GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Rhodanobacter denitrificans 2APBS1

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_000230695.2:WP_015446959.1
          Length = 400

 Score =  501 bits (1289), Expect = e-146
 Identities = 252/395 (63%), Positives = 307/395 (77%)

Query: 6   YICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGEDN 65
           ++ DA RTP GR GG+LA VRADDLAA+P+ AL+ R+P +DW+ LDEV LGCANQAGEDN
Sbjct: 5   WLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQAGEDN 64

Query: 66  RNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRAP 125
           RNVARMA LLAGLP SVP VT+NRLCASG++A+G A RAIA GEAELV+AGGVESMSRAP
Sbjct: 65  RNVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAP 124

Query: 126 YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDAF 185
           YV+ KAD A+ RGQ++EDTT+GWR +NP M+A YG+D+M +TA+N+A ++ + R  QDA+
Sbjct: 125 YVLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDSQDAY 184

Query: 186 ALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGPD 245
           ALRSQQ    AQA G+ AEEI  V     K   VV  DEH R DTT   LA LKP+ G  
Sbjct: 185 ALRSQQRTAHAQAQGWLAEEITAVHAPHGKESLVVQVDEHPRADTTAAKLAALKPLLGAG 244

Query: 246 KTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVRK 305
            ++TAGNASG+NDG+ A++LAS  A+ ++GL+  A+++GMA+AGVAPRVMGIGPVPA+ K
Sbjct: 245 SSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPVPAIHK 304

Query: 306 LLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGAR 365
           LL R  L  +DFD IE+NEAFAAQ LA TR LG+ DD   VN NGGAIALGHPLGASGAR
Sbjct: 305 LLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGASGAR 364

Query: 366 LVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           L LTA   L +    R L ++CVGVGQG+ALA+ER
Sbjct: 365 LALTAAFALRRHRQHRALVSLCVGVGQGLALALER 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: 506
Number of extensions: 18
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_015446959.1 R2APBS1_RS03900 (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.4085530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-194  630.5  14.0   6.6e-194  630.4  14.0    1.0  1  NCBI__GCF_000230695.2:WP_015446959.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015446959.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.4  14.0  6.6e-194  6.6e-194       2     399 ..       3     399 ..       2     400 .] 0.99

  Alignments for each domain:
  == domain 1  score: 630.4 bits;  conditional E-value: 6.6e-194
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           ++++vda rtp+Gr gG+l+ vraddlaa+p++al+ar+p+ld+aa+d+vilGcanqaGednrnvarma+lla
  NCBI__GCF_000230695.2:WP_015446959.1   3 SAWLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQAGEDNRNVARMATLLA 75 
                                           589********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp+svp++tvnrlc+sgl+a+g aarai++Gea+lv+aGGvesmsrap+vl kad a++r ++ledtt+Gwr
  NCBI__GCF_000230695.2:WP_015446959.1  76 GLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAPYVLAKADVAYARGQQLEDTTLGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           +vnp+++a yG+dsm +taen+a+e+g++r+ qda+alrsqqrta+aqa+G++aeei+ v+ ++ k  + vv+
  NCBI__GCF_000230695.2:WP_015446959.1 149 LVNPRMQAGYGIDSMTQTAENLAREHGIDRDSQDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGKE-SLVVQ 220
                                           **************************************************************99886.89*** PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                            deh+ra+tt  +la lk+++ ++ ++taGnasG+ndGaaa+llase a++r+gl+p ari+++a+aGv+prv
  NCBI__GCF_000230695.2:WP_015446959.1 221 VDEHPRADTTAAKLAALKPLLGAGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRV 293
                                           ************************************************************************* PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gpvpa++kllar+gl  +d+d ie+neafaaq la++r+lgl+dd+++vn+nGGaialGhplGasGarl+
  NCBI__GCF_000230695.2:WP_015446959.1 294 MGIGPVPAIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGASGARLA 366
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvier 399
                                           lta   l+++ +++al++lc+GvGqG+al++er
  NCBI__GCF_000230695.2:WP_015446959.1 367 LTAAFALRRHRQHRALVSLCVGVGQGLALALER 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.29
//
[ok]

This GapMind analysis is from Sep 24 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