Alignments for a candidate for pcaB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Cupriavidus basilensis 4G11

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate RR42_RS32055 RR42_RS32055 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__Cup4G11:RR42_RS32055
          Length = 442

 Score =  856 bits (2212), Expect = 0.0
 Identities = 442/442 (100%), Positives = 442/442 (100%)

Query: 11  MFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEIDFDALA 70
           MFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEIDFDALA
Sbjct: 1   MFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEIDFDALA 60

Query: 71  AAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREALQAVDAD 130
           AAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREALQAVDAD
Sbjct: 61  AAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREALQAVDAD 120

Query: 131 LKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDAARAQAA 190
           LKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDAARAQAA
Sbjct: 121 LKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDAARAQAA 180

Query: 191 TLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGMLTGSLG 250
           TLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGMLTGSLG
Sbjct: 181 TLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGMLTGSLG 240

Query: 251 KIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLVATMLAG 310
           KIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLVATMLAG
Sbjct: 241 KIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLVATMLAG 300

Query: 311 MVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVTHGLILA 370
           MVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVTHGLILA
Sbjct: 301 MVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVTHGLILA 360

Query: 371 EAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDAAALDRV 430
           EAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDAAALDRV
Sbjct: 361 EAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDAAALDRV 420

Query: 431 CDPANYAGQAAGFVDAVLAAWR 452
           CDPANYAGQAAGFVDAVLAAWR
Sbjct: 421 CDPANYAGQAAGFVDAVLAAWR 442


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: 705
Number of extensions: 17
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: 470
Length of database: 442
Length adjustment: 33
Effective length of query: 437
Effective length of database: 409
Effective search space:   178733
Effective search space used:   178733
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 RR42_RS32055 RR42_RS32055 (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.29396.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-131  422.9  30.4   3.9e-131  422.9  30.4    2.1  2  lcl|FitnessBrowser__Cup4G11:RR42_RS32055  RR42_RS32055 3-carboxy-cis,cis-m


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS32055  RR42_RS32055 3-carboxy-cis,cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.9  30.4  3.9e-131  3.9e-131       6     338 .]       2     340 ..       1     340 [. 0.98
   2 ?   -0.9   0.4     0.032     0.032      28      51 ..     399     422 ..     375     435 .. 0.74

  Alignments for each domain:
  == domain 1  score: 422.9 bits;  conditional E-value: 3.9e-131
                                 TIGR02426   6 fgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnvv 74 
                                               fg  +  ++fsd a+++ mld+Eaalara+a++G+ipa+aaeaiaa++++ ++D  ala+aa  +gn++
  lcl|FitnessBrowser__Cup4G11:RR42_RS32055   2 FGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEIDFDALAAAAVAGGNLA 70 
                                               78889999************************************************************* PP

                                 TIGR02426  75 iplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtp 140
                                               iplv++l+++va+   +aaryvH+GaTSQD iDT+++Lqlr+al++++adl++l +a a+laa+hrdtp
  lcl|FitnessBrowser__Cup4G11:RR42_RS32055  71 IPLVRQLTARVAArdaQAARYVHWGATSQDAIDTGMVLQLREALQAVDADLKALGHACAALAAQHRDTP 139
                                               ************99999**************************************************** PP

                                 TIGR02426 141 ltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAae 209
                                               ++arT+lQ+A+ptt+glkaagwl+a+ r  +rl+a r++a +lqfGGAaGtla+l++++ ava al ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS32055 140 MVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDAARAQAATLQFGGAAGTLASLGAAAPAVATALGSA 208
                                               ********************************************************************* PP

                                 TIGR02426 210 lgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle.agg..GGSSampHKrNP 275
                                               l L+ + +pWh+ rdr++e+a++L++++g+lgkia+Dv+l++qtev+ev+e +g+  GGSS+mpHKrNP
  lcl|FitnessBrowser__Cup4G11:RR42_RS32055 209 LSLAVAPTPWHAYRDRMVEVATTLGMLTGSLGKIARDVSLMMQTEVAEVAEpTGPgrGGSSTMPHKRNP 277
                                               ***************************************************766689************ PP

                                 TIGR02426 276 vaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                               v+++++++aa r+p lvat++a ++qe+eR++ggW+aeW tL+++v+l+agalrq+ e++ gl
  lcl|FitnessBrowser__Cup4G11:RR42_RS32055 278 VGCAAVLTAAVRVPPLVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGL 340
                                               **********************************************************99886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.032
                                 TIGR02426  28 EaalaraqadvGlipaeaaeaiaa 51 
                                                a la+ +a++Gl++a+a ++++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS32055 399 GATLAEDAAHAGLMDAAALDRVCD 422
                                               467888888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (442 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: 8.70
//
[ok]

This GapMind analysis is from Sep 17 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