BLASTP 2.2.23 [Feb-03-2010] 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. Reference for composition-based statistics starting in round 2: Schaffer, Alejandro A., L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005. Query= Q13253 (232 letters) Database: ../databases/nrPDB-GO_2019.06.18_sequences.fasta 36,641 sequences; 10,336,785 total letters Searching..................................................done Results from round 1 Score E Sequences producing significant alignments: (bits) Value 1M4U-A nrPDB 422 e-119 5YXW-B nrPDB 28 2.9 1E3A-B nrPDB 27 6.2 >1M4U-A nrPDB Length = 206 Score = 422 bits (1086), Expect = e-119, Method: Compositional matrix adjust. Identities = 205/205 (100%), Positives = 205/205 (100%) Query: 28 QHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDR 87 QHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDR Sbjct: 2 QHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDR 61 Query: 88 PGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQM 147 PGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQM Sbjct: 62 PGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQM 121 Query: 148 WLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRC 207 WLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRC Sbjct: 122 WLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRC 181 Query: 208 QRRGGQRCGWIPIQYPIISECKCSC 232 QRRGGQRCGWIPIQYPIISECKCSC Sbjct: 182 QRRGGQRCGWIPIQYPIISECKCSC 206 >5YXW-B nrPDB Length = 419 Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust. Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 9/63 (14%) Query: 163 DLGSRFW----PRYVKVG----SCFSKRSCS-VPEGMVCKPSKSVHLTVLRWRCQRRGGQ 213 ++GS+ W P+YV S F + SC+ +PEG VC + ++ L C R + Sbjct: 193 NIGSQEWYTTVPKYVATQGYLISNFDESSCTFMPEGTVCSQNALYPMSPLLQECLRGSTK 252 Query: 214 RCG 216 C Sbjct: 253 SCA 255 >1E3A-B nrPDB Length = 560 Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust. Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 7/46 (15%) Query: 74 YDP--GFMAT---SPPEDRPGGGGGAA--GGAEDLAELDQLLRQRP 112 Y+P G++A SP +D P A GGA+ + E+D+LL Q+P Sbjct: 233 YNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKP 278 Searching..................................................done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: 1M4U-A nrPDB 445 e-126 Sequences not found previously or not previously below threshold: 5YXW-B nrPDB 30 1.2 1E3A-B nrPDB 29 1.8 4B46-A nrPDB 28 3.0 CONVERGED! >1M4U-A nrPDB Length = 206 Score = 445 bits (1144), Expect = e-126, Method: Composition-based stats. Identities = 205/205 (100%), Positives = 205/205 (100%) Query: 28 QHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDR 87 QHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDR Sbjct: 2 QHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDR 61 Query: 88 PGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQM 147 PGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQM Sbjct: 62 PGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQM 121 Query: 148 WLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRC 207 WLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRC Sbjct: 122 WLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRC 181 Query: 208 QRRGGQRCGWIPIQYPIISECKCSC 232 QRRGGQRCGWIPIQYPIISECKCSC Sbjct: 182 QRRGGQRCGWIPIQYPIISECKCSC 206 >5YXW-B nrPDB Length = 419 Score = 29.6 bits (65), Expect = 1.2, Method: Composition-based stats. Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 9/63 (14%) Query: 163 DLGSRFW----PRYVKVG----SCFSKRSCS-VPEGMVCKPSKSVHLTVLRWRCQRRGGQ 213 ++GS+ W P+YV S F + SC+ +PEG VC + ++ L C R + Sbjct: 193 NIGSQEWYTTVPKYVATQGYLISNFDESSCTFMPEGTVCSQNALYPMSPLLQECLRGSTK 252 Query: 214 RCG 216 C Sbjct: 253 SCA 255 >1E3A-B nrPDB Length = 560 Score = 28.8 bits (63), Expect = 1.8, Method: Composition-based stats. Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 7/46 (15%) Query: 74 YDP--GFMAT---SPPEDRPGGGGGAA--GGAEDLAELDQLLRQRP 112 Y+P G++A SP +D P A GGA+ + E+D+LL Q+P Sbjct: 233 YNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLLEQKP 278 >4B46-A nrPDB Length = 395 Score = 28.4 bits (62), Expect = 3.0, Method: Composition-based stats. Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 15/104 (14%) Query: 65 LLRSLLGGHYDPGFMATSPPEDRPGGGGGA----AGGAEDLAELD---------QLLRQR 111 ++ +L GG A+ E R GGG GG E LD L+R+ Sbjct: 219 IINTLAGGGVSTVGYASEGVEPRKNNGGGLLSRLTGGDEPDDNLDTAHTTNRITSLVRKA 278 Query: 112 PSG--AMPSEIKGLEFSEGLAQGKKQRLSKKLRRKLQMWLWSQT 153 G +P EI+G E + + G + L++K + + W+ QT Sbjct: 279 ALGRLTLPCEIEGAERALLVLAGPPEHLNRKGIERGRKWIEEQT 322 Database: ../databases/nrPDB-GO_2019.06.18_sequences.fasta Posted date: Jan 3, 2023 9:05 PM Number of letters in database: 10,336,785 Number of sequences in database: 36,641 Lambda K H 0.321 0.140 0.461 Lambda K H 0.267 0.0430 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 11,126,589 Number of Sequences: 36641 Number of extensions: 516504 Number of successful extensions: 1229 Number of sequences better than 10.0: 7 Number of HSP's better than 10.0 without gapping: 6 Number of HSP's successfully gapped in prelim test: 9 Number of HSP's that attempted gapping in prelim test: 1215 Number of HSP's gapped (non-prelim): 17 length of query: 232 length of database: 10,336,785 effective HSP length: 94 effective length of query: 138 effective length of database: 6,892,531 effective search space: 951169278 effective search space used: 951169278 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 58 (26.9 bits)