Alignments for a candidate for gloB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Escherichia coli BW25113

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate 14352 b0212 predicted hydroxyacylglutathione hydrolase (NCBI)

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__Keio:14352
          Length = 251

 Score =  520 bits (1339), Expect = e-152
 Identities = 251/251 (100%), Positives = 251/251 (100%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVG 60
           MNLNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVG
Sbjct: 1   MNLNSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVG 60

Query: 61  GVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK 120
           GVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK
Sbjct: 61  GVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK 120

Query: 121 PYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSILP 180
           PYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSILP
Sbjct: 121 PYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSILP 180

Query: 181 HDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQPEER 240
           HDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQPEER
Sbjct: 181 HDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQPEER 240

Query: 241 FAWLRSKKDRF 251
           FAWLRSKKDRF
Sbjct: 241 FAWLRSKKDRF 251


Lambda     K      H
   0.321    0.138    0.425 

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: 407
Number of extensions: 1
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: 251
Length of database: 251
Length adjustment: 24
Effective length of query: 227
Effective length of database: 227
Effective search space:    51529
Effective search space used:    51529
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 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate 14352 b0212 (predicted hydroxyacylglutathione hydrolase (NCBI))
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.2432.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.3e-108  346.8   0.0   3.6e-108  346.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:14352  b0212 predicted hydroxyacylgluta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14352  b0212 predicted hydroxyacylglutathione hydrolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.6   0.0  3.6e-108  3.6e-108       2     248 .]       4     251 .]       3     251 .] 0.99

  Alignments for each domain:
  == domain 1  score: 346.6 bits;  conditional E-value: 3.6e-108
                       TIGR03413   2 iaipalsdNyiwllkdekseavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp.vkvvgpaeeri 79 
                                     ++ipa++dNyiw+l+de+ ++++vDpg+aepvl+a++++++++eai+lTHhH+DHvggv+el+ekfp + v+gp+e++ 
  lcl|FitnessBrowser__Keio:14352   4 NSIPAFDDNYIWVLNDEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVGGVKELVEKFPqIVVYGPQETQD 82 
                                     689**************************************************************************** PP

                       TIGR03413  80 pgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslqklaaLpeet 158
                                     +g+t+ vk+g++  +l++e++v+++pGHtlgHi+y+++  ++lFcgDtLfs GCGrlfegta+qm++sl+kl+aLp++t
  lcl|FitnessBrowser__Keio:14352  83 KGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK--PYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDT 159
                                     **************************************..*************************************** PP

                       TIGR03413 159 kvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaevkaalee..ekaeev 235
                                     +v+caHEYtlsN++Fal++ p++ ++++++++v++lrak+++tlP+ l++e+++N+FLr+e+ ++ + ++e    ++++
  lcl|FitnessBrowser__Keio:14352 160 LVCCAHEYTLSNMKFALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEetLLQQPE 238
                                     *********************************************************************99777899** PP

                       TIGR03413 236 evfaelRekkdkf 248
                                     e fa lR+kkd+f
  lcl|FitnessBrowser__Keio:14352 239 ERFAWLRSKKDRF 251
                                     ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (251 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.97
//
[ok]

This GapMind analysis is from Sep 17 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