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.
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:
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