Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate Pf6N2E2_2831 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2)
Query= uniprot:A0A0C4YE08 (470 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 Length = 454 Score = 429 bits (1104), Expect = e-125 Identities = 226/445 (50%), Positives = 288/445 (64%), Gaps = 4/445 (0%) Query: 5 SRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCRAGEI 64 ++L D F + F D VQ MLD EAALARAEA GVIP A I CRA Sbjct: 7 NQLFDAYFTARDMREVFCDAGRVQAMLDVEAALARAEARVGVIPQSAVAPIEKACRAALY 66 Query: 65 DFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQLREAL 124 DF AL+ A + GN AIPLV+ L R+A DA+A RYVH GATSQD +D+G+VLQLR AL Sbjct: 67 DFSALSEAIASAGNSAIPLVKALGKRIAVEDAEAERYVHLGATSQDVMDSGLVLQLRLAL 126 Query: 125 QAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLRRLDA 184 ++ +L L A A + TP+ RTWLQHA P T G+K AGWL A+ R +RL Sbjct: 127 GLIEGELAQLAATLARQAEHYAATPLAGRTWLQHATPVTLGMKIAGWLGAITRSRQRLKE 186 Query: 185 ARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVATTLGM 244 + + LQFGGA+GTLA+LG A +A AL + L L + PWH RDR+VE + LG+ Sbjct: 187 LKPRLLVLQFGGASGTLAALGEHALPIAEALAAELQLNLPEQPWHTQRDRLVEFGSVLGL 246 Query: 245 LTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRVPPLV 304 + GSLGK+ RD+SL+MQTE E EP+ PG+GGSSTMPHKRNPVG A ++ AA RVP L+ Sbjct: 247 IAGSLGKLGRDISLLMQTEAGEAFEPSAPGKGGSSTMPHKRNPVGAAVLIGAATRVPGLL 306 Query: 305 ATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRANLGVT 364 +T+ + M QEHER+LG W AEW+TLP+I L +GAL+Q + GL+VDAARM NL +T Sbjct: 307 STLFSAMPQEHERSLGLWHAEWETLPEICCLVSGALQQARLLAEGLEVDAARMARNLELT 366 Query: 365 HGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAGLMDA 424 GL+LAEA + L ++GR AHHL+E C+RAVAE LR LG ++ + A Sbjct: 367 QGLVLAEAVSIVLAQRVGRDAAHHLLEQCCKRAVAEQRHLRDVLG----DEPQVTAQLSA 422 Query: 425 AALDRVCDPANYAGQAAGFVDAVLA 449 LD + DPA+Y GQA +V +A Sbjct: 423 TELDHLLDPAHYLGQAQTWVARAVA 447 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: 485 Number of extensions: 16 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: 454 Length adjustment: 33 Effective length of query: 437 Effective length of database: 421 Effective search space: 183977 Effective search space used: 183977 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 Pf6N2E2_2831 (3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))
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.27786.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-144 466.4 9.3 3e-144 466.0 9.3 1.2 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 3-carboxy-cis,cis-muconate cyclo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.0 9.3 3e-144 3e-144 1 338 [] 9 352 .. 9 352 .. 0.99 Alignments for each domain: == domain 1 score: 466.0 bits; conditional E-value: 3e-144 TIGR02426 1 lldglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDleala 64 l+d++f++ +++e+f d++r++amldvEaalara+a+vG+ip++a++ i+ a++++ +D +al+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 9 LFDAYFTARDMREVFCDAGRVQAMLDVEAALARAEARVGVIPQSAVAPIEKACRAALYDFSALS 72 7899************************************************************ PP TIGR02426 65 eaaaeagnvviplvkalrkavae...eaaryvHlGaTSQDviDTalmLqlrdaldllladlerl 125 ea+a+agn++iplvkal k++a ea+ryvHlGaTSQDv+D +l+Lqlr al l++ +l++l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 73 EAIASAGNSAIPLVKALGKRIAVedaEAERYVHLGATSQDVMDSGLVLQLRLALGLIEGELAQL 136 *********************9888899************************************ PP TIGR02426 126 aeaLaelaarhrdtpltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAa 189 a++La++a++ ++tpl +rT+lQ+A+p+t+g+k+agwl a++r+r+rl++l+ ++l+lqfGGA+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 137 AATLARQAEHYAATPLAGRTWLQHATPVTLGMKIAGWLGAITRSRQRLKELKPRLLVLQFGGAS 200 **************************************************************** PP TIGR02426 190 GtlaalekkglavaealAaelgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqt 253 Gtlaal++++l +aealAael+L++p++pWhtqrdr++e++++L+l+ag+lgk+++D++ll+qt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 201 GTLAALGEHALPIAEALAAELQLNLPEQPWHTQRDRLVEFGSVLGLIAGSLGKLGRDISLLMQT 264 **************************************************************** PP TIGR02426 254 evgevle.agg..GGSSampHKrNPvaaevlaaaarrapglvatLfaalaqedeRsaggWhaeW 314 e+ge++e +++ GGSS+mpHKrNPv+a+vl++aa+r+pgl++tLf+a++qe+eRs+g WhaeW lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 265 EAGEAFEpSAPgkGGSSTMPHKRNPVGAAVLIGAATRVPGLLSTLFSAMPQEHERSLGLWHAEW 328 *******766689*************************************************** PP TIGR02426 315 etLrelvaltagalrqaaellegl 338 etL+e+++l++gal+qa+ l+egl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2831 329 ETLPEICCLVSGALQQARLLAEGL 352 *********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (338 nodes) Target sequences: 1 (454 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: 9.64 // [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