Alignments for a candidate for pcaB in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Pseudomonas stutzeri A1501

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate WP_011912438.1 PST_RS06395 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>NCBI__GCF_000013785.1:WP_011912438.1
          Length = 453

 Score =  455 bits (1171), Expect = e-132
 Identities = 242/446 (54%), Positives = 300/446 (67%), Gaps = 4/446 (0%)

Query: 4   SSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGE 63
           S++L D  F SA     FSD   VQ MLDFEAALARAEA  GVIPA A +AI A C A  
Sbjct: 5   SNQLFDVYFTSAPMREVFSDRGRVQGMLDFEAALARAEARTGVIPATAVDAIEAACHAEH 64

Query: 64  IDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREA 123
            D  ALA A    GN AIPLV+ L  +VAA D  A +YVH GATSQDA+D+G+VLQLR+A
Sbjct: 65  YDLCALAEAVATAGNSAIPLVKALGRQVAANDPDAEKYVHLGATSQDAMDSGLVLQLRQA 124

Query: 124 LQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLD 183
           L  ++ DL+ LG A A  AA+H +TPM  RTWLQHA P T G+K AGWL A+ R  +RL 
Sbjct: 125 LALLETDLRRLGDALADQAARHAETPMAGRTWLQHATPVTLGMKIAGWLGAVTRHRQRLA 184

Query: 184 AARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLG 243
             R +   LQFGGA+G+LA+LG  A  V+ AL   L L +   PWH  RDR+VE A+ LG
Sbjct: 185 ELRPRLLCLQFGGASGSLAALGEQAWPVSEALAGELGLNLPDQPWHTQRDRLVEFASLLG 244

Query: 244 MLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPL 303
           ++ GSLGK+ RD++L+MQT+V EV EP  PG+GGSSTMPHKRNPVGCA ++ AA R P L
Sbjct: 245 LIAGSLGKLGRDLALLMQTDVGEVFEPAAPGKGGSSTMPHKRNPVGCAVMIAAATRAPGL 304

Query: 304 VATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGV 363
           VATML+ + QEHER+LG W AEW+TLP++  L +GAL Q L  V  L+VD  R+R NL +
Sbjct: 305 VATMLSALPQEHERSLGLWLAEWETLPELCCLVSGALSQALIAVPALEVDGERLRGNLEL 364

Query: 364 THGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMD 423
           T GL+LAEA  + L   +GR  AH LVE  C++AVAEG  LR      L +    +   +
Sbjct: 365 TRGLVLAEAVSIALAQLVGREKAHELVEQCCKQAVAEGRHLR----GVLRDSPEVSSRFN 420

Query: 424 AAALDRVCDPANYAGQAAGFVDAVLA 449
            A LDR+ DPANY GQA  +V+  +A
Sbjct: 421 DAELDRLLDPANYLGQARRWVERAVA 446


Lambda     K      H
   0.319    0.130    0.380 

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: 475
Number of extensions: 11
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: 470
Length of database: 453
Length adjustment: 33
Effective length of query: 437
Effective length of database: 420
Effective search space:   183540
Effective search space used:   183540
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_011912438.1 PST_RS06395 (3-carboxy-cis,cis-muconate cycloisomerase)
to HMM TIGR02426 (pcaB: 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))

# 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/TIGR02426.hmm
# target sequence database:        /tmp/gapView.27701.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02426  [M=338]
Accession:   TIGR02426
Description: protocat_pcaB: 3-carboxy-cis,cis-muconate cycloisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.5e-144  464.7  11.0   9.5e-144  464.4  11.0    1.1  1  lcl|NCBI__GCF_000013785.1:WP_011912438.1  PST_RS06395 3-carboxy-cis,cis-mu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011912438.1  PST_RS06395 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.4  11.0  9.5e-144  9.5e-144       1     333 [.       8     346 ..       8     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 464.4 bits;  conditional E-value: 9.5e-144
                                 TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaae 69 
                                               l+d +f+   ++e+fsdr+r+++mld+Eaalara+a++G+ipa a++ai+aa+++ ++Dl alaea+a+
  lcl|NCBI__GCF_000013785.1:WP_011912438.1   8 LFDVYFTSAPMREVFSDRGRVQGMLDFEAALARAEARTGVIPATAVDAIEAACHAEHYDLCALAEAVAT 76 
                                               6788999999*********************************************************** PP

                                 TIGR02426  70 agnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaar 135
                                               agn++iplvkal ++va+   +a++yvHlGaTSQD +D +l+Lqlr+al+ll+ dl+rl +aLa++aar
  lcl|NCBI__GCF_000013785.1:WP_011912438.1  77 AGNSAIPLVKALGRQVAAndpDAEKYVHLGATSQDAMDSGLVLQLRQALALLETDLRRLGDALADQAAR 145
                                               *****************99999*********************************************** PP

                                 TIGR02426 136 hrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavae 204
                                               h++tp+ +rT+lQ+A+p+t+g+k+agwl av+r+r+rl++lr ++l lqfGGA+G+laal++++  v e
  lcl|NCBI__GCF_000013785.1:WP_011912438.1 146 HAETPMAGRTWLQHATPVTLGMKIAGWLGAVTRHRQRLAELRPRLLCLQFGGASGSLAALGEQAWPVSE 214
                                               ********************************************************************* PP

                                 TIGR02426 205 alAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSamp 270
                                               alA+elgL++p +pWhtqrdr++e+a++L+l+ag+lgk+++D+all+qt+vgev+e a++  GGSS+mp
  lcl|NCBI__GCF_000013785.1:WP_011912438.1 215 ALAGELGLNLPDQPWHTQRDRLVEFASLLGLIAGSLGKLGRDLALLMQTDVGEVFEpAAPgkGGSSTMP 283
                                               ********************************************************877689******* PP

                                 TIGR02426 271 HKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaae 333
                                               HKrNPv+++v++aaa+rapglvat+++al+qe+eRs+g W aeWetL+el++l++gal+qa  
  lcl|NCBI__GCF_000013785.1:WP_011912438.1 284 HKRNPVGCAVMIAAATRAPGLVATMLSALPQEHERSLGLWLAEWETLPELCCLVSGALSQALI 346
                                               ***********************************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (453 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: 12.72
//
[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:

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