Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate BPHYT_RS07565 BPHYT_RS07565 urocanate hydratase
Query= reanno::Smeli:SM_b21163 (557 letters) >FitnessBrowser__BFirm:BPHYT_RS07565 Length = 562 Score = 848 bits (2191), Expect = 0.0 Identities = 402/558 (72%), Positives = 467/558 (83%), Gaps = 6/558 (1%) Query: 1 MNNPRH------NIREVRSPRGTEISAKSWLTEAPLRMLMNNLDPDVAENPHELVVYGGI 54 MNNP+H R +R+PRG E + K+W+ EA RM+ NNLDP+VAE+PH LVVYGGI Sbjct: 1 MNNPKHIDPRLDPTRTIRAPRGAEKTCKTWIAEAAYRMIQNNLDPEVAEHPHALVVYGGI 60 Query: 55 GRAARTWADFDRIVASLKDLNEDETLLVQSGKPVGVFRTHKDAPRVLIANSNLVPHWATW 114 GRAAR W FD+I+ SLKDL E+ETLL+QSGKPVGVFRTH DAPRVL+ANSNLVPHWATW Sbjct: 61 GRAARNWDCFDQILKSLKDLEENETLLIQSGKPVGVFRTHADAPRVLLANSNLVPHWATW 120 Query: 115 DHFNELDKKGLAMYGQMTAGSWIYIGTQGIVQGTYETFVEAGRQHYGGSLKGKWILTGGL 174 +HF+ELD+KGL MYGQMTAGSWIYIG+QGIVQGTYETF QH+ G G+WILTGGL Sbjct: 121 EHFHELDRKGLMMYGQMTAGSWIYIGSQGIVQGTYETFFSVANQHFNGDPSGRWILTGGL 180 Query: 175 GGMGGAQPLAAVMAGACCLAVECNPDSIDFRLRTRYLDEKAETLEEAMEMIERWTKAGEP 234 GGMGGAQPLAA MAG +AVEC+ IDFRL+TRY+D+KA TL+EA+ M+E KAG+P Sbjct: 181 GGMGGAQPLAATMAGFSMIAVECDETRIDFRLKTRYVDKKAATLDEALAMLEEAKKAGKP 240 Query: 235 KSVGLLGNAAEILPEMVRRGIRPDMVTDQTSAHDPINGYLPKGWTMAEWKAKRESDPKAV 294 S+GLLGNAA++ E V RGI PD VTDQTSAHDPI+GYLP+GW + +W+ ++++ P ++ Sbjct: 241 VSIGLLGNAADVFAECVTRGITPDCVTDQTSAHDPIHGYLPQGWNVEDWRERQKTVPDSI 300 Query: 295 EKAARASMRDHVEAMLAFWDSGVPTLDYGNNIRQVAKDEGLERAFDFPGFVPAYIRPLFC 354 A+ SM V+AML + G TLDYGNNIRQ+A + G+E AFDFPGFVPAYIRPLFC Sbjct: 301 VLPAKQSMAKQVQAMLTLQERGAATLDYGNNIRQMALEMGVENAFDFPGFVPAYIRPLFC 360 Query: 355 RGIGPFRWAALSGDPEDIYRTDRKVKELLPDNKHLHNWLDMARERIAFQGLPARICWVGL 414 G GPFRW ALSGDPEDIY+TD KVKEL+PD+ HLHNWLDMARERIAFQGLPARICWVG+ Sbjct: 361 EGKGPFRWVALSGDPEDIYKTDAKVKELIPDDPHLHNWLDMARERIAFQGLPARICWVGV 420 Query: 415 GDRHRLGLAFNEMVRSGELKAPIVIGRDHLDSGSVASPNRETEAMKDGSDAVSDWPLLNA 474 DR+RLG AFNEMV++GELKAPIVIGRDHLD+GSVASPNRETE+MKDGSDAVSDWPLLNA Sbjct: 421 KDRYRLGQAFNEMVKNGELKAPIVIGRDHLDTGSVASPNRETESMKDGSDAVSDWPLLNA 480 Query: 475 LLNTASGATWVSLHHGGGVGMGFSQHSGMVICCDGTDDAARRIERVLWNDPATGVMRHAD 534 LLNTA GA+WVSLHHGGGVGMGFSQHSG+VI DGTD A R+ RVL+NDPATGVMRHAD Sbjct: 481 LLNTAGGASWVSLHHGGGVGMGFSQHSGVVIVADGTDAAKERLGRVLFNDPATGVMRHAD 540 Query: 535 AGYDIAVDCAREKGLRLP 552 AGY++A + ARE GL LP Sbjct: 541 AGYELAQETAREAGLNLP 558 Lambda K H 0.319 0.137 0.431 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: 1130 Number of extensions: 52 Number of successful extensions: 1 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: 557 Length of database: 562 Length adjustment: 36 Effective length of query: 521 Effective length of database: 526 Effective search space: 274046 Effective search space used: 274046 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 BPHYT_RS07565 BPHYT_RS07565 (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.1950206.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-294 964.0 0.2 1.3e-294 963.8 0.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS07565 BPHYT_RS07565 urocanate hydratas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS07565 BPHYT_RS07565 urocanate hydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 963.8 0.2 1.3e-294 1.3e-294 1 545 [] 15 559 .. 15 559 .. 1.00 Alignments for each domain: == domain 1 score: 963.8 bits; conditional E-value: 1.3e-294 TIGR01228 1 keiraprGkeleakgweqeaalrllmnnldpevaedpeelvvyGGkGkaarnweafdkiveelkrledde 70 ++iraprG e+++k+w+ eaa r+++nnldpevae+p+ lvvyGG+G+aarnw++fd+i+++lk le++e lcl|FitnessBrowser__BFirm:BPHYT_RS07565 15 RTIRAPRGAEKTCKTWIAEAAYRMIQNNLDPEVAEHPHALVVYGGIGRAARNWDCFDQILKSLKDLEENE 84 689******************************************************************* PP TIGR01228 71 tllvqsGkpvgvfkthekaprvliansnlvpkwadwekfeeleakGlimyGqmtaGswiyiGtqGilqGt 140 tll+qsGkpvgvf+th +aprvl+ansnlvp+wa+we+f+el++kGl+myGqmtaGswiyiG+qGi+qGt lcl|FitnessBrowser__BFirm:BPHYT_RS07565 85 TLLIQSGKPVGVFRTHADAPRVLLANSNLVPHWATWEHFHELDRKGLMMYGQMTAGSWIYIGSQGIVQGT 154 ********************************************************************** PP TIGR01228 141 yetlaelarkhfggslkgklvltaGlGgmGGaqplavtlneavsiavevdeeridkrletkyldektddl 210 yet+ ++a++hf g+ +g+++lt GlGgmGGaqpla+t+++ ++iave+de+rid+rl+t+y+d+k++ l lcl|FitnessBrowser__BFirm:BPHYT_RS07565 155 YETFFSVANQHFNGDPSGRWILTGGLGGMGGAQPLAATMAGFSMIAVECDETRIDFRLKTRYVDKKAATL 224 ********************************************************************** PP TIGR01228 211 dealaraeeakaeGkalsigllGnaaevleellergvvpdvvtdqtsahdellGyipegytvedadklrd 280 deala+ eeak++Gk++sigllGnaa+v+ e ++rg++pd vtdqtsahd++ Gy+p+g+ ved +++++ lcl|FitnessBrowser__BFirm:BPHYT_RS07565 225 DEALAMLEEAKKAGKPVSIGLLGNAADVFAECVTRGITPDCVTDQTSAHDPIHGYLPQGWNVEDWRERQK 294 ********************************************************************** PP TIGR01228 281 eepeeyvkaakaslakhvrallalqkkGavtfdyGnnirqvakeeGvedafdfpGfvpayirdlfceGkG 350 + p+ +v ak+s+ak+v+a+l+lq++Ga t+dyGnnirq+a e Gve+afdfpGfvpayir+lfceGkG lcl|FitnessBrowser__BFirm:BPHYT_RS07565 295 TVPDSIVLPAKQSMAKQVQAMLTLQERGAATLDYGNNIRQMALEMGVENAFDFPGFVPAYIRPLFCEGKG 364 ********************************************************************** PP TIGR01228 351 pfrwvalsGdpadiyrtdkavkelfpedeelhrwidlakekvafqGlparicwlgygereklalainelv 420 pfrwvalsGdp+diy+td++vkel+p+d +lh+w+d+a+e++afqGlparicw+g ++r +l+ a+ne+v lcl|FitnessBrowser__BFirm:BPHYT_RS07565 365 PFRWVALSGDPEDIYKTDAKVKELIPDDPHLHNWLDMARERIAFQGLPARICWVGVKDRYRLGQAFNEMV 434 ********************************************************************** PP TIGR01228 421 rsGelkapvvigrdhldaGsvaspnreteamkdGsdavadwpllnallntaaGaswvslhhGGGvglGfs 490 ++Gelkap+vigrdhld+Gsvaspnrete+mkdGsdav+dwpllnallnta+GaswvslhhGGGvg+Gfs lcl|FitnessBrowser__BFirm:BPHYT_RS07565 435 KNGELKAPIVIGRDHLDTGSVASPNRETESMKDGSDAVSDWPLLNALLNTAGGASWVSLHHGGGVGMGFS 504 ********************************************************************** PP TIGR01228 491 lhaglvivadGtdeaaerlkrvltadpGlGvirhadaGyesaldvakeqgldlpm 545 +h+g+vivadGtd+a+erl rvl +dp +Gv+rhadaGye a ++a+e gl+lpm lcl|FitnessBrowser__BFirm:BPHYT_RS07565 505 QHSGVVIVADGTDAAKERLGRVLFNDPATGVMRHADAGYELAQETAREAGLNLPM 559 ******************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (545 nodes) Target sequences: 1 (562 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 34.40 // [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