Alignments for a candidate for gloB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gloB in Pseudomonas stutzeri RCH2

Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate GFF2028 Psest_2071 hydroxyacylglutathione hydrolase

Query= CharProtDB::CH_024825
         (251 letters)



>FitnessBrowser__psRCH2:GFF2028
          Length = 259

 Score =  220 bits (560), Expect = 3e-62
 Identities = 119/260 (45%), Positives = 163/260 (62%), Gaps = 11/260 (4%)

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

Query: 59  VGGVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYF 118
           VGGV+ L  +     VYGP         + + DG+   VL  +  VIA PGHTLGHI Y 
Sbjct: 62  VGGVERLKTQ-TGARVYGPAAENIPARDEALSDGQRIRVLDKDLEVIAVPGHTLGHIAYV 120

Query: 119 ----SKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKF 174
                +P+L  GDTLF+ GCGRLFEGT  QM+ SL++L++LPDDTLV C HEYTLSN++F
Sbjct: 121 HSDAEQPWLLSGDTLFAAGCGRLFEGTPEQMFASLQRLASLPDDTLVYCTHEYTLSNLRF 180

Query: 175 ALSILPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLL 234
           A ++ P++  I    R+V  LR +N  +LP  +  ER  N FLR+  ++ +     E   
Sbjct: 181 AQAVEPYNQEIQQRVREVTALREENHFSLPTRMNIERATNPFLRS-SVEAVQQAASEHCG 239

Query: 235 QQPEER---FAWLRSKKDRF 251
           ++ E+    FA LR+ KDRF
Sbjct: 240 RRLEDEVAVFAALRAWKDRF 259


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: 231
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: 251
Length of database: 259
Length adjustment: 24
Effective length of query: 227
Effective length of database: 235
Effective search space:    53345
Effective search space used:    53345
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: 47 (22.7 bits)

Align candidate GFF2028 Psest_2071 (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.15438.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.4e-107  343.9   0.0   2.7e-107  343.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2028  Psest_2071 hydroxyacylglutathion


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2028  Psest_2071 hydroxyacylglutathione hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.7   0.0  2.7e-107  2.7e-107       1     248 []       4     259 .]       4     259 .] 0.98

  Alignments for each domain:
  == domain 1  score: 343.7 bits;  conditional E-value: 2.7e-107
                           TIGR03413   1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeek.glkleaillTHhHaDHvggvaellekfpvkvvg 73 
                                         i+a+pa++dNyiwll+d+++ ++++vDpg+a+pvl++l+++ +++l++il+THhH+DHvggv++l+++++++v+g
  lcl|FitnessBrowser__psRCH2:GFF2028   4 IEALPAFTDNYIWLLQDDATqRCAAVDPGDAAPVLSWLQDHlDWRLSDILITHHHHDHVGGVERLKTQTGARVYG 78 
                                         6789**************999*****************98879******************************** PP

                           TIGR03413  74 paeeripgltkevkegdevellelevevlevpGHtlgHiayyleee..kvlFcgDtLfsaGCGrlfegtaeqmle 146
                                         pa+e+ip+ ++++++g+++++l++++ev++vpGHtlgHiay+ +++  ++l +gDtLf+aGCGrlfegt+eqm++
  lcl|FitnessBrowser__psRCH2:GFF2028  79 PAAENIPARDEALSDGQRIRVLDKDLEVIAVPGHTLGHIAYVHSDAeqPWLLSGDTLFAAGCGRLFEGTPEQMFA 153
                                         ******************************************9876669************************** PP

                           TIGR03413 147 slqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLraeea 221
                                         slq+la+Lp++t+vyc+HEYtlsNlrFa+avep n+++++r++ev+alr++++ +lP++++ e+atNpFLr + +
  lcl|FitnessBrowser__psRCH2:GFF2028 154 SLQRLASLPDDTLVYCTHEYTLSNLRFAQAVEPYNQEIQQRVREVTALREENHFSLPTRMNIERATNPFLRSSVE 228
                                         *************************************************************************** PP

                           TIGR03413 222 evkaalee....ekaeevevfaelRekkdkf 248
                                         +v++a++e    + ++ev+vfa+lR++kd+f
  lcl|FitnessBrowser__psRCH2:GFF2028 229 AVQQAASEhcgrRLEDEVAVFAALRAWKDRF 259
                                         ***999998998999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (259 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: 9.06
//
[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