Alignments for a candidate for gloA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloA in Stenotrophomonas chelatiphaga DSM 21508

Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate WP_057508877.1 ABB28_RS12120 lactoylglutathione lyase

Query= BRENDA::Q88GF8
         (175 letters)



>NCBI__GCF_001431535.1:WP_057508877.1
          Length = 172

 Score =  257 bits (656), Expect = 8e-74
 Identities = 120/169 (71%), Positives = 138/169 (81%), Gaps = 1/169 (0%)

Query: 1   MSLHDLQTLPGVTAQPDAATAQFVFNHTMLRVKDIEKSLDFYTRVLGFRLVDKRDFPEAA 60
           MSL DLQT+PGV AQP A TA FVFNHTMLRVKD   SLDFYTRVLG+RL+DKRDF EA 
Sbjct: 1   MSLSDLQTVPGVAAQPPAETAGFVFNHTMLRVKDATASLDFYTRVLGYRLIDKRDFAEAQ 60

Query: 61  FSLYFLALVDPAQI-PADDTARHQWMKSIPGVLELTHNHGTENDADFAYHNGNTDPRGFG 119
           FSLYFLAL+    + P  D  R  WM  IPGVLELTHNHGTE      YH+GN+DPRGFG
Sbjct: 61  FSLYFLALLPAGTVVPESDAERRLWMAGIPGVLELTHNHGTEAQDGPVYHDGNSDPRGFG 120

Query: 120 HICISVPDVRAACARFEELEVPFQKRLQDGRMNHLAFVKDPDGYWVEVI 168
           HIC+SVPD+++AC RF++L+VP+QKRL+DGRM HLAF+KDPDGYWVE+I
Sbjct: 121 HICVSVPDIQSACKRFDDLQVPYQKRLEDGRMKHLAFIKDPDGYWVEII 169


Lambda     K      H
   0.323    0.139    0.431 

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: 192
Number of extensions: 5
Number of successful extensions: 2
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: 175
Length of database: 172
Length adjustment: 19
Effective length of query: 156
Effective length of database: 153
Effective search space:    23868
Effective search space used:    23868
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 44 (21.6 bits)

Align candidate WP_057508877.1 ABB28_RS12120 (lactoylglutathione lyase)
to HMM TIGR00068 (gloA: lactoylglutathione lyase (EC 4.4.1.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00068.hmm
# target sequence database:        /tmp/gapView.1942.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00068  [M=150]
Accession:   TIGR00068
Description: glyox_I: lactoylglutathione lyase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      3e-46  142.7   0.0    3.7e-46  142.4   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508877.1  ABB28_RS12120 lactoylglutathione


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508877.1  ABB28_RS12120 lactoylglutathione lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.0   3.7e-46   3.7e-46      11     141 ..      18     171 ..       9     172 .] 0.95

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 3.7e-46
                                 TIGR00068  11 eatkkylllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessa............ 67 
                                                +t ++++ htmlrv+d  +sldfyt+vlG +l+ k+df e +fsl+fl+  +  +             
  lcl|NCBI__GCF_001431535.1:WP_057508877.1  18 AETAGFVFNHTMLRVKDATASLDFYTRVLGYRLIDKRDFAEAQFSLYFLALLPAGTVvpesdaerrlwm 86 
                                               568899********************************************9998888899999****** PP

                                 TIGR00068  68 ....avieLtynwgtek.....ydlGn....gfGhiaiavddvykacervkakGgkvvrepgpvkggtk 123
                                                    v+eLt+n+gte      y+ Gn    gfGhi ++v+d+++ac+r+ ++ + + ++    +g++k
  lcl|NCBI__GCF_001431535.1:WP_057508877.1  87 agipGVLELTHNHGTEAqdgpvYHDGNsdprGFGHICVSVPDIQSACKRFDDLQVPYQKRL--EDGRMK 153
                                               ****************99*****************************************99..****** PP

                                 TIGR00068 124 viafvkDPDGykiellek 141
                                               ++af+kDPDGy++e++ +
  lcl|NCBI__GCF_001431535.1:WP_057508877.1 154 HLAFIKDPDGYWVEIISN 171
                                               ***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (150 nodes)
Target sequences:                          1  (172 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.92
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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