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= P04039 (78 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 6GIQ-h nrPDB 162 2e-41 2Y69-L nrPDB 33 0.021 2DB3-A nrPDB 28 1.2 6QKC-A nrPDB 25 8.8 >6GIQ-h nrPDB Length = 78 Score = 162 bits (411), Expect = 2e-41, Method: Compositional matrix adjust. Identities = 78/78 (100%), Positives = 78/78 (100%) Query: 1 MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG 60 MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG Sbjct: 1 MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG 60 Query: 61 FAVPFVACYVQLKKSGAF 78 FAVPFVACYVQLKKSGAF Sbjct: 61 FAVPFVACYVQLKKSGAF 78 >2Y69-L nrPDB Length = 63 Score = 33.5 bits (75), Expect = 0.021, Method: Compositional matrix adjust. Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 1/49 (2%) Query: 26 RSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKK 74 R H+++G +NIPF V+ + A+ FF GFA PF QL K Sbjct: 15 RRSHYEEGPGKNIPFSVENKWRLLAMMTL-FFGSGFAAPFFIVRHQLLK 62 >2DB3-A nrPDB Length = 434 Score = 27.7 bits (60), Expect = 1.2, Method: Compositional matrix adjust. Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%) Query: 28 VHFKDGVYENIPFKVKGRKTPYALSHF 54 +HF Y NIP KV G P + HF Sbjct: 34 IHFSK--YNNIPVKVTGSDVPQPIQHF 58 >6QKC-A nrPDB Length = 915 Score = 24.6 bits (52), Expect = 8.8, Method: Composition-based stats. Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 5/35 (14%) Query: 32 DGVYENIPFKVKGRKTPYAL-----SHFGFFAIGF 61 +G+ N+ F KGR+T Y L H G IG+ Sbjct: 355 EGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGY 389 Searching..................................................done Results from round 2 Score E Sequences producing significant alignments: (bits) Value Sequences used in model and found again: 6GIQ-h nrPDB 148 3e-37 Sequences not found previously or not previously below threshold: 2Y69-L nrPDB 32 0.086 2DB3-A nrPDB 28 1.3 4TM5-A nrPDB 27 1.9 CONVERGED! >6GIQ-h nrPDB Length = 78 Score = 148 bits (375), Expect = 3e-37, Method: Composition-based stats. Identities = 78/78 (100%), Positives = 78/78 (100%) Query: 1 MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG 60 MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG Sbjct: 1 MLCQQMIRTTAKRSSNIMTRPIIMKRSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIG 60 Query: 61 FAVPFVACYVQLKKSGAF 78 FAVPFVACYVQLKKSGAF Sbjct: 61 FAVPFVACYVQLKKSGAF 78 >2Y69-L nrPDB Length = 63 Score = 31.5 bits (70), Expect = 0.086, Method: Composition-based stats. Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 1/49 (2%) Query: 26 RSVHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKK 74 R H+++G +NIPF V+ + A+ FF GFA PF QL K Sbjct: 15 RRSHYEEGPGKNIPFSVENKWRLLAMMTL-FFGSGFAAPFFIVRHQLLK 62 >2DB3-A nrPDB Length = 434 Score = 27.7 bits (60), Expect = 1.3, Method: Composition-based stats. Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%) Query: 28 VHFKDGVYENIPFKVKGRKTPYALSHF 54 +HF Y NIP KV G P + HF Sbjct: 34 IHFSK--YNNIPVKVTGSDVPQPIQHF 58 >4TM5-A nrPDB Length = 311 Score = 26.9 bits (58), Expect = 1.9, Method: Composition-based stats. Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 7/52 (13%) Query: 20 RPIIMKRSVHFKDGVYENIPFKVKG-RKTPYALS-HFGFFA-----IGFAVP 64 R ++ R F DGVYE +P +G R+ P+ ++ H A IG A P Sbjct: 35 RVPVLDRGFIFGDGVYEVVPIYAEGARRAPFRIAQHLARLARSLKKIGIADP 86 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 0.331 0.140 0.430 Lambda K H 0.267 0.0450 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 3,449,397 Number of Sequences: 36641 Number of extensions: 129162 Number of successful extensions: 275 Number of sequences better than 10.0: 12 Number of HSP's better than 10.0 without gapping: 8 Number of HSP's successfully gapped in prelim test: 8 Number of HSP's that attempted gapping in prelim test: 265 Number of HSP's gapped (non-prelim): 16 length of query: 78 length of database: 10,336,785 effective HSP length: 48 effective length of query: 30 effective length of database: 8,578,017 effective search space: 257340510 effective search space used: 257340510 T: 11 A: 40 X1: 16 ( 7.6 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 53 (24.9 bits)