Alignments for a candidate for pcaB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Stenotrophomonas chelatiphaga DSM 21508

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate WP_057508463.1 ABB28_RS09870 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>NCBI__GCF_001431535.1:WP_057508463.1
          Length = 451

 Score =  427 bits (1099), Expect = e-124
 Identities = 240/455 (52%), Positives = 294/455 (64%), Gaps = 4/455 (0%)

Query: 1   MPTSSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCR 60
           M  +  L   +FG     A F+D A +Q MLD E ALA A+A CGVIP  A  AI A C 
Sbjct: 1   MSETHSLLGALFGDPLVDAGFTDAARLQAMLDVERALACAQARCGVIPQTALPAIEAACH 60

Query: 61  AGEIDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQL 120
           A   D  ALA A    GN AIPLV+ LTARV A DA+AAR+VHWGATSQD IDTG VLQL
Sbjct: 61  AQLYDIAALAQATALAGNPAIPLVKALTARVRADDAEAARWVHWGATSQDIIDTGAVLQL 120

Query: 121 REALQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLR 180
           R+A+  V A L+ L  A AALA   RDT +  RT LQ A+P TFGLKAAGWLDAL+R  +
Sbjct: 121 RQAVGQVQAKLQQLCSALAALAEAERDTGLPGRTLLQQAVPVTFGLKAAGWLDALQRSQQ 180

Query: 181 RLDAARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVAT 240
           RL A  A    LQFGGAAGTLASL      VA AL   L L +   PWHA RDR+ E+ +
Sbjct: 181 RLHALHADTLVLQFGGAAGTLASLQDRGLDVAQALAEELQLPLPALPWHAARDRIAELGS 240

Query: 241 TLGMLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRV 300
              +L GSLGKIA D+ L+MQ+EVAE  EP G G+GGSS MPHKRNPVGC A + AA RV
Sbjct: 241 VFALLVGSLGKIATDIVLLMQSEVAEAFEPAGEGKGGSSAMPHKRNPVGCVAAIAAATRV 300

Query: 301 PPLVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRAN 360
           P L++T+ + M Q HERA G W AEW+T+P+IV L AG+L Q+  VV GLQ+D  RM+ +
Sbjct: 301 PGLLSTLFSAMPQAHERAAGQWHAEWETVPEIVRLCAGSLAQVTVVVRGLQLDRERMQEH 360

Query: 361 LGVTHGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAG 420
           LG   GL+ AEA  + L  +IG+  AH LVE A ++A+A    LR+ L A   E + H  
Sbjct: 361 LGSHGGLLYAEAVAVTLAEQIGKAAAHALVEQAAQQALAHARPLREVLQAN-PEVSRH-- 417

Query: 421 LMDAAALDRVCDPANYAGQAAGFVDAVLAAWRHEA 455
            +D+A LD +    ++ G A  ++D VLA   H+A
Sbjct: 418 -LDSAQLDALFAADSWRGMADTWIDRVLARVPHDA 451


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: 461
Number of extensions: 24
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: 451
Length adjustment: 33
Effective length of query: 437
Effective length of database: 418
Effective search space:   182666
Effective search space used:   182666
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_057508463.1 ABB28_RS09870 (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.16413.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-141  456.9  21.4   1.7e-141  456.9  21.4    1.4  2  lcl|NCBI__GCF_001431535.1:WP_057508463.1  ABB28_RS09870 3-carboxy-cis,cis-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508463.1  ABB28_RS09870 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.9  21.4  1.7e-141  1.7e-141       1     338 []       7     350 ..       7     350 .. 0.98
   2 ?   -3.7   0.3      0.22      0.22      35      46 ..     378     389 ..     365     408 .. 0.43

  Alignments for each domain:
  == domain 1  score: 456.9 bits;  conditional E-value: 1.7e-141
                                 TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaae 69 
                                               ll +lfgd+ +++ f+d+arl+amldvE ala aqa++G+ip+ a  ai+aa+++  +D++ala+a+a 
  lcl|NCBI__GCF_001431535.1:WP_057508463.1   7 LLGALFGDPLVDAGFTDAARLQAMLDVERALACAQARCGVIPQTALPAIEAACHAQLYDIAALAQATAL 75 
                                               67899**************************************************************** PP

                                 TIGR02426  70 agnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaar 135
                                               agn++iplvkal+++v +   eaar+vH+GaTSQD+iDT+ +Lqlr+a+  ++a+l++l+ aLa+la+ 
  lcl|NCBI__GCF_001431535.1:WP_057508463.1  76 AGNPAIPLVKALTARVRAddaEAARWVHWGATSQDIIDTGAVLQLRQAVGQVQAKLQQLCSALAALAEA 144
                                               **************99767899*********************************************** PP

                                 TIGR02426 136 hrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavae 204
                                               +rdt l++rTllQqAvp+t+glkaagwl+a++r+++rl+al++++l+lqfGGAaGtla+l+ +gl+va+
  lcl|NCBI__GCF_001431535.1:WP_057508463.1 145 ERDTGLPGRTLLQQAVPVTFGLKAAGWLDALQRSQQRLHALHADTLVLQFGGAAGTLASLQDRGLDVAQ 213
                                               ********************************************************************* PP

                                 TIGR02426 205 alAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSamp 270
                                               alA+el+L++palpWh++rdriael++++al+ g+lgkia+D++ll+q+ev+e++e ag   GGSSamp
  lcl|NCBI__GCF_001431535.1:WP_057508463.1 214 ALAEELQLPLPALPWHAARDRIAELGSVFALLVGSLGKIATDIVLLMQSEVAEAFEpAGEgkGGSSAMP 282
                                               ********************************************************644379******* PP

                                 TIGR02426 271 HKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                               HKrNPv++++++aaa+r+pgl++tLf+a++q +eR+ag+WhaeWet++e+v+l ag+l+q+++++ gl
  lcl|NCBI__GCF_001431535.1:WP_057508463.1 283 HKRNPVGCVAAIAAATRVPGLLSTLFSAMPQAHERAAGQWHAEWETVPEIVRLCAGSLAQVTVVVRGL 350
                                               ***************************************************************99987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.22
                                 TIGR02426  35 qadvGlipaeaa 46 
                                               + ++G + a+a 
  lcl|NCBI__GCF_001431535.1:WP_057508463.1 378 AEQIGKAAAHAL 389
                                               222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (451 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.64
//
[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