GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas stutzeri RCH2

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF2603 Psest_2653 fatty oxidation complex, beta subunit FadA

Query= BRENDA::P28790
         (391 letters)



>FitnessBrowser__psRCH2:GFF2603
          Length = 391

 Score =  707 bits (1824), Expect = 0.0
 Identities = 347/391 (88%), Positives = 368/391 (94%)

Query: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWG 60
           MSLNPRD VIVDFGRTPMGRSKGGMHRNTRAE MSAHLI  VL RN K+DP EVEDVIWG
Sbjct: 1   MSLNPRDAVIVDFGRTPMGRSKGGMHRNTRAETMSAHLIDGVLARNPKIDPAEVEDVIWG 60

Query: 61  CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMT+IPHTSA QTVSRLCGSSMSALHTA QAI T NGDVFV+G
Sbjct: 61  CVNQTLEQGWNIARMASLMTRIPHTSAGQTVSRLCGSSMSALHTAVQAIQTNNGDVFVIG 120

Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180
           GVEHMGHVSMMHGVDPNP +SLYAAKASGMMGLTAEMLGKMHGI+REQQDAF  RSH+LA
Sbjct: 121 GVEHMGHVSMMHGVDPNPQLSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGERSHRLA 180

Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240
           HKAT+EG FKDEIIPM+GYDE+GFLK+FDYDETIRPDTTLESLAALKPAFNPKGGTVTAG
Sbjct: 181 HKATLEGNFKDEIIPMEGYDEDGFLKVFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240

Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300
           TSSQITDGASCMIVMSAQRAKDLG++PLAV+R+MA+AGVDPAIMGYGPVP+TQK LKRAG
Sbjct: 241 TSSQITDGASCMIVMSAQRAKDLGIQPLAVVRAMALAGVDPAIMGYGPVPSTQKVLKRAG 300

Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360
           L M DI  +ELNEAFAAQALPVLKDLK+LDKM EKVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LTMDDISHVELNEAFAAQALPVLKDLKLLDKMEEKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391
           LNVMKQN GT G++TMCIGLGQGI+TVFERV
Sbjct: 361 LNVMKQNNGTIGVATMCIGLGQGISTVFERV 391


Lambda     K      H
   0.318    0.133    0.386 

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: 631
Number of extensions: 16
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF2603 Psest_2653 (fatty oxidation complex, beta subunit FadA)
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

# 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/TIGR02445.hmm
# target sequence database:        /tmp/gapView.4483.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02445  [M=385]
Accession:   TIGR02445
Description: fadA: acetyl-CoA C-acyltransferase FadA
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.9e-229  745.7   6.9   5.5e-229  745.6   6.9    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2603  Psest_2653 fatty oxidation compl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2603  Psest_2653 fatty oxidation complex, beta subunit FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  745.6   6.9  5.5e-229  5.5e-229       1     385 []       7     391 .]       7     391 .] 1.00

  Alignments for each domain:
  == domain 1  score: 745.6 bits;  conditional E-value: 5.5e-229
                           TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallae 75 
                                         d vivd++rtpmgrskgg++rntrae +sahl+ ++larnpk+++aeved++wgcv+qtleqg+niar+a+l+++
  lcl|FitnessBrowser__psRCH2:GFF2603   7 DAVIVDFGRTPMGRSKGGMHRNTRAETMSAHLIDGVLARNPKIDPAEVEDVIWGCVNQTLEQGWNIARMASLMTR 81 
                                         579************************************************************************ PP

                           TIGR02445  76 vphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltae 150
                                         +ph++a +tv+rlcgssm+alh+a +ai t++++v++iggvehmghvsm+hgvd++p+ls  +aka+gmmgltae
  lcl|FitnessBrowser__psRCH2:GFF2603  82 IPHTSAGQTVSRLCGSSMSALHTAVQAIQTNNGDVFVIGGVEHMGHVSMMHGVDPNPQLSLYAAKASGMMGLTAE 156
                                         *************************************************************************** PP

                           TIGR02445 151 mlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafd 225
                                         mlgk+hgi+reqqdaf+ rsh +ah+atleg+fk+eiip+egyd+dg+lkv+dyde+irp+tt+e+laal+paf+
  lcl|FitnessBrowser__psRCH2:GFF2603 157 MLGKMHGITREQQDAFGERSHRLAHKATLEGNFKDEIIPMEGYDEDGFLKVFDYDETIRPDTTLESLAALKPAFN 231
                                         *************************************************************************** PP

                           TIGR02445 226 pkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdi 300
                                         pk+gtvtagtss+++dgas+m+vms++ra++lg++p+a++r+ma+agvdp+imgygpvp+t+k lkragl+++di
  lcl|FitnessBrowser__psRCH2:GFF2603 232 PKGGTVTAGTSSQITDGASCMIVMSAQRAKDLGIQPLAVVRAMALAGVDPAIMGYGPVPSTQKVLKRAGLTMDDI 306
                                         *************************************************************************** PP

                           TIGR02445 301 dvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglg 375
                                           +elneafaaqalpvlkdl+lldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++ g+atmciglg
  lcl|FitnessBrowser__psRCH2:GFF2603 307 SHVELNEAFAAQALPVLKDLKLLDKMEEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNNGTIGVATMCIGLG 381
                                         *************************************************************************** PP

                           TIGR02445 376 qgiatvferv 385
                                         qgi+tvferv
  lcl|FitnessBrowser__psRCH2:GFF2603 382 QGISTVFERV 391
                                         *********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 00:00:00.01
# Mc/sec: 10.68
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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