Alignments for a candidate for treF in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Stenotrophomonas chelatiphaga DSM 21508

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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources