Alignments for a candidate for pcaD in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Pseudomonas simiae WCS417

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate GFF1325 PS417_06735 3-oxoadipate enol-lactonase

Query= reanno::pseudo3_N2E3:AO353_17230
         (266 letters)



>FitnessBrowser__WCS417:GFF1325
          Length = 263

 Score =  458 bits (1178), Expect = e-134
 Identities = 226/261 (86%), Positives = 243/261 (93%)

Query: 1   VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR 60
           + FVQLA+GEL YQLDGPE APVLVLSNSLGT+LHMWD+QIPAFT+HFRVLRFDTRGHG+
Sbjct: 1   MAFVQLAEGELHYQLDGPEGAPVLVLSNSLGTDLHMWDLQIPAFTQHFRVLRFDTRGHGK 60

Query: 61  SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT 120
           SLVTPGPYSIEQLG+DV+ALLDAL+I+RAHFCGLSMGGLIGQWLGINAG+RL +LVVCNT
Sbjct: 61  SLVTPGPYSIEQLGQDVIALLDALDIQRAHFCGLSMGGLIGQWLGINAGQRLQRLVVCNT 120

Query: 121 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS 180
           AAKIG P VWNPRIE VLRDG AAMVALRDASIARWFT DFA ANP  AKQITDMLAATS
Sbjct: 121 AAKIGTPEVWNPRIEMVLRDGAAAMVALRDASIARWFTADFAAANPYQAKQITDMLAATS 180

Query: 181 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA 240
           P+GYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPP+G  FIQ  V+GAEYAEFYA
Sbjct: 181 PEGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPAGSHFIQNHVQGAEYAEFYA 240

Query: 241 AHLSNVQAGSAFSDRVLSFLL 261
           AHLSNVQAG+AFSD V+ FLL
Sbjct: 241 AHLSNVQAGAAFSDCVIEFLL 261


Lambda     K      H
   0.321    0.136    0.410 

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: 358
Number of extensions: 5
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: 266
Length of database: 263
Length adjustment: 25
Effective length of query: 241
Effective length of database: 238
Effective search space:    57358
Effective search space used:    57358
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: 47 (22.7 bits)

Align candidate GFF1325 PS417_06735 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

# 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/TIGR02427.hmm
# target sequence database:        /tmp/gapView.20859.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02427  [M=251]
Accession:   TIGR02427
Description: protocat_pcaD: 3-oxoadipate enol-lactonase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.3e-110  351.9   0.2     1e-109  351.7   0.2    1.0  1  lcl|FitnessBrowser__WCS417:GFF1325  PS417_06735 3-oxoadipate enol-la


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1325  PS417_06735 3-oxoadipate enol-lactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.7   0.2    1e-109    1e-109       2     250 ..      11     260 ..      10     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: 351.7 bits;  conditional E-value: 1e-109
                           TIGR02427   2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallDal 76 
                                         lhy+l+g+e ++pvlvl+nSLGtdl++wd +++a+t++frvlr+D+rGHG+S v+ gpysie+l++dv+allDal
  lcl|FitnessBrowser__WCS417:GFF1325  11 LHYQLDGPE-GAPVLVLSNSLGTDLHMWDLQIPAFTQHFRVLRFDTRGHGKSLVTPGPYSIEQLGQDVIALLDAL 84 
                                         9********.***************************************************************** PP

                           TIGR02427  77 giekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeG...laaladavlerwFtp 148
                                         +i++a++cGlS+GGli+q+L++++++r+++lv++ntaakigt+e+W++Ri+ v ++G   + al+da+++rwFt+
  lcl|FitnessBrowser__WCS417:GFF1325  85 DIQRAHFCGLSMGGLIGQWLGINAGQRLQRLVVCNTAAKIGTPEVWNPRIEMVLRDGaaaMVALRDASIARWFTA 159
                                         *********************************************************8888999*********** PP

                           TIGR02427 149 afreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpgar 223
                                         +f++a+p +++++++ml++++pegYaa+caA+rdad+re+l +i+vPtlviaG+eD++tPp+  + i+++v ga+
  lcl|FitnessBrowser__WCS417:GFF1325 160 DFAAANPYQAKQITDMLAATSPEGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPAGSHFIQNHVQGAE 234
                                         *************************************************************************** PP

                           TIGR02427 224 faeieeaaHlpnleqpeafaallrdfl 250
                                         +ae++ aaHl+n+++++af++ +++fl
  lcl|FitnessBrowser__WCS417:GFF1325 235 YAEFY-AAHLSNVQAGAAFSDCVIEFL 260
                                         *****.********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (263 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: 00:00:00.01
# Mc/sec: 5.95
//
[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