Alignments for a candidate for pcaF in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaF in Rhizorhabdus wittichii RW1

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_011950736.1 SWIT_RS26775 3-oxoadipyl-CoA thiolase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_000016765.1:WP_011950736.1
          Length = 400

 Score =  505 bits (1300), Expect = e-147
 Identities = 251/398 (63%), Positives = 317/398 (79%), Gaps = 2/398 (0%)

Query: 4   EVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGE 63
           + +ICDA+RTPIG+  GSLA VRADDLAA+P+KAL++RNP  DWS LD+V LGCANQAGE
Sbjct: 3   QAFICDAIRTPIGKLNGSLATVRADDLAALPIKALMDRNPDTDWSTLDDVILGCANQAGE 62

Query: 64  DNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSR 123
           DNRNVARMA+LLAGLP+ VPGVT+NRLC+SG++A+G A +AI SG+A+ +IAGGVESM+R
Sbjct: 63  DNRNVARMAVLLAGLPECVPGVTVNRLCSSGLNALGIASQAIRSGDADFMIAGGVESMTR 122

Query: 124 APYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQD 183
           APYV+GKA SAFGR QKIEDTT+GWRF+NP M+A YGVD MP+T +NVA ++ VSR  QD
Sbjct: 123 APYVLGKAGSAFGRDQKIEDTTLGWRFVNPAMQAAYGVDTMPQTGENVAQEWGVSREAQD 182

Query: 184 AFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVV-DADEHLRPDTTLEALAKLKPVN 242
            FAL SQ+ A RAQA G FA EI+PV +   +G+ V+ +ADEHLR  T+L+ LAKLKPV 
Sbjct: 183 RFALASQEKAARAQAGGRFAAEIIPVSVPQHRGDHVLFEADEHLRA-TSLDILAKLKPVT 241

Query: 243 GPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPA 302
           GP  TVTAGNASG+NDG+ A+++A+       GL  RA+V+GMA++G+APR+MG GP+ A
Sbjct: 242 GPGGTVTAGNASGLNDGAAAMLVATEATAAAQGLVTRARVVGMAASGIAPRIMGAGPIEA 301

Query: 303 VRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGAS 362
            R+++ R +++    DVIELNEAFA+Q +A    LGI   D RVNPNGGAIALGHPLG S
Sbjct: 302 ARRVMARHSITTDALDVIELNEAFASQAIATLSSLGIDPLDPRVNPNGGAIALGHPLGMS 361

Query: 363 GARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           GAR+ L+AV +L +  G+  L  MCVGVGQGVA+ +ER
Sbjct: 362 GARIALSAVEELHRVQGRYALAFMCVGVGQGVAVLLER 399


Lambda     K      H
   0.317    0.134    0.379 

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: 501
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_011950736.1 SWIT_RS26775 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.1923145.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-194  632.2  12.9   2.1e-194  632.0  12.9    1.0  1  NCBI__GCF_000016765.1:WP_011950736.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_011950736.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.0  12.9  2.1e-194  2.1e-194       2     399 ..       3     399 ..       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 632.0 bits;  conditional E-value: 2.1e-194
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           +++i+dairtpiG+  Gsl++vraddlaa+p+kal++rnp+ d++++ddvilGcanqaGednrnvarma+lla
  NCBI__GCF_000016765.1:WP_011950736.1   3 QAFICDAIRTPIGKLNGSLATVRADDLAALPIKALMDRNPDTDWSTLDDVILGCANQAGEDNRNVARMAVLLA 75 
                                           69*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp+ vpg+tvnrlc+sgl+alg+a +ai++G+ad++iaGGvesm+rap+vlGka saf+r++k+edtt+Gwr
  NCBI__GCF_000016765.1:WP_011950736.1  76 GLPECVPGVTVNRLCSSGLNALGIASQAIRSGDADFMIAGGVESMTRAPYVLGKAGSAFGRDQKIEDTTLGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           fvnp+++a yGvd+mp+t enva+e+gvsre qd fal sq+++a+aqa G fa+ei+pv+++q++G+++ ++
  NCBI__GCF_000016765.1:WP_011950736.1 149 FVNPAMQAAYGVDTMPQTGENVAQEWGVSREAQDRFALASQEKAARAQAGGRFAAEIIPVSVPQHRGDHVLFE 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +dehlr  t+l+ laklk+v+ ++gtvtaGnasG+ndGaaa+l+a+e +++++gl++rar++++a++G++pr+
  NCBI__GCF_000016765.1:WP_011950736.1 222 ADEHLR-ATSLDILAKLKPVTGPGGTVTAGNASGLNDGAAAMLVATEATAAAQGLVTRARVVGMAASGIAPRI 293
                                           ******.8***************************************************************** PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG gp+ a+++++ar +++ + ldvielneafa+qa+a+l +lg+   d rvnpnGGaialGhplG+sGar++
  NCBI__GCF_000016765.1:WP_011950736.1 294 MGAGPIEAARRVMARHSITTDALDVIELNEAFASQAIATLSSLGIDPLDPRVNPNGGAIALGHPLGMSGARIA 366
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvier 399
                                           l+a+++l++ +gryala +c+GvGqG+a+++er
  NCBI__GCF_000016765.1:WP_011950736.1 367 LSAVEELHRVQGRYALAFMCVGVGQGVAVLLER 399
                                           ********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.44
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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