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.2510.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.23
//
[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:

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:

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:

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:

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