Align p-hydroxybenzoate hydroxylase; PHBH; PHBHase; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate WP_042118977.1 RHE_RS17600 4-hydroxybenzoate 3-monooxygenase
Query= SwissProt::P00438 (394 letters) >NCBI__GCF_000092045.1:WP_042118977.1 Length = 389 Score = 524 bits (1349), Expect = e-153 Identities = 254/390 (65%), Positives = 307/390 (78%), Gaps = 1/390 (0%) Query: 1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60 M+TQVAIIG+GPSGLLLGQLL +AG+DNVIL+R + +Y+LGR+RAGVLE+G V LL EA Sbjct: 1 MRTQVAIIGSGPSGLLLGQLLTEAGVDNVILDRVSKNYILGRVRAGVLEEGTVGLLDEAK 60 Query: 61 VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120 R+ +GL H+G +AF G+ RIDL L+G + VTVYGQTEVTRDLM+ REACG+ + Sbjct: 61 AGARLHAEGLPHDGFSLAFDGRDHRIDLHELTG-RRVTVYGQTEVTRDLMQRREACGSLS 119 Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180 +Y AA+V HD+ G P+VT+ +DG R+DCD+IAGCDGFHG SR+++P ++ FE+V Sbjct: 120 IYDAADVAPHDVDGGSPFVTYTKDGIGHRIDCDFIAGCDGFHGTSRRALPEGAVRSFEKV 179 Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFW 240 YPFGWLGLLAD PVS+ELIYANHPRGFALCS RSATRSRYY+Q PL K+EDWSD+RFW Sbjct: 180 YPFGWLGLLADVAPVSNELIYANHPRGFALCSMRSATRSRYYIQCPLDAKIEDWSDDRFW 239 Query: 241 TELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300 EL+ RLPA AE L T PS EKSIAPLRSFV EPM+ GRLFL GDAAHIVPPTGAKGLN Sbjct: 240 DELRRRLPAHHAEALTTAPSFEKSIAPLRSFVTEPMRFGRLFLVGDAAHIVPPTGAKGLN 299 Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360 LAASDV L+ LL+ YREG ++ YS L R+WKA RFSWWMT+++HRFPDT F Sbjct: 300 LAASDVHYLFGGLLEHYREGSDSGIDAYSQTALTRVWKAVRFSWWMTTMMHRFPDTSDFD 359 Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLPY 390 Q+IQ+ EL+Y S A +AENYVGLP+ Sbjct: 360 QKIQEAELDYLTHSRAASMVLAENYVGLPF 389 Lambda K H 0.321 0.138 0.414 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: 522 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: 394 Length of database: 389 Length adjustment: 31 Effective length of query: 363 Effective length of database: 358 Effective search space: 129954 Effective search space used: 129954 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: 50 (23.9 bits)
Align candidate WP_042118977.1 RHE_RS17600 (4-hydroxybenzoate 3-monooxygenase)
to HMM TIGR02360 (pobA: 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2))
# 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/TIGR02360.hmm # target sequence database: /tmp/gapView.522862.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02360 [M=390] Accession: TIGR02360 Description: pbenz_hydroxyl: 4-hydroxybenzoate 3-monooxygenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-206 669.1 0.0 1e-205 668.9 0.0 1.0 1 NCBI__GCF_000092045.1:WP_042118977.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092045.1:WP_042118977.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 668.9 0.0 1e-205 1e-205 1 390 [] 1 389 [] 1 389 [] 1.00 Alignments for each domain: == domain 1 score: 668.9 bits; conditional E-value: 1e-205 TIGR02360 1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglvhe 73 m+tqvaiig+GpsGlllgqll +aG+d+vil+r s++y+lgr+raGvle+gtv ll+ea+++ rl++egl+h+ NCBI__GCF_000092045.1:WP_042118977.1 1 MRTQVAIIGSGPSGLLLGQLLTEAGVDNVILDRVSKNYILGRVRAGVLEEGTVGLLDEAKAGARLHAEGLPHD 73 9************************************************************************ PP TIGR02360 74 GveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfekdge 146 G+ +af+g+ +r+dl++ltg + v+vyGqtevtrdl++ rea+g+ ++y+a++v +hd+++ +p vt++kdg NCBI__GCF_000092045.1:WP_042118977.1 74 GFSLAFDGRDHRIDLHELTG-RRVTVYGQTEVTRDLMQRREACGSLSIYDAADVAPHDVDGGSPFVTYTKDGI 145 *******************9.**************************************************** PP TIGR02360 147 ekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrs 219 +r+dcdfiaGcdGfhG sr+++p+ ++++fekvypfGwlG+l+++ pvs+eliy+n+ rGfalcs+rs+trs NCBI__GCF_000092045.1:WP_042118977.1 146 GHRIDCDFIAGCDGFHGTSRRALPEGAVRSFEKVYPFGWLGLLADVAPVSNELIYANHPRGFALCSMRSATRS 218 ************************************************************************* PP TIGR02360 220 ryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivp 292 ryy+q++l+ k+edwsddrfw+el+rrl+ + ae l t+ps+eksiaplrsfv+epmr+Grlfl+Gdaahivp NCBI__GCF_000092045.1:WP_042118977.1 219 RYYIQCPLDAKIEDWSDDRFWDELRRRLPAHHAEALTTAPSFEKSIAPLRSFVTEPMRFGRLFLVGDAAHIVP 291 ************************************************************************* PP TIGR02360 293 ptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqq 365 ptGakGlnlaasdv+yl+ +lle+y+e++++g+++ys+ al+rvwka rfsww+t+++hrfpd+++fd+kiq+ NCBI__GCF_000092045.1:WP_042118977.1 292 PTGAKGLNLAASDVHYLFGGLLEHYREGSDSGIDAYSQTALTRVWKAVRFSWWMTTMMHRFPDTSDFDQKIQE 364 ************************************************************************* PP TIGR02360 366 aeleylleseaaqktlaenyvGlpy 390 ael+yl++s+aa +laenyvGlp+ NCBI__GCF_000092045.1:WP_042118977.1 365 AELDYLTHSRAASMVLAENYVGLPF 389 ************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (390 nodes) Target sequences: 1 (389 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: 31.12 // [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