Alignments for a candidate for gloB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Pseudomonas simiae WCS417

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate GFF2397 PS417_12220 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__WCS417:GFF2397
          Length = 255

 Score =  222 bits (566), Expect = 5e-63
 Identities = 117/255 (45%), Positives = 159/255 (62%), Gaps = 5/255 (1%)

Query: 1   MNLNSIPAFDDNYIWVLNDEAG-RCLIVDPGDAEPVLNAIAAN-NWQPEAIFLTHHHHDH 58
           + ++++PAF DNYIW+L D +  RC +VDPGDA PVL  +  N  W    I +THHHHDH
Sbjct: 2   IQISALPAFTDNYIWLLQDPSTQRCAVVDPGDAAPVLAWLKQNPEWALSDILITHHHHDH 61

Query: 59  VGGVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYF 118
           VGGV+ L ++     VYGP   +       + D +   VLG +F +   PGHTLGHI ++
Sbjct: 62  VGGVEHL-KRVTDAKVYGPANEKIPARDVALNDNDRISVLGWDFDIYTVPGHTLGHIAFY 120

Query: 119 SKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSI 178
               LFCGDTLF+ GCGRLFEGT +QM+ SL+ L+ALP DTLV C HEYT SN+KFA ++
Sbjct: 121 HLGVLFCGDTLFAAGCGRLFEGTPAQMHTSLESLAALPADTLVYCTHEYTQSNLKFAQAV 180

Query: 179 LPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLL--QQ 236
            P +  I      V++LR + +ITLP  L  E++ N FLRT +  +    +E +    + 
Sbjct: 181 EPDNADIAQRVEIVRQLRERGEITLPSNLALEKRTNPFLRTSETSVKQKADERSGRDNRS 240

Query: 237 PEERFAWLRSKKDRF 251
             E FA LR+ KD+F
Sbjct: 241 GAEVFASLRAWKDKF 255


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: 224
Number of extensions: 6
Number of successful extensions: 3
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: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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 GFF2397 PS417_12220 (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.3315.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     3e-108  346.9   0.0   3.4e-108  346.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2397  PS417_12220 hydroxyacylglutathio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2397  PS417_12220 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.7   0.0  3.4e-108  3.4e-108       1     248 []       4     255 .]       4     255 .] 0.98

  Alignments for each domain:
  == domain 1  score: 346.7 bits;  conditional E-value: 3.4e-108
                           TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeek.glkleaillTHhHaDHvggvaellekfpvkvvg 73 
                                         i a+pa++dNyiwll+d+++ +++vvDpg+a+pvl++l+++ ++ l++il+THhH+DHvggv++l++ +++kv+g
  lcl|FitnessBrowser__WCS417:GFF2397   4 ISALPAFTDNYIWLLQDPSTqRCAVVDPGDAAPVLAWLKQNpEWALSDILITHHHHDHVGGVEHLKRVTDAKVYG 78 
                                         5789***************99*****************99879******************************** PP

                           TIGR03413  74 paeeripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmlesl 148
                                         pa+e+ip+ +++++++d++++l+ ++++++vpGHtlgHia+y    +vlFcgDtLf+aGCGrlfegt++qm++sl
  lcl|FitnessBrowser__WCS417:GFF2397  79 PANEKIPARDVALNDNDRISVLGWDFDIYTVPGHTLGHIAFYHL--GVLFCGDTLFAAGCGRLFEGTPAQMHTSL 151
                                         ******************************************99..***************************** PP

                           TIGR03413 149 qklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeeaev 223
                                         + laaLp++t+vyc+HEYt+sNl+Fa+avep+n+++++r++ v++lr++g++tlPs+la ek+tNpFLr++e++v
  lcl|FitnessBrowser__WCS417:GFF2397 152 ESLAALPADTLVYCTHEYTQSNLKFAQAVEPDNADIAQRVEIVRQLRERGEITLPSNLALEKRTNPFLRTSETSV 226
                                         *************************************************************************** PP

                           TIGR03413 224 kaalee....ekaeevevfaelRekkdkf 248
                                         k++++e    ++++ +evfa+lR++kdkf
  lcl|FitnessBrowser__WCS417:GFF2397 227 KQKADErsgrDNRSGAEVFASLRAWKDKF 255
                                         ****99999888999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (255 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 6.78
//
[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