BLASTP 2.2.21 [Jun-14-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= gi|3298468|dbj|BAA31520.1| SAMIPF (472 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 8,994,603 sequences; 3,078,807,967 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value pdb|1JLX|A Chain A, Agglutinin In Complex With T-Disaccharide >g... 640 0.0 gb|AAQ03084.1|AF401479_1 agglutinin [Amaranthus caudatus] 630 e-179 gb|AAL05954.1| agglutinin [Amaranthus caudatus] 627 e-178 gb|AAD33922.1|AF143954_1 agglutinin [Amaranthus hypochondriacus]... 625 e-177 gb|AAM09540.1|AF491291_1 seed protein AmA1 [Amaranthus hypochond... 624 e-177 ref|XP_002264858.1| PREDICTED: hypothetical protein [Vitis vinif... 245 6e-63 ref|XP_002264911.1| PREDICTED: hypothetical protein [Vitis vinif... 244 1e-62 emb|CAN71829.1| hypothetical protein [Vitis vinifera] 239 5e-61 ref|XP_002264098.1| PREDICTED: hypothetical protein [Vitis vinif... 237 2e-60 ref|XP_002264775.1| PREDICTED: hypothetical protein [Vitis vinif... 231 9e-59 >pdb|1JLX|A Chain A, Agglutinin In Complex With T-Disaccharide pdb|1JLX|B Chain B, Agglutinin In Complex With T-Disaccharide pdb|1JLY|A Chain A, Crystal Structure Of Amaranthus Caudatus Agglutinin pdb|1JLY|B Chain B, Crystal Structure Of Amaranthus Caudatus Agglutinin Length = 303 Score = 640 bits (1652), Expect = 0.0, Method: Compositional matrix adjust. Identities = 303/303 (100%), Positives = 303/303 (100%) Query: 170 AGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIK 229 AGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIK Sbjct: 1 AGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIK 60 Query: 230 SRYTNKYLVRWSPNHYWITASANEPDENKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHY 289 SRYTNKYLVRWSPNHYWITASANEPDENKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHY Sbjct: 61 SRYTNKYLVRWSPNHYWITASANEPDENKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHY 120 Query: 290 TQNYTVGGSFVSYLFAESSQIDTGSKDVFHVIDWKSIFQFPKGYVTFKGNNGKYLGVITI 349 TQNYTVGGSFVSYLFAESSQIDTGSKDVFHVIDWKSIFQFPKGYVTFKGNNGKYLGVITI Sbjct: 121 TQNYTVGGSFVSYLFAESSQIDTGSKDVFHVIDWKSIFQFPKGYVTFKGNNGKYLGVITI 180 Query: 350 NQLPCLQFGYDNLNDPKVAHQMFVTSNGTICIKSNYMNKFWRLSTDDWILVDGNDPRETN 409 NQLPCLQFGYDNLNDPKVAHQMFVTSNGTICIKSNYMNKFWRLSTDDWILVDGNDPRETN Sbjct: 181 NQLPCLQFGYDNLNDPKVAHQMFVTSNGTICIKSNYMNKFWRLSTDDWILVDGNDPRETN 240 Query: 410 EAAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELG 469 EAAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELG Sbjct: 241 EAAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELG 300 Query: 470 QNN 472 QNN Sbjct: 301 QNN 303 BLASTP 2.2.21 [Jun-14-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING finger protein (600 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 8,994,603 sequences; 3,078,807,967 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value sp|Q9WTV7.1|RNF12_MOUSE RecName: Full=E3 ubiquitin-protein ligas... 684 0.0 ref|NP_035406.3| ring finger protein, LIM domain interacting [Mu... 676 0.0 dbj|BAB28712.1| unnamed protein product [Mus musculus] 674 0.0 dbj|BAC26379.1| unnamed protein product [Mus musculus] 672 0.0 ref|NP_001020063.1| ring finger protein, LIM domain interacting ... 620 e-175 ref|NP_057204.2| ring finger protein, LIM domain interacting [Ho... 606 e-171 ref|XP_001141975.1| PREDICTED: ring finger protein 12 isoform 1 ... 605 e-171 ref|XP_001096367.1| PREDICTED: similar to ring finger protein 12... 605 e-171 dbj|BAA91632.1| unnamed protein product [Homo sapiens] 604 e-170 ref|XP_001505028.1| PREDICTED: similar to E3 ubiquitin-protein l... 602 e-170 >sp|Q9WTV7.1|RNF12_MOUSE RecName: Full=E3 ubiquitin-protein ligase RNF12; AltName: Full=RING finger protein 12; AltName: Full=LIM domain-interacting RING finger protein; AltName: Full=RING finger LIM domain-binding protein; Short=R-LIM gb|AAD34209.1|AF069992_1 LIM domain interacting RING finger protein [Mus musculus] Length = 600 Score = 684 bits (1765), Expect = 0.0, Method: Compositional matrix adjust. Identities = 353/414 (85%), Positives = 353/414 (85%) Query: 1 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE 60 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE Sbjct: 1 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE 60 Query: 61 EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS 120 EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS Sbjct: 61 EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS 120 Query: 121 WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMXXXXX 180 WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQM Sbjct: 121 WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSAS 180 Query: 181 XXXXXXXXXXXXXXTEAVTEVXXXXXXXXXXXXXXXXXXXXXXXERSMSPLQPTSEIPRR 240 TEAVTEV ERSMSPLQPTSEIPRR Sbjct: 181 ESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRR 240 Query: 241 APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPXXXXXXXXXXXXX 300 APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNP Sbjct: 241 APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS 300 Query: 301 XXXXXXQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF 360 QRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF Sbjct: 301 ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF 360 Query: 361 SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMY 414 SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMY Sbjct: 361 SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMY 414 Score = 258 bits (658), Expect = 2e-66, Method: Compositional matrix adjust. Identities = 115/115 (100%), Positives = 115/115 (100%) Query: 486 KDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKT 545 KDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKT Sbjct: 486 KDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKT 545 Query: 546 CSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV 600 CSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV Sbjct: 546 CSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV 600 BLASTP 2.2.21 [Jun-14-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= gi|671626|emb|CAA85685.1| rubisco large subunit (473 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 8,994,603 sequences; 3,078,807,967 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value emb|CAA85685.1| rubisco large subunit [Rosmarinus officinalis] 947 0.0 emb|CAA85698.1| rubisco large subunit [Salvia sclarea] >gi|14192... 942 0.0 emb|CAA85688.1| rubisco large subunit [Salvia bucharica] >gi|141... 942 0.0 emb|CAA85670.1| rubisco large subunit [Monarda menthaefolia] 941 0.0 emb|CAA85667.1| rubisco large subunit [Mentha suaveolens] 941 0.0 emb|CAA85676.1| rubisco large subunit [Origanum laevigatum] >gi|... 941 0.0 emb|CAA85684.1| rubisco large subunit [Rosmarinus officinalis] 940 0.0 emb|CAA85687.1| rubisco large subunit [Salvia argentea] 939 0.0 emb|CAA85686.1| rubisco large subunit [Salvia aethiopis] 939 0.0 emb|CAA85718.1| rubisco large subunit [Thymus alsinoides] 939 0.0 >emb|CAA85685.1| rubisco large subunit [Rosmarinus officinalis] Length = 473 Score = 947 bits (2449), Expect = 0.0, Method: Compositional matrix adjust. Identities = 458/473 (96%), Positives = 458/473 (96%) Query: 1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQXXXXXXXXXXXXXXX 60 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQ Sbjct: 1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAE 60 Query: 61 SSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSI 120 SSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSI Sbjct: 61 SSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSI 120 Query: 121 VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180 VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL Sbjct: 121 VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180 Query: 181 SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYL 240 SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYL Sbjct: 181 SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYL 240 Query: 241 NATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAV 300 NATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAV Sbjct: 241 NATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAV 300 Query: 301 IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSR 360 IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSR Sbjct: 301 IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSR 360 Query: 361 GIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN 420 GIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN Sbjct: 361 GIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN 420 Query: 421 RVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD 473 RVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD Sbjct: 421 RVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD 473 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects Posted date: Jun 4, 2009 5:40 PM Number of letters in database: 3,078,807,967 Number of sequences in database: 8,994,603 Lambda K H 0.325 0.138 0.426 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 8994603 Number of Hits to DB: 8,456,431,703 Number of extensions: 350268212 Number of successful extensions: 843324 Number of sequences better than 1.0e-05: 30452 Number of HSP's gapped: 835403 Number of HSP's successfully gapped: 30847 Length of database: 3,078,807,967 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 133 (55.8 bits)