Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate WP_057507494.1 ABB28_RS04560 alpha,alpha-trehalase TreA
Query= BRENDA::P13482 (565 letters) >NCBI__GCF_001431535.1:WP_057507494.1 Length = 538 Score = 637 bits (1642), Expect = 0.0 Identities = 300/526 (57%), Positives = 378/526 (71%) Query: 16 PACIFLCFAALSVQAEETPVTPQPPDILLGPLFNDVQNAKLFPDQKTFADAVPNSDPLMI 75 P L A + P PPD L PLF VQ A LFPDQKTFADAVP P I Sbjct: 5 PCLASLLLAPMLWSTAAVAAAPAPPDQRLQPLFQQVQGAHLFPDQKTFADAVPRRAPEAI 64 Query: 76 LADYRMQQNQSGFDLRHFVNVNFTLPKEGEKYVPPEGQSLREHIDGLWPVLTRSTENTEK 135 + ++ + Q+GF L+ FVN NF +P + YVPP G++LR HI+GLWPVLTR T + Sbjct: 65 VQAWQREHTQAGFSLQSFVNDNFDVPGDAAPYVPPAGETLRAHIEGLWPVLTRQTGTVDP 124 Query: 136 WDSLLPLPEPYVVPGGRFREVYYWDSYFTMLGLAESGHWDKVADMVANFAHEIDTYGHIP 195 SLLPLP+PYVVPGGRFREVYYWDSYFT+LGLA SG W +V DMV NFA++ID++GHIP Sbjct: 125 NGSLLPLPKPYVVPGGRFREVYYWDSYFTLLGLASSGQWQRVRDMVDNFAYQIDSHGHIP 184 Query: 196 NGNRSYYLSRSQPPFFALMVELLAQHEGDAALKQYLPQMQKEYAYWMDGVENLQAGQQEK 255 NGNRSYYLSRSQPPFF+LMV+LLA HEGD A ++YLPQ++ E+A+WMDGV+ L GQ Sbjct: 185 NGNRSYYLSRSQPPFFSLMVDLLATHEGDEAYRRYLPQLRAEHAFWMDGVDGLPPGQAHA 244 Query: 256 RVVKLQDGTLLNRYWDDRDTPRPESWVEDIATAKSNPNRPATEIYRDLRSAAASGWDFSS 315 RVV+L DG++LNRY+D R PR ESW +D+ATA P R +++YRDLR+ A SGWDFSS Sbjct: 245 RVVRLADGSVLNRYYDARAVPRTESWTDDLATAAQAPQRAPSQVYRDLRAGAESGWDFSS 304 Query: 316 RWMDNPQQLNTLRTTSIVPVDLNSLMFKMEKILARASKAAGDNAMANQYETLANARQKGI 375 RW+D+P L+++RTT I+PVDLNSL+F +E+ LA AS + ++ A ARQ+ I Sbjct: 305 RWLDDPAALSSIRTTDILPVDLNSLLFHLERTLAHASGVTKNTRARREFNRQAQARQRAI 364 Query: 376 EKYLWNDQQGWYADYDLKSHKVRNQLTAAALFPLYVNAAAKDRANKMATATKTHLLQPGG 435 LW+ QGWY D DL++ R LTAAALFPL+++ A K +A + A A + L++ GG Sbjct: 365 NTLLWDPSQGWYVDRDLQTGHTRPALTAAALFPLWLDIAGKPQARRTADAVEAQLVKQGG 424 Query: 436 LNTTSVKSGQQWDAPNGWAPLQWVATEGLQNYGQKEVAMDISWHFLTNVQHTYDREKKLV 495 L TT++ +GQQWDAPNGWAPLQWVA +GLQ YGQ +A + FL VQ YDRE+KLV Sbjct: 425 LLTTTLTTGQQWDAPNGWAPLQWVAVDGLQRYGQDRLARQLGTRFLRTVQSVYDREQKLV 484 Query: 496 EKYDVSTTGTGGGGGEYPLQDGFGWTNGVTLKMLDLICPKEQPCDN 541 EKY V + GGGGGEYPLQDGFGW+NGVTL +LD +C ++ C++ Sbjct: 485 EKYVVDGSAGGGGGGEYPLQDGFGWSNGVTLALLDRLCAPKKKCES 530 Lambda K H 0.315 0.132 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1017 Number of extensions: 37 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 565 Length of database: 538 Length adjustment: 36 Effective length of query: 529 Effective length of database: 502 Effective search space: 265558 Effective search space used: 265558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory