Alignments for a candidate for gloB in Thiomicrorhabdus arctica DSM 13458

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Thiomicrorhabdus arctica DSM 13458

Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate WP_019556343.1 F612_RS0103390 hydroxyacylglutathione hydrolase

Query= curated2:Q31H51
         (268 letters)



>NCBI__GCF_000381085.1:WP_019556343.1
          Length = 258

 Score =  207 bits (526), Expect = 2e-58
 Identities = 112/262 (42%), Positives = 156/262 (59%), Gaps = 10/262 (3%)

Query: 1   MKIVGLPTLSD---NYTWVIQSENADDKRAWIVDPGESQKVIHYFEENQLQLDGILLTHH 57
           M IVGLP+L D   NY W++     +  +AW+VDPGES +VI +  +N+L L  IL+TH 
Sbjct: 1   MNIVGLPSLIDTYENYIWILY----EGDKAWVVDPGESTQVIDFLNQNKLNLQAILITHT 56

Query: 58  HYDHTDGIMGVMDALGEVAIVSNAQGPFKPVTHPVKEGDQVQV-LNETFQVIETPGHTDE 116
           H+DH DGI G+ +A  E  I   A+     +   + EGD + + +N +  V++TPGHT  
Sbjct: 57  HFDHIDGIPGLKEAFPETVIYGPAKNQHHIIQTGLFEGDVIPLTMNFSLTVLDTPGHTAN 116

Query: 117 HICFYHPEALFSGDTLFTGGCGKIWQNPPEQMAESLLKLRALNDDCMVYCGHEYTYANLN 176
           HI FY+ +ALF GDTLFT GCG++     E+  +S++KLR L D    YC HEYT  NL 
Sbjct: 117 HISFYNDQALFCGDTLFTAGCGRLLGGTVEEFTQSIIKLRDLPDSVSFYCAHEYTEDNLK 176

Query: 177 FAKIAEPNTPAILDRLAEVKTNTQRNIPCVPARLGLEKQTNPFLRFDHPPLMQTLMERQA 236
           FA + EP+  A+  R+ +      +      + L  EK TNPF+RFD   L   LME  A
Sbjct: 177 FALLVEPDNEALQQRVKQPLFKYPQIHKGPLSTLLEEKNTNPFMRFDDLTLKGKLMEHGA 236

Query: 237 QPNESVSTLFATLRAWKDELDQ 258
             ++S ++LF TLR WKD+ DQ
Sbjct: 237 --SDSPTSLFKTLREWKDQFDQ 256


Lambda     K      H
   0.318    0.135    0.417 

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: 243
Number of extensions: 12
Number of successful extensions: 5
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: 268
Length of database: 258
Length adjustment: 25
Effective length of query: 243
Effective length of database: 233
Effective search space:    56619
Effective search space used:    56619
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_019556343.1 F612_RS0103390 (hydroxyacylglutathione hydrolase)
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))

# 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/TIGR03413.hmm
# target sequence database:        /tmp/gapView.1645800.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03413  [M=248]
Accession:   TIGR03413
Description: GSH_gloB: hydroxyacylglutathione hydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.1e-82  261.7   0.0    3.6e-82  261.4   0.0    1.0  1  NCBI__GCF_000381085.1:WP_019556343.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381085.1:WP_019556343.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.4   0.0   3.6e-82   3.6e-82       8     248 .]      13     254 ..       6     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 3.6e-82
                             TIGR03413   8 sdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.vkvvgpaeeri 79 
                                            +Nyiw+l + + +a+vvDpge++ v+++l++++l+l+ail+TH H DH++g+  l+e+fp + ++gpa+++ 
  NCBI__GCF_000381085.1:WP_019556343.1  13 YENYIWILYEGD-KAWVVDPGESTQVIDFLNQNKLNLQAILITHTHFDHIDGIPGLKEAFPeTVIYGPAKNQH 84 
                                           58**********.************************************************9999******** PP

                             TIGR03413  80 pgltkevkegdevel.lelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslqkl 151
                                           + +++ + egd + l ++ +++vl++pGHt++Hi++y +  ++lFcgDtLf+aGCGrl+ gt e++++s+ kl
  NCBI__GCF_000381085.1:WP_019556343.1  85 HIIQTGLFEGDVIPLtMNFSLTVLDTPGHTANHISFYND--QALFCGDTLFTAGCGRLLGGTVEEFTQSIIKL 155
                                           **************98899********************..9******************************* PP

                             TIGR03413 152 aaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevk 224
                                           ++Lp++   ycaHEYt++Nl+Fal vep+neal++r+k+   +  + +    stl eek+tNpF+r+++ ++k
  NCBI__GCF_000381085.1:WP_019556343.1 156 RDLPDSVSFYCAHEYTEDNLKFALLVEPDNEALQQRVKQPLFKYPQIHKGPLSTLLEEKNTNPFMRFDDLTLK 228
                                           **************************************9988888877777799******************* PP

                             TIGR03413 225 aalee..ekaeevevfaelRekkdkf 248
                                            +l e  +++++++ f++lRe+kd+f
  NCBI__GCF_000381085.1:WP_019556343.1 229 GKLMEhgASDSPTSLFKTLREWKDQF 254
                                           999887888999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (258 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: 19.62
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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