# /home/username/fasta-36.3.4/bin/fasta36 -E 1 -m 10 NC_002127.faa NC_009649.faa
FASTA searches a protein or DNA sequence data bank
 version 36.3.4 Apr, 2011
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: NC_002127.faa
  1>>>gi|10955263|ref|NP_052604.1| plasmid mobilization [Escherichia coli O157:H7 s - 107 aa
Library: NC_009649.faa
    45119 residues in   180 sequences

Statistics: (shuffled [498]) Expectation_n fit: rho(ln(x))= 3.0739+/-0.0105; mu= 13.5811+/- 0.558
 mean_var=50.3269+/-12.335, 0's: 0 Z-trim(86.3): 0  B-trim: 0 in 0/33
 Lambda= 0.180790
 statistics sampled from 68 (68) to 498 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.783), E-opt: 0.2 (0.378), width:  16
 Scan time:  0.030

The best scores are:                                      opt bits E(180)
gi|152973457|ref|YP_001338508.1| ATPase with chape ( 931)   71 28.5   0.048
gi|152973588|ref|YP_001338639.1| F pilus assembly  ( 459)   63 25.9    0.14
gi|152973480|ref|YP_001338531.1| Arsenate reductas ( 141)   51 22.0    0.63

>>>gi|10955263|ref|NP_052604.1|, 107 aa vs NC_009649.faa library
; pg_name: /Users/pjcock/Downloads/Software/fasta-36.3.4/bin/fasta36
; pg_ver: 36.3.4 Apr, 2011
; pg_argv: /Users/pjcock/Downloads/Software/fasta-36.3.4/bin/fasta36 -E 1 -m 10 NC_002127.faa NC_009649.faa
; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Nov 2010
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_join_E(): 1 (0.783)
; pg_optcut_E(): 0.2 (0.378)
; mp_extrap: 60000 498
; mp_stats: (shuffled [498]) Expectation_n fit: rho(ln(x))= 3.0739+/-0.0105; mu= 13.5811+/- 0.558  mean_var=50.3269+/-12.335, 0's: 0 Z-trim(86.3): 0  B-trim: 0 in 0/33  Lambda= 0.180790
; mp_KS: -0.0000 (N=0) at  30
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: BL50 matrix (15:-5), open/ext: -10/-2  ktup: 2, E-join: 1 (0.783), E-opt: 0.2 (0.378), width:  16
>>gi|152973457|ref|YP_001338508.1| ATPase with chaperone activity, ATP-binding subunit [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  97
; fa_init1:  43
; fa_opt:  71
; fa_z-score: 109.6
; fa_bits: 28.5
; fa_expect:  0.048
; sw_score: 71
; sw_ident: 0.250
; sw_sim: 0.574
; sw_overlap: 108
>gi|10955263| ..
; sq_len: 107
; sq_offset: 1
; sq_type: p
; al_start: 5
; al_stop: 103
; al_display_start: 1
--------------------------MTKRSGSNT-RRRAISRPVRLTAE
ED---QEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVM-----
RLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD
>gi|152973457|ref|YP_001338508.1| ..
; sq_len: 931
; sq_offset: 1
; sq_type: p
; al_start: 96
; al_stop: 195
; al_display_start: 66
SDFFRIGDDATPVAADTDDVVDASFGEPAAAGSGAPRRRGSGLASRISEQ
SEALLQEAAKHAAEFGRS------EVDTEHLLLALADSDVVKTILGQFKI
KVDDLKRQIESEAKR-GDKPF-EGEIGVSPRVKDALSRAFVASNELGHSY
VGPEHFLIGLAEEGEGLAANLLRRYGLTPQ
; al_cons:
                              .::..-:::. .   :.. .
 .---::  :.::: :..------ .   . . .:.:. :.: ..-----
..  :....  ..::-::. .-:  :...   .  :::
>>gi|152973588|ref|YP_001338639.1| F pilus assembly protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  66
; fa_init1:  33
; fa_opt:  63
; fa_z-score: 101.4
; fa_bits: 25.9
; fa_expect:   0.14
; sw_score: 63
; sw_ident: 0.266
; sw_sim: 0.656
; sw_overlap: 64
>gi|10955263| ..
; sq_len: 107
; sq_offset: 1
; sq_type: p
; al_start: 32
; al_stop: 94
; al_display_start: 2
TKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKK
VNSLTDDRVLKEV-MRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRAL
LSRLMAD
>gi|152973588|ref|YP_001338639.1| ..
; sq_len: 459
; sq_offset: 1
; sq_type: p
; al_start: 191
; al_stop: 248
; al_display_start: 161
VGGLFPRTQVAQQKVCQDIAGESNIFSDWAASRQGCTVGG--KMDSVQDK
ASDKDKERVMKNINIMWNALSKNRLFDG----NKELKEFIMTLTGTLIFG
ENSEITPLPARTTDQDLIRAMMEGGTAKIYHCNDSDKCLKVVADATVTIT
SNKALKSQISALLSSIQNKAVADEKLTDQE
; al_cons:
                              :.. : ::.:--.  ..  :
...   .::.:..-.  .::.:. ..::----..:  : ....:
>>gi|152973480|ref|YP_001338531.1| Arsenate reductase (Arsenical pump modifier) [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  45
; fa_init1:  37
; fa_opt:  51
; fa_z-score: 89.6
; fa_bits: 22.0
; fa_expect:   0.63
; sw_score: 51
; sw_ident: 0.267
; sw_sim: 0.622
; sw_overlap: 45
>gi|10955263| ..
; sq_len: 107
; sq_offset: 1
; sq_type: p
; al_start: 27
; al_stop: 66
; al_display_start: 1
----MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAA
A-----LGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLI
AITEYHRALLSRLMAD
>gi|152973480|ref|YP_001338531.1| ..
; sq_len: 141
; sq_offset: 1
; sq_type: p
; al_start: 43
; al_stop: 87
; al_display_start: 13
GTSRNTLEMIRNSGNEPTVIHYLENPPSRDELVKLIADMGISVRALLRKN
VEPYEELGLEEDKFTDDQLIDFMLQHPILINRPIVVTPLGTRLCRPSEVV
LDILPDAQKGAFAKEDGEKV
; al_cons:
                              :. :  :. : .: ..::  
.-----:: . ...:::...  ...
>>><<<
  2>>>gi|10955264|ref|NP_052605.1| hypothetical protein pOSAK1_02 [Escherichia coli O157:H7 s - 126 aa
Library: NC_009649.faa
    45119 residues in   180 sequences

Statistics: (shuffled [493]) Expectation_n fit: rho(ln(x))= 4.1464+/-0.0105; mu= 7.4394+/- 0.556
 mean_var=56.5622+/-13.483, 0's: 0 Z-trim(85.2): 0  B-trim: 0 in 0/33
 Lambda= 0.170534
 statistics sampled from 51 (51) to 493 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.728), E-opt: 0.2 (0.331), width:  16
 Scan time:  0.050

The best scores are:                                      opt bits E(180)
gi|152973462|ref|YP_001338513.1| hypothetical prot ( 101)   58 23.9    0.15
gi|152973509|ref|YP_001338560.1| probable sensor k ( 448)   56 24.0     0.6
gi|152973581|ref|YP_001338632.1| inner membrane pr (  84)   48 21.3    0.72
gi|152973536|ref|YP_001338587.1| putative inner me (  84)   48 21.3    0.72

>>>gi|10955264|ref|NP_052605.1|, 126 aa vs NC_009649.faa library
; pg_name: /Users/pjcock/Downloads/Software/fasta-36.3.4/bin/fasta36
; pg_ver: 36.3.4 Apr, 2011
; pg_argv: /Users/pjcock/Downloads/Software/fasta-36.3.4/bin/fasta36 -E 1 -m 10 NC_002127.faa NC_009649.faa
; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Nov 2010
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_join_E(): 1 (0.728)
; pg_optcut_E(): 0.2 (0.331)
; mp_extrap: 60000 493
; mp_stats: (shuffled [493]) Expectation_n fit: rho(ln(x))= 4.1464+/-0.0105; mu= 7.4394+/- 0.556  mean_var=56.5622+/-13.483, 0's: 0 Z-trim(85.2): 0  B-trim: 0 in 0/33  Lambda= 0.170534
; mp_KS: -0.0000 (N=0) at  30
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: BL50 matrix (15:-5), open/ext: -10/-2  ktup: 2, E-join: 1 (0.728), E-opt: 0.2 (0.331), width:  16
>>gi|152973462|ref|YP_001338513.1| hypothetical protein KPN_pKPN3p05904 [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  78
; fa_init1:  50
; fa_opt:  58
; fa_z-score: 100.8
; fa_bits: 23.9
; fa_expect:   0.15
; sw_score: 58
; sw_ident: 0.289
; sw_sim: 0.632
; sw_overlap: 38
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 1
; al_stop: 38
; al_display_start: 1
------------------------------MKKDKKYQIEAIKNKDKTLF
IVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSF
NGEKFSSYTLNKVTKTDEYN
>gi|152973462|ref|YP_001338513.1| ..
; sq_len: 101
; sq_offset: 1
; sq_type: p
; al_start: 44
; al_stop: 81
; al_display_start: 14
DALLGEIQRLRKQVHQLQLERDILTKANELIKKDLGVSFLKLKNREKTLI
VDALKKKYPVAELLSVLQLARSCYFYQNVCTISMRKYA
; al_cons:
                              .:::   ..  .::..:::.
.      :  .:..: ..
>>gi|152973509|ref|YP_001338560.1| probable sensor kinase (silver resistance) [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  73
; fa_init1:  56
; fa_opt:  56
; fa_z-score: 89.9
; fa_bits: 24.0
; fa_expect:    0.6
; sw_score: 56
; sw_ident: 0.727
; sw_sim: 0.818
; sw_overlap: 11
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 51
; al_stop: 61
; al_display_start: 21
IVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSF
NGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFAL
KKGIPI
>gi|152973509|ref|YP_001338560.1| ..
; sq_len: 448
; sq_offset: 1
; sq_type: p
; al_start: 408
; al_stop: 418
; al_display_start: 378
RRAINNLLSNALRYTPEGQAITVSIREQESFFDLVIENPGKPIPEEHLSR
LFDRFYRVDPSRQRKGEALRL
; al_cons:
                              ::::.: : ::
>>gi|152973581|ref|YP_001338632.1| inner membrane protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  61
; fa_init1:  46
; fa_opt:  48
; fa_z-score: 88.5
; fa_bits: 21.3
; fa_expect:   0.72
; sw_score: 48
; sw_ident: 0.300
; sw_sim: 0.675
; sw_overlap: 40
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 16
; al_stop: 53
; al_display_start: 1
---------------MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSE-FF
SKIESDLKKKKSKGD-VFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKV
TKTDEYNDLSELSASFFKKN
>gi|152973581|ref|YP_001338632.1| ..
; sq_len: 84
; sq_offset: 1
; sq_type: p
; al_start: 45
; al_stop: 84
; al_display_start: 15
LRLTLTIIIISPVIYFSWDAVKGTSGSDYVESVVFILMAGFAMSVCYLFF
SVLEKVINARKSKDESIYHD
; al_cons:
                              ....::..:   .:   -::
: .:. .. .::: .-.. :
>>gi|152973536|ref|YP_001338587.1| putative inner membrane protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  63
; fa_init1:  42
; fa_opt:  48
; fa_z-score: 88.5
; fa_bits: 21.3
; fa_expect:   0.72
; sw_score: 48
; sw_ident: 0.267
; sw_sim: 0.667
; sw_overlap: 30
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 97
; al_stop: 126
; al_display_start: 67
YTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKAT
SFALKKGIPI
>gi|152973536|ref|YP_001338587.1| ..
; sq_len: 84
; sq_offset: 1
; sq_type: p
; al_start: 7
; al_stop: 36
; al_display_start: 1
------------------------MSQWNIASFSKEEQDKVAVDKVAADV
AWQERMNKPVMPELVEREQPEHLREYFHERFRVHRLNSQQLPRANAPEYN
KPGDDQQN
; al_cons:
                              ::: :.. ::. :. ..  .
..  . . :.
>>><<<
  3>>>gi|10955265|ref|NP_052606.1| hypothetical protein pOSAK1_03 [Escherichia coli O157:H7 s - 346 aa
Library: NC_009649.faa
    45119 residues in   180 sequences

Statistics: (shuffled [445]) Expectation_n fit: rho(ln(x))= 3.1750+/-0.0113; mu= 16.4403+/- 0.606
 mean_var=50.7026+/-12.811, 0's: 0 Z-trim(83.1): 0  B-trim: 0 in 0/32
 Lambda= 0.180119
 statistics sampled from 31 (31) to 444 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.678), E-opt: 0.2 (0.278), width:  16
 Scan time:  0.060

The best scores are:                                      opt bits E(180)
gi|152973545|ref|YP_001338596.1| putative plasmid  ( 242)   70 28.4   0.041
gi|152973505|ref|YP_001338556.1| putative membrane ( 430)   57 25.4    0.59

>>>gi|10955265|ref|NP_052606.1|, 346 aa vs NC_009649.faa library
; pg_name: /Users/pjcock/Downloads/Software/fasta-36.3.4/bin/fasta36
; pg_ver: 36.3.4 Apr, 2011
; pg_argv: /Users/pjcock/Downloads/Software/fasta-36.3.4/bin/fasta36 -E 1 -m 10 NC_002127.faa NC_009649.faa
; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Nov 2010
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_join_E(): 1 (0.678)
; pg_optcut_E(): 0.2 (0.278)
; mp_extrap: 60000 444
; mp_stats: (shuffled [445]) Expectation_n fit: rho(ln(x))= 3.1750+/-0.0113; mu= 16.4403+/- 0.606  mean_var=50.7026+/-12.811, 0's: 0 Z-trim(83.1): 0  B-trim: 0 in 0/32  Lambda= 0.180119
; mp_KS: -0.0000 (N=0) at  30
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: BL50 matrix (15:-5), open/ext: -10/-2  ktup: 2, E-join: 1 (0.678), E-opt: 0.2 (0.278), width:  16
>>gi|152973545|ref|YP_001338596.1| putative plasmid SOS inhibition protein A [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  72
; fa_init1:  52
; fa_opt:  70
; fa_z-score: 110.9
; fa_bits: 28.4
; fa_expect:  0.041
; sw_score: 70
; sw_ident: 0.279
; sw_sim: 0.651
; sw_overlap: 43
>gi|10955265| ..
; sq_len: 346
; sq_offset: 1
; sq_type: p
; al_start: 197
; al_stop: 238
; al_display_start: 167
DFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKK
QLSC-SLIMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNL
GEYFTENKPKYIIREIHQET
>gi|152973545|ref|YP_001338596.1| ..
; sq_len: 242
; sq_offset: 1
; sq_type: p
; al_start: 52
; al_stop: 94
; al_display_start: 22
IMTVEEARQRGARLPSMPHVRTFLRLLTGCSRINSDVARRIPGIHRDPKD
RLSSLKQVEEALDMLISSHGEYCPLPLTMDVQAENFPEVLHTRTVRRLKR
QDFAFTRKMRREARQVEQSW
; al_cons:
                              :...: . . :  ::.: : 
.:: -. . . .:. . ... ::
>>gi|152973505|ref|YP_001338556.1| putative membrane fusion protein SilB [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
; fa_frame: f
; fa_initn:  95
; fa_init1:  52
; fa_opt:  57
; fa_z-score: 90.1
; fa_bits: 25.4
; fa_expect:   0.59
; sw_score: 57
; sw_ident: 0.234
; sw_sim: 0.609
; sw_overlap: 64
>gi|10955265| ..
; sq_len: 346
; sq_offset: 1
; sq_type: p
; al_start: 40
; al_stop: 101
; al_display_start: 10
NINIDKIESALTQNGVTNYSSNVKNERETHISGTYKGIDFLIKLMPSGGN
TTIGRASGQNNTYFDEIALIIKENCLY--SDTKNFEYTIPKFSDDDRANL
FEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGK
YLQIASLINDFMCSILNMKEIVEQKNKEFN
>gi|152973505|ref|YP_001338556.1| ..
; sq_len: 430
; sq_offset: 1
; sq_type: p
; al_start: 222
; al_stop: 281
; al_display_start: 192
RLRLAGMPEEDIQRLRSTRTIQTRFTIKAPIDGVITAFD-LRTGMNISKD
KVVAQIQGMDPVW---ISAAVPESIAYLLKDTSQFEISVPAYPDKTFHVE
KWNILPSVDQTTRTLQVRLQVSNKDEFLKPGMNAYLKLNTKSQEMLLIPS
QAVIDTGKEQRVITVDDEGKFVPKQIHVLH
; al_cons:
                              :.:.  ..:-:   :  . .
 .... .:.. ..---:.  . :.  :--.::..:: ..: . :
>>><<<
>>>///


579 residues in 3 query   sequences
45119 residues in 180 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Apr 22 16:31:22 2011 done: Fri Apr 22 16:31:22 2011
 Total Scan time:  0.140 Total Display time:  0.020

Function used was FASTA [36.3.4 Apr, 2011]