Alignments for a candidate for pcaD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaD in Pseudomonas fluorescens GW456-L13

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate PfGW456L13_4585 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585
          Length = 263

 Score =  462 bits (1188), Expect = e-135
 Identities = 228/262 (87%), Positives = 245/262 (93%)

Query: 1   VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR 60
           V FVQLA+GEL YQLDGP  APVLVLSNSLGT+LHMWD QIPAF+KHFRVLRFDTRGHG+
Sbjct: 1   VAFVQLAEGELHYQLDGPVDAPVLVLSNSLGTDLHMWDAQIPAFSKHFRVLRFDTRGHGQ 60

Query: 61  SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT 120
           SLVTPGPYSIEQLGRDVLALLDAL+IERAHFCGLSMGGLIGQWLGINAG+RL++L+VCNT
Sbjct: 61  SLVTPGPYSIEQLGRDVLALLDALHIERAHFCGLSMGGLIGQWLGINAGDRLNQLIVCNT 120

Query: 121 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS 180
           AAKIGDPSVWNPRIE VLRDG AAMVALRDASIARWFTPDF++ANPA AKQITDMLAATS
Sbjct: 121 AAKIGDPSVWNPRIEMVLRDGQAAMVALRDASIARWFTPDFSEANPAAAKQITDMLAATS 180

Query: 181 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA 240
           P+GYAANCAAVRDADFR+QL+SI  P LVIAGTEDAVTPPSGG FIQE V GAEYAEFYA
Sbjct: 181 PEGYAANCAAVRDADFRDQLSSIKAPLLVIAGTEDAVTPPSGGHFIQEHVPGAEYAEFYA 240

Query: 241 AHLSNVQAGSAFSDRVLSFLLA 262
           AHLSNVQAG+ FS+ VL+FL A
Sbjct: 241 AHLSNVQAGADFSECVLAFLKA 262


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: 370
Number of extensions: 8
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 PfGW456L13_4585 (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.936.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.5e-109  350.5   0.0   2.8e-109  350.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585  Beta-ketoadipate enol-lactone hy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585  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 !  350.3   0.0  2.8e-109  2.8e-109       2     251 .]      11     261 ..      10     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: 350.3 bits;  conditional E-value: 2.8e-109
                                               TIGR02427   2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvp 56 
                                                             lhy+l+g+  d+pvlvl+nSLGtdl++wd++++a++k+frvlr+D+rGHG+S v+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585  11 LHYQLDGPV-DAPVLVLSNSLGTDLHMWDAQIPAFSKHFRVLRFDTRGHGQSLVT 64 
                                                             9********.********************************************* PP

                                               TIGR02427  57 egpysiedladdvlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsn 111
                                                              gpysie+l++dvlallDal+ie+a++cGlS+GGli+q+L+++++dr+++l+++n
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585  65 PGPYSIEQLGRDVLALLDALHIERAHFCGLSMGGLIGQWLGINAGDRLNQLIVCN 119
                                                             ******************************************************* PP

                                               TIGR02427 112 taakigtaesWeaRiaavraeG...laaladavlerwFtpafreaepaelelvrn 163
                                                             taakig++++W++Ri+ v ++G   + al+da+++rwFtp+f ea+pa+++++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585 120 TAAKIGDPSVWNPRIEMVLRDGqaaMVALRDASIARWFTPDFSEANPAAAKQITD 174
                                                             **********************999999*************************** PP

                                               TIGR02427 164 mlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadl 218
                                                             ml++++pegYaa+caA+rdad+r++l++i++P+lviaG+eD++tPp+  + i+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585 175 MLAATSPEGYAANCAAVRDADFRDQLSSIKAPLLVIAGTEDAVTPPSGGHFIQEH 229
                                                             ******************************************************* PP

                                               TIGR02427 219 vpgarfaeieeaaHlpnleqpeafaallrdflk 251
                                                             vpga++ae++ aaHl+n+++++ f++ + +flk
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4585 230 VPGAEYAEFY-AAHLSNVQAGADFSECVLAFLK 261
                                                             **********.********************96 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: 00:00:00.00
# Mc/sec: 6.92
//
[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