Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate AO353_17225 AO353_17225 3-carboxy-cis,cis-muconate cycloisomerase
Query= uniprot:A0A0C4YE08 (470 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17225 Length = 453 Score = 452 bits (1162), Expect = e-131 Identities = 237/445 (53%), Positives = 297/445 (66%), Gaps = 4/445 (0%) Query: 5 SRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEI 64 ++L D F + FSD VQ MLDFEAALARAEA G+IPA A I A CRA Sbjct: 6 NQLFDAYFTARNMREVFSDQGRVQAMLDFEAALARAEARVGLIPASAVAPIEAACRAEHY 65 Query: 65 DFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREAL 124 DF AL A GN AIPLV+ L ++AA D A RYVH GATSQD +DTG+VLQ+R+AL Sbjct: 66 DFAALGEAIAIAGNSAIPLVKALGKQIAAHDQDAERYVHLGATSQDVMDTGLVLQVRQAL 125 Query: 125 QAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDA 184 +D+DL LG A A A H TP+ RTWLQHA P T G+K AGWL A+ R +RL A Sbjct: 126 HLIDSDLARLGEALAIQARHHVLTPLAGRTWLQHATPVTLGMKVAGWLGAVTRSRQRLHA 185 Query: 185 ARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGM 244 + + LQFGGA+GTLA+LG A +A AL L L + PWH RDR+VE LG+ Sbjct: 186 LKPRLLVLQFGGASGTLAALGEQAMPIAEALAQELQLTLPEQPWHTQRDRLVEFGAALGL 245 Query: 245 LTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLV 304 + GSLGK+ RD+SL+MQTE AEV EP+ PG+GGSSTMPHKRNPVG A ++ AA RVP L+ Sbjct: 246 IAGSLGKLGRDISLLMQTEAAEVFEPSAPGKGGSSTMPHKRNPVGAAVLIGAATRVPGLL 305 Query: 305 ATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVT 364 +T+ + M QEHER+LG W AEW+TLP+I L +GAL+Q L + GL+VDA RM NL +T Sbjct: 306 STLFSAMPQEHERSLGLWHAEWETLPEICCLVSGALQQALLITEGLEVDAERMAQNLDLT 365 Query: 365 HGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDA 424 GL+LAEA + L +IGR AHHL+E C+RAVAE LR LG ++ + + Sbjct: 366 QGLVLAEAVSIVLAQRIGRDKAHHLLELCCKRAVAEQRHLRAVLG----DEPQVTAELSS 421 Query: 425 AALDRVCDPANYAGQAAGFVDAVLA 449 A LD++ +PA+Y GQA +V+ LA Sbjct: 422 AELDQLMNPAHYLGQAQTWVERALA 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: 474 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: 470 Length of database: 453 Length adjustment: 33 Effective length of query: 437 Effective length of database: 420 Effective search space: 183540 Effective search space used: 183540 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 AO353_17225 AO353_17225 (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.4765.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-146 473.9 11.8 1.6e-146 473.5 11.8 1.2 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 AO353_17225 3-carboxy-cis,cis-mu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 AO353_17225 3-carboxy-cis,cis-muconate cycloisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.5 11.8 1.6e-146 1.6e-146 1 338 [] 8 351 .. 8 351 .. 0.99 Alignments for each domain: == domain 1 score: 473.5 bits; conditional E-value: 1.6e-146 TIGR02426 1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealae 65 l+d++f++ +++e+fsd++r++amld+Eaalara+a+vGlipa+a++ i+aa+++ ++D +al e lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 8 LFDAYFTARNMREVFSDQGRVQAMLDFEAALARAEARVGLIPASAVAPIEAACRAEHYDFAALGE 72 7899************************************************************* PP TIGR02426 66 aaaeagnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerlae 127 a+a agn++iplvkal k++a+ +a+ryvHlGaTSQDv+DT+l+Lq+r+al+l++ dl+rl e lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 73 AIAIAGNSAIPLVKALGKQIAAhdqDAERYVHLGATSQDVMDTGLVLQVRQALHLIDSDLARLGE 137 *********************99999*************************************** PP TIGR02426 128 aLaelaarhrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtl 192 aLa +a++h tpl +rT+lQ+A+p+t+g+k+agwl av+r+r+rl+al+ ++l+lqfGGA+Gtl lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 138 ALAIQARHHVLTPLAGRTWLQHATPVTLGMKVAGWLGAVTRSRQRLHALKPRLLVLQFGGASGTL 202 ***************************************************************** PP TIGR02426 193 aalekkglavaealAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevge 257 aal+++++ +aealA+el+L++p++pWhtqrdr++e++aaL+l+ag+lgk+++D++ll+qte++e lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 203 AALGEQAMPIAEALAQELQLTLPEQPWHTQRDRLVEFGAALGLIAGSLGKLGRDISLLMQTEAAE 267 ***************************************************************** PP TIGR02426 258 vle.agg..GGSSampHKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLre 319 v+e +++ GGSS+mpHKrNPv+a+vl++aa+r+pgl++tLf+a++qe+eRs+g WhaeWetL+e lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 268 VFEpSAPgkGGSSTMPHKRNPVGAAVLIGAATRVPGLLSTLFSAMPQEHERSLGLWHAEWETLPE 332 ***766689******************************************************** PP TIGR02426 320 lvaltagalrqaaellegl 338 +++l++gal+qa + egl lcl|FitnessBrowser__pseudo3_N2E3:AO353_17225 333 ICCLVSGALQQALLITEGL 351 ************9999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (338 nodes) Target sequences: 1 (453 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: 8.55 // [ok]
This GapMind analysis is from Sep 17 2021. 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