Align Urocanate hydratase; Urocanase; Imidazolonepropionate hydrolase; EC 4.2.1.49 (characterized)
to candidate WP_110805607.1 C8J30_RS09465 urocanate hydratase
Query= SwissProt::Q5L084 (551 letters) >NCBI__GCF_003217355.1:WP_110805607.1 Length = 552 Score = 569 bits (1466), Expect = e-166 Identities = 279/536 (52%), Positives = 365/536 (68%), Gaps = 2/536 (0%) Query: 10 PAGTERRAKGWIQEAALRMLNNNLHPDVAERPDELIVYGGIGKAARNWECYEAIVDTLLR 69 P+G + RAK W E LR+L N L V E P++LIVY +GKAARNW + AIV +L Sbjct: 14 PSGPDLRAKNWRAEGLLRLLENVL--SVGEAPEKLIVYAALGKAARNWPAHAAIVKSLTE 71 Query: 70 LENDETLLIQSGKPVAVFRTHPDAPRVLIANSNLVPAWATWDHFHELDKKGLIMYGQMTA 129 +E DETL+IQSGKPV + +TH AP V++AN N+V WA + F++L++KGLI +G +TA Sbjct: 72 IEEDETLIIQSGKPVGILKTHAGAPMVIMANCNIVGQWAKAEVFYDLERKGLICWGGLTA 131 Query: 130 GSWIYIGSQGIVQGTYETFAEVARQHFGGTLAGTITLTAGLGGMGGAQPLAVTMNGGVCL 189 G+W YIGSQG++QGTYE F +A + F +LAG LTAGLGGMGGAQPLA M G L Sbjct: 132 GAWQYIGSQGVIQGTYEIFMRIAERRFNSSLAGRFILTAGLGGMGGAQPLAGRMAGAAIL 191 Query: 190 AIEVDPARIQRRIDTNYLDTMTDSLDAALEMAKQAKEEKKALSIGLVGNAAEVLPRLVEM 249 ++VD AR + R + +LD + LD+AL M A+ E +A S+ L+GNAAE+ P + Sbjct: 192 CVDVDEARAKMRQEIGFLDAIAPDLDSALAMIDAARAEGRATSVALIGNAAEIYPEIAAR 251 Query: 250 GFVPDVLTDQTSAHDPLNGYIPAGLTLDEAAELRARDPKQYIARAKQSIAAHVRAMLAMQ 309 G PD++TDQTSAHD + GY+PAG L LR ++P++ I + SIAAHV AML Q Sbjct: 252 GITPDIVTDQTSAHDLVYGYVPAGYDLPRVRRLREQNPEELIEAGRASIAAHVSAMLEFQ 311 Query: 310 KQGAVTFDYGNNIRQVAKDEGVDDAFSFPGFVPAYIRPLFCEGKGPFRWVALSGDPEDIY 369 +GA FD GN IR AK GV++AF P F AY+RPLFC GPFRW+ALSGDPEDI Sbjct: 312 SRGAEVFDNGNLIRTQAKQGGVENAFDIPIFTEAYLRPLFCRAIGPFRWMALSGDPEDIR 371 Query: 370 KTDEVILREFSDNERLCHWIRMAQKRIKFQGLPARICWLGYGERAKFGKIINDMVAKGEL 429 + D+++L+ F DN+ + +WIR+A++ + F+GLPARI WLG+GER +N MVA GEL Sbjct: 372 RIDDLVLKMFPDNQIVTNWIRLARENVPFEGLPARIAWLGHGERTDLAVAVNRMVASGEL 431 Query: 430 KAPIVIGRDHLDSGSVASPNRETEGMKDGSDAIADWPILNALLNAVGGASWVSVHHGGGV 489 P+ RDHLD+G +A PN TE M+DGSDAIADWP+L+A+ GA V+VH GGG Sbjct: 432 AGPVAFSRDHLDAGGMAHPNIMTEKMRDGSDAIADWPLLDAMTLCASGADLVTVHSGGGG 491 Query: 490 GMGYSIHAGMVIVADGTKEAEKRLERVLTTDPGLGVVRHADAGYELAIRTAKEKGI 545 GY AG+ IVA+G+ AE RL LT D LGV+R+ADAGY A+ A +K + Sbjct: 492 YAGYMTSAGVTIVAEGSAAAETRLRLALTNDTALGVIRYADAGYADALDEAAQKAV 547 Lambda K H 0.319 0.136 0.411 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: 771 Number of extensions: 28 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: 551 Length of database: 552 Length adjustment: 36 Effective length of query: 515 Effective length of database: 516 Effective search space: 265740 Effective search space used: 265740 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 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_110805607.1 C8J30_RS09465 (urocanate hydratase)
to HMM TIGR01228 (hutU: urocanate hydratase (EC 4.2.1.49))
# 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/TIGR01228.hmm # target sequence database: /tmp/gapView.174199.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01228 [M=545] Accession: TIGR01228 Description: hutU: urocanate hydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-215 702.6 0.9 2.3e-215 702.2 0.9 1.0 1 NCBI__GCF_003217355.1:WP_110805607.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217355.1:WP_110805607.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 702.2 0.9 2.3e-215 2.3e-215 6 540 .. 14 546 .. 10 549 .. 0.99 Alignments for each domain: == domain 1 score: 702.2 bits; conditional E-value: 2.3e-215 TIGR01228 6 prGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrleddetllvqsGk 78 p G +l ak w+ e lrll+n l v e pe+l+vy Gkaarnw a+ +iv++l+ +e+detl++qsGk NCBI__GCF_003217355.1:WP_110805607.1 14 PSGPDLRAKNWRAEGLLRLLENVL--SVGEAPEKLIVYAALGKAARNWPAHAAIVKSLTEIEEDETLIIQSGK 84 89*********************9..69********************************************* PP TIGR01228 79 pvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGtyetlaelarkh 151 pvg++kth ap v++an+n+v++wa+ e+f +le+kGli +G +taG+w yiG+qG++qGtye + +a ++ NCBI__GCF_003217355.1:WP_110805607.1 85 PVGILKTHAGAPMVIMANCNIVGQWAKAEVFYDLERKGLICWGGLTAGAWQYIGSQGVIQGTYEIFMRIAERR 157 ************************************************************************* PP TIGR01228 152 fggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddldealaraeeakaeG 224 f sl g+++ltaGlGgmGGaqpla ++++a+ + v+vde+r + r e +ld + dld ala++++a+aeG NCBI__GCF_003217355.1:WP_110805607.1 158 FNSSLAGRFILTAGLGGMGGAQPLAGRMAGAAILCVDVDEARAKMRQEIGFLDAIAPDLDSALAMIDAARAEG 230 ************************************************************************* PP TIGR01228 225 kalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrdeepeeyvkaakaslakh 297 +a+s++l Gnaae+++e+ rg++pd+vtdqtsahd + Gy+p+gy + ++lr+++pee ++a +as+a+h NCBI__GCF_003217355.1:WP_110805607.1 231 RATSVALIGNAAEIYPEIAARGITPDIVTDQTSAHDLVYGYVPAGYDLPRVRRLREQNPEELIEAGRASIAAH 303 ************************************************************************* PP TIGR01228 298 vrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkGpfrwvalsGdpadiyrtdka 370 v a+l++q++Ga +fd Gn ir++ak+ Gve+afd+p f ay+r+lfc+ Gpfrw+alsGdp+di r+d+ NCBI__GCF_003217355.1:WP_110805607.1 304 VSAMLEFQSRGAEVFDNGNLIRTQAKQGGVENAFDIPIFTEAYLRPLFCRAIGPFRWMALSGDPEDIRRIDDL 376 ************************************************************************* PP TIGR01228 371 vkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelvrsGelkapvvigrdhldaGsvas 443 v+++fp+++ +++wi la+e+v f+Glpari wlg+ger la+a+n +v sGel pv+ +rdhldaG +a NCBI__GCF_003217355.1:WP_110805607.1 377 VLKMFPDNQIVTNWIRLARENVPFEGLPARIAWLGHGERTDLAVAVNRMVASGELAGPVAFSRDHLDAGGMAH 449 ************************************************************************* PP TIGR01228 444 pnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfslhaglvivadGtdeaaerlkrvltad 516 pn te+m+dGsda+adwpll+a+ a+Ga++v++h GGG G+ ag+ iva+G+ +a+ rl+ +lt+d NCBI__GCF_003217355.1:WP_110805607.1 450 PNIMTEKMRDGSDAIADWPLLDAMTLCASGADLVTVHSGGGGYAGYMTSAGVTIVAEGSAAAETRLRLALTND 522 ************************************************************************* PP TIGR01228 517 pGlGvirhadaGyesaldvakeqg 540 lGvir+adaGy++ald+a ++ NCBI__GCF_003217355.1:WP_110805607.1 523 TALGVIRYADAGYADALDEAAQKA 546 ******************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (545 nodes) Target sequences: 1 (552 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: 00:00:00.00 # Mc/sec: 36.10 // [ok]
This GapMind analysis is from Sep 24 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