GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaB in Rhizobium etli CFN 42

Align 3-Carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) (characterized)
to candidate WP_042119916.1 RHE_RS24300 3-carboxy-cis,cis-muconate cycloisomerase

Query= BRENDA::Q2HNZ1
         (353 letters)



>NCBI__GCF_000092045.1:WP_042119916.1
          Length = 348

 Score =  355 bits (911), Expect = e-102
 Identities = 190/349 (54%), Positives = 236/349 (67%), Gaps = 3/349 (0%)

Query: 1   MSLSPFEHPFLSGLFGDSEIIELFSAKADIDAMIRFETALAQAEAEASIFADDEAEAIVS 60
           M+ SPF+HPFLSGL GD EI   FSA+ADI AM+ FE ALA+AEA   +   + A  I  
Sbjct: 1   MTASPFDHPFLSGLLGDDEIAPHFSAEADIRAMLSFEAALARAEAAHGLIPAEAARKIAE 60

Query: 61  GLSEFAADMSALRHGVAKDGVVVPELIRQMRAAVAGQGADKVHFGATSQDVIDTSLMLRL 120
             + F+ D+++LR  +AKDGVVVP+ ++Q+RA V  +    +H GATSQDVIDTSLM+RL
Sbjct: 61  ACTGFSPDLASLRSAMAKDGVVVPDFVKQLRAKVGEEAGKNLHLGATSQDVIDTSLMIRL 120

Query: 121 KMAAEIIATRLGHLIDTLGDLASRDGHKPLTGYTRMQAAIGITVADRAAGWIAPLERHLL 180
           K    + A RL  +I  L  L  + G   L G+TRMQAAI I+V+DR   W APL  +  
Sbjct: 121 KAVVFLFAGRLSAIIAALEGLDRQFGGNRLMGHTRMQAAIAISVSDRLNVWRAPLATYRD 180

Query: 181 RLETFAQNGFALQFGGAAGTLEKLGDNAGAVRADLAKRLGLADRPQWHNQRDGIPEFANL 240
           RL    +  F +QFGGAAGTL+KLG    AVRA LA+ LGL+D  QW + R  I + A L
Sbjct: 181 RL---TEQSFPVQFGGAAGTLDKLGPQGPAVRASLAQELGLSDTRQWQSARLPIADIAGL 237

Query: 241 LSLVTGTLGKFGQDIALMAEIGSEIRLSGGGGSSAMPHKQNPVNAETLVTLARFNAVQIS 300
            + ++G+LGK GQDIAL+AE+G EI +SGGG SSAM HKQNPV AE LV+LARFNA  +S
Sbjct: 238 FASISGSLGKIGQDIALLAEMGGEIEVSGGGASSAMAHKQNPVAAEVLVSLARFNATALS 297

Query: 301 ALHQSLVQEQERSGAGWMLEWLTLPQMVTATGTSLLVAERLAAQIDRLG 349
            +HQSL+ EQERSGA W LEWL LPQM   T  SL +A  L   I RLG
Sbjct: 298 GIHQSLIHEQERSGAAWTLEWLLLPQMTMGTAASLRLARELTGNIKRLG 346


Lambda     K      H
   0.318    0.133    0.376 

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: 372
Number of extensions: 14
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: 353
Length of database: 348
Length adjustment: 29
Effective length of query: 324
Effective length of database: 319
Effective search space:   103356
Effective search space used:   103356
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_042119916.1 RHE_RS24300 (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.242378.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-116  373.2  10.4     6e-116  373.0  10.4    1.0  1  NCBI__GCF_000092045.1:WP_042119916.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092045.1:WP_042119916.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.0  10.4    6e-116    6e-116       1     337 [.      10     341 ..      10     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: 373.0 bits;  conditional E-value: 6e-116
                             TIGR02426   1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeagnv 73 
                                           +l+gl gd+e+a +fs++a++raml++Eaalara+a+ Glipaeaa++ia a+  +++Dl++l++a+a++g+v
  NCBI__GCF_000092045.1:WP_042119916.1  10 FLSGLLGDDEIAPHFSAEADIRAMLSFEAALARAEAAHGLIPAEAARKIAEACTGFSPDLASLRSAMAKDGVV 82 
                                           6899********************************************************************* PP

                             TIGR02426  74 viplvkalrkavaeeaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtpltarTl 146
                                           v++ vk+lr++v+eea++ +HlGaTSQDviDT+lm++l++++ l + +l++ ++aL  l ++++ + l+++T+
  NCBI__GCF_000092045.1:WP_042119916.1  83 VPDFVKQLRAKVGEEAGKNLHLGATSQDVIDTSLMIRLKAVVFLFAGRLSAIIAALEGLDRQFGGNRLMGHTR 155
                                           ************************************************************************* PP

                             TIGR02426 147 lQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAaelgLeapalpW 219
                                           +Q+A+++ v++++  w+a+++ +rdrl++     +++qfGGAaGtl +l+ +g av++ lA+elgL++ + +W
  NCBI__GCF_000092045.1:WP_042119916.1 156 MQAAIAISVSDRLNVWRAPLATYRDRLTEQ---SFPVQFGGAAGTLDKLGPQGPAVRASLAQELGLSD-TRQW 224
                                           ****************************94...5**********************************.99** PP

                             TIGR02426 220 htqrdriaelaaaLalvagalgkiaqDvallaqtevgevleaggGGSSampHKrNPvaaevlaaaarrapglv 292
                                           +++r +ia++a ++a ++g+lgki+qD+alla++  ++ ++ ggG SSam+HK+NPvaaevl+++ar++++ +
  NCBI__GCF_000092045.1:WP_042119916.1 225 QSARLPIADIAGLFASISGSLGKIGQDIALLAEMGGEIEVS-GGGASSAMAHKQNPVAAEVLVSLARFNATAL 296
                                           *********************************99999998.999**************************** PP

                             TIGR02426 293 atLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaelleg 337
                                           ++++++l +e+eRs+++W +eW  L++++  ta++lr a+el  +
  NCBI__GCF_000092045.1:WP_042119916.1 297 SGIHQSLIHEQERSGAAWTLEWLLLPQMTMGTAASLRLARELTGN 341
                                           ***************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (348 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.80
//
[ok]

This GapMind analysis is from Apr 09 2024. 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