Alignments for a candidate for pcaD in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Pseudomonas fluorescens FW300-N1B4

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate Pf1N1B4_3238 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238
          Length = 268

 Score =  462 bits (1189), Expect = e-135
 Identities = 231/267 (86%), Positives = 247/267 (92%), Gaps = 5/267 (1%)

Query: 1   VGFVQLADGELKYQ-----LDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDT 55
           V FVQLA+GEL YQ     LDGP  APVLVLSNSLGT+LHMWD QIPAFT+HFRVLRFDT
Sbjct: 1   VAFVQLAEGELHYQIQGPQLDGPADAPVLVLSNSLGTDLHMWDAQIPAFTEHFRVLRFDT 60

Query: 56  RGHGRSLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKL 115
           RGHG+SLVTPGPYSIEQLGRDVLALLDAL+IERAHFCGLSMGGLIGQWLGINA +RL+KL
Sbjct: 61  RGHGQSLVTPGPYSIEQLGRDVLALLDALHIERAHFCGLSMGGLIGQWLGINASQRLNKL 120

Query: 116 VVCNTAAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDM 175
           +VCNTAAKIGDPSVWNPRIETVLRDG AAMVALRDASIARWFT DFA+ANPA  K+ITDM
Sbjct: 121 IVCNTAAKIGDPSVWNPRIETVLRDGSAAMVALRDASIARWFTADFAEANPAAVKRITDM 180

Query: 176 LAATSPQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEY 235
           LAATSP+GYAANCAAVRDADFR+QL+SI VP LVIAGTEDAVTPPSGG FIQE V+GAEY
Sbjct: 181 LAATSPEGYAANCAAVRDADFRDQLSSIKVPLLVIAGTEDAVTPPSGGHFIQEHVQGAEY 240

Query: 236 AEFYAAHLSNVQAGSAFSDRVLSFLLA 262
           AEFYAAHLSNVQAG+AFSDRVL+FL A
Sbjct: 241 AEFYAAHLSNVQAGAAFSDRVLAFLSA 267


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: 372
Number of extensions: 7
Number of successful extensions: 2
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: 268
Length adjustment: 25
Effective length of query: 241
Effective length of database: 243
Effective search space:    58563
Effective search space used:    58563
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 Pf1N1B4_3238 (Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24))
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.13212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     6e-108  346.0   0.1   6.7e-108  345.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238  Beta-ketoadipate enol-lactone hy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238  Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.8   0.1  6.7e-108  6.7e-108       2     250 ..      11     265 ..      10     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 345.8 bits;  conditional E-value: 6.7e-108
                                      TIGR02427   2 lhyrlegae....adkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpys 61 
                                                    lhy+++g++    ad+pvlvl+nSLGtdl++wd++++a+t++frvlr+D+rGHG+S v+ gpys
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238  11 LHYQIQGPQldgpADAPVLVLSNSLGTDLHMWDAQIPAFTEHFRVLRFDTRGHGQSLVTPGPYS 74 
                                                    7888776653333499************************************************ PP

                                      TIGR02427  62 iedladdvlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaR 125
                                                    ie+l++dvlallDal+ie+a++cGlS+GGli+q+L++++++r+++l+++ntaakig++++W++R
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238  75 IEQLGRDVLALLDALHIERAHFCGLSMGGLIGQWLGINASQRLNKLIVCNTAAKIGDPSVWNPR 138
                                                    **************************************************************** PP

                                      TIGR02427 126 iaavraeG...laaladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlr 186
                                                    i++v ++G   + al+da+++rwFt++f+ea+pa+++ +++ml++++pegYaa+caA+rdad+r
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238 139 IETVLRDGsaaMVALRDASIARWFTADFAEANPAAVKRITDMLAATSPEGYAANCAAVRDADFR 202
                                                    ********999999************************************************** PP

                                      TIGR02427 187 erleeiavPtlviaGdeDgstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdfl 250
                                                    ++l++i+vP+lviaG+eD++tPp+  + i+++v ga++ae++ aaHl+n+++++af++++ +fl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3238 203 DQLSSIKVPLLVIAGTEDAVTPPSGGHFIQEHVQGAEYAEFY-AAHLSNVQAGAAFSDRVLAFL 265
                                                    ******************************************.********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (251 nodes)
Target sequences:                          1  (268 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: 7.07
//
[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