Alignments for a candidate for pcaD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Pseudomonas stutzeri RCH2

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate GFF3011 Psest_3069 3-oxoadipate enol-lactonase

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



>FitnessBrowser__psRCH2:GFF3011
          Length = 262

 Score =  358 bits (919), Expect = e-104
 Identities = 179/257 (69%), Positives = 205/257 (79%)

Query: 4   VQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLV 63
           V+LAD  L Y+ DG E+APVLVLSNSLGT+L MWD QI AF +HFRVLR+DTRGHG S V
Sbjct: 4   VKLADVSLNYRFDGAENAPVLVLSNSLGTDLQMWDDQIAAFAEHFRVLRYDTRGHGGSGV 63

Query: 64  TPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAK 123
           TPGPYSIEQLG+DVL +LDA  IER  FCGLSMGGLIGQWLGI+AGERL +LV+CNT AK
Sbjct: 64  TPGPYSIEQLGQDVLGMLDAFGIERFAFCGLSMGGLIGQWLGIHAGERLQRLVLCNTGAK 123

Query: 124 IGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQG 183
           IG   VWN RI++VL      M  +RDASIARWFT DFAQANPAVA +ITDM+A+TSP G
Sbjct: 124 IGTDEVWNTRIDSVLAGREQTMRDMRDASIARWFTADFAQANPAVAARITDMIASTSPDG 183

Query: 184 YAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAHL 243
           YAANCAAVRDAD+REQLA+I  PTL++ G +D VT    G FIQ  + GAE   F AAHL
Sbjct: 184 YAANCAAVRDADYREQLATIKTPTLIVCGAKDPVTTVEHGEFIQANIPGAELVAFEAAHL 243

Query: 244 SNVQAGSAFSDRVLSFL 260
           SNV+AG AF+ RVL+FL
Sbjct: 244 SNVEAGDAFTQRVLTFL 260


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: 292
Number of extensions: 9
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: 262
Length adjustment: 25
Effective length of query: 241
Effective length of database: 237
Effective search space:    57117
Effective search space used:    57117
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 GFF3011 Psest_3069 (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.20217.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-102  326.4   0.1   6.4e-102  326.2   0.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3011  Psest_3069 3-oxoadipate enol-lac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3011  Psest_3069 3-oxoadipate enol-lactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.2   0.1  6.4e-102  6.4e-102       2     251 .]      11     261 ..      10     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 326.2 bits;  conditional E-value: 6.4e-102
                           TIGR02427   2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallDal 76 
                                         l+yr++gae ++pvlvl+nSLGtdl++wd++++a++++frvlryD+rGHG S v+ gpysie+l++dvl++lDa+
  lcl|FitnessBrowser__psRCH2:GFF3011  11 LNYRFDGAE-NAPVLVLSNSLGTDLQMWDDQIAAFAEHFRVLRYDTRGHGGSGVTPGPYSIEQLGQDVLGMLDAF 84 
                                         89*******.***************************************************************** PP

                           TIGR02427  77 giekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaav...raeGlaaladavlerwFtp 148
                                         gie++a+cGlS+GGli+q+L++++++r+++lvl+nt akigt e+W++Ri+ v   r++ +  ++da+++rwFt+
  lcl|FitnessBrowser__psRCH2:GFF3011  85 GIERFAFCGLSMGGLIGQWLGIHAGERLQRLVLCNTGAKIGTDEVWNTRIDSVlagREQTMRDMRDASIARWFTA 159
                                         ***************************************************994445677*************** PP

                           TIGR02427 149 afreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpgar 223
                                         +f++a+pa ++ +++m+++++p+gYaa+caA+rdad+re+l  i+ Ptl++ G++D++t  e+ + i++ +pga+
  lcl|FitnessBrowser__psRCH2:GFF3011 160 DFAQANPAVAARITDMIASTSPDGYAANCAAVRDADYREQLATIKTPTLIVCGAKDPVTTVEHGEFIQANIPGAE 234
                                         *************************************************************************** PP

                           TIGR02427 224 faeieeaaHlpnleqpeafaallrdflk 251
                                         ++ +e aaHl+n+e+++af++++ +fl+
  lcl|FitnessBrowser__psRCH2:GFF3011 235 LVAFE-AAHLSNVEAGDAFTQRVLTFLR 261
                                         *****.********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (262 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: 9.68
//
[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