Alignments for a candidate for pcaB in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Pseudomonas benzenivorans DSM 8628

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate WP_090446761.1 BLS63_RS16760 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>NCBI__GCF_900100495.1:WP_090446761.1
          Length = 450

 Score =  465 bits (1196), Expect = e-135
 Identities = 249/449 (55%), Positives = 305/449 (67%), Gaps = 4/449 (0%)

Query: 4   SSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGE 63
           S++L D  F SAA  A FSD   VQ MLDFEAALARAEA  GVIPA A   I   C A  
Sbjct: 2   SNQLFDRYFSSAAMAALFSDAGRVQGMLDFEAALARAEARVGVIPAGAVAPIETACHAER 61

Query: 64  IDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREA 123
            DF  LA A    GN AIPLV+ L  +VAA DA+A RY+H GATSQDA+D+G+VLQLR+A
Sbjct: 62  YDFSELAEAIATAGNSAIPLVKALGRQVAAADAEAERYLHLGATSQDAMDSGLVLQLRQA 121

Query: 124 LQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLD 183
           ++ ++ADL  LG   A  A +H D  +  RTWLQHA P T G+K AG L A+ R  +RL 
Sbjct: 122 VELLEADLTELGQVLALQAERHADCVLPGRTWLQHATPVTLGMKLAGVLGAVSRHRQRLS 181

Query: 184 AARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLG 243
             + +   LQFGGAAGTLA+LG    AV+ AL   L LA+   PWH+ RDR+VE A  LG
Sbjct: 182 ELKPRLLVLQFGGAAGTLAALGEQGWAVSEALAEELGLALPEQPWHSQRDRLVEFAALLG 241

Query: 244 MLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPL 303
           ++ GSLGK+ RD+SL+MQT+V EV EP  PG+GGSSTMPHKRNPVG A ++ AA R P L
Sbjct: 242 LIAGSLGKLGRDLSLLMQTDVGEVFEPAAPGKGGSSTMPHKRNPVGAAVLIGAATRAPGL 301

Query: 304 VATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGV 363
           V+T+LA M QEHER+LG W AEW+TLPQ+  L +GAL+Q L  V GL+VDAARMR+NL +
Sbjct: 302 VSTLLAAMPQEHERSLGLWHAEWETLPQLCCLVSGALQQALLAVPGLEVDAARMRSNLEL 361

Query: 364 THGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMD 423
           T GL+LAEA  + L  +IGR  AHHL+E  CR+A  EG  LRQ LGA    +A     + 
Sbjct: 362 TQGLVLAEAVSIALAQRIGRDAAHHLLEDCCRQAAKEGVHLRQVLGA----NAEVTAQLS 417

Query: 424 AAALDRVCDPANYAGQAAGFVDAVLAAWR 452
           AA LD + DPA+Y GQA  +V   +A  R
Sbjct: 418 AAELDHLLDPAHYLGQARRWVARAVAEHR 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: 473
Number of extensions: 12
Number of successful extensions: 3
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: 450
Length adjustment: 33
Effective length of query: 437
Effective length of database: 417
Effective search space:   182229
Effective search space used:   182229
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_090446761.1 BLS63_RS16760 (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.918.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-141  454.8  13.0   1.1e-140  454.4  13.0    1.2  1  lcl|NCBI__GCF_900100495.1:WP_090446761.1  BLS63_RS16760 3-carboxy-cis,cis-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090446761.1  BLS63_RS16760 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.4  13.0  1.1e-140  1.1e-140       1     336 [.       5     346 ..       5     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 454.4 bits;  conditional E-value: 1.1e-140
                                 TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaae 69 
                                               l+d++f+  ++a+lfsd++r+++mld+Eaalara+a+vG+ipa a++ i++a+++ ++D ++laea+a+
  lcl|NCBI__GCF_900100495.1:WP_090446761.1   5 LFDRYFSSAAMAALFSDAGRVQGMLDFEAALARAEARVGVIPAGAVAPIETACHAERYDFSELAEAIAT 73 
                                               789****************************************************************** PP

                                 TIGR02426  70 agnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaar 135
                                               agn++iplvkal ++va+   ea+ry+HlGaTSQD +D +l+Lqlr+a++ll+adl +l ++La +a+r
  lcl|NCBI__GCF_900100495.1:WP_090446761.1  74 AGNSAIPLVKALGRQVAAadaEAERYLHLGATSQDAMDSGLVLQLRQAVELLEADLTELGQVLALQAER 142
                                               ****************999999*********************************************** PP

                                 TIGR02426 136 hrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavae 204
                                               h+d  l++rT+lQ+A+p+t+g+k+ag+l av+r+r+rl++l+ ++l+lqfGGAaGtlaal+++g av e
  lcl|NCBI__GCF_900100495.1:WP_090446761.1 143 HADCVLPGRTWLQHATPVTLGMKLAGVLGAVSRHRQRLSELKPRLLVLQFGGAAGTLAALGEQGWAVSE 211
                                               ********************************************************************* PP

                                 TIGR02426 205 alAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSamp 270
                                               alA+elgL++p++pWh+qrdr++e+aa+L+l+ag+lgk+++D++ll+qt+vgev+e a++  GGSS+mp
  lcl|NCBI__GCF_900100495.1:WP_090446761.1 212 ALAEELGLALPEQPWHSQRDRLVEFAALLGLIAGSLGKLGRDLSLLMQTDVGEVFEpAAPgkGGSSTMP 280
                                               ********************************************************877689******* PP

                                 TIGR02426 271 HKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaelle 336
                                               HKrNPv+a+vl++aa+rapglv+tL+aa++qe+eRs+g WhaeWetL++l++l++gal+qa   + 
  lcl|NCBI__GCF_900100495.1:WP_090446761.1 281 HKRNPVGAAVLIGAATRAPGLVSTLLAAMPQEHERSLGLWHAEWETLPQLCCLVSGALQQALLAVP 346
                                               ************************************************************976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (450 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: 12.15
//
[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