Align p-hydroxybenzoate hydroxylase; PHBH; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate WP_011382706.1 AMB_RS01315 4-hydroxybenzoate 3-monooxygenase
Query= SwissProt::P20586 (394 letters) >NCBI__GCF_000009985.1:WP_011382706.1 Length = 391 Score = 542 bits (1397), Expect = e-159 Identities = 271/392 (69%), Positives = 312/392 (79%), Gaps = 1/392 (0%) Query: 1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60 M+ QVAIIGAGPSGL+LGQLL KAGID +ILE QTPDYVLGRIRAGVLEQ VDLL EAG Sbjct: 1 MRVQVAIIGAGPSGLILGQLLAKAGIDALILEAQTPDYVLGRIRAGVLEQVCVDLLDEAG 60 Query: 61 VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120 V R+ +GL H+G+E+ G R RIDL L+GGK VTVYGQTE+TRDLMEAR T Sbjct: 61 VGERLHAEGLPHQGIELLVDGTRHRIDLAGLTGGKQVTVYGQTELTRDLMEARTRAALKT 120 Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180 VY+A EV + D + P V++ +DG R ++CD+IAGCDG+HG+ R S+P + L+ FERV Sbjct: 121 VYEAKEVMVSDFDTDHPRVSYLKDGVRHEVECDFIAGCDGYHGVCRASVPKDALRTFERV 180 Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFW 240 YPFGWLGLL+DTPPV+HELIYA RGFALCSQRS TRSRYY+QVPLSEKVEDWSDERFW Sbjct: 181 YPFGWLGLLSDTPPVNHELIYAKSERGFALCSQRSLTRSRYYLQVPLSEKVEDWSDERFW 240 Query: 241 TELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300 EL+ RL + LVTGPSLEKSIAPLRSFV EPM+ GRLFLAGDAAHIVPPTGAKGLN Sbjct: 241 GELRQRLDGRANDALVTGPSLEKSIAPLRSFVAEPMRFGRLFLAGDAAHIVPPTGAKGLN 300 Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360 LAASDV TL L++ Y G E ++RYS CLRRIWKAERFSWWMT++LHRFPDT F Sbjct: 301 LAASDVRTLGHALIEFY-GGSLEGIDRYSERCLRRIWKAERFSWWMTNLLHRFPDTPPFE 359 Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLPYEE 392 QR + EL+Y + S AG TIAENYVGLP+E+ Sbjct: 360 QRALEAELDYVVHSLAGRTTIAENYVGLPFED 391 Lambda K H 0.321 0.138 0.413 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: 559 Number of extensions: 21 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: 391 Length adjustment: 31 Effective length of query: 363 Effective length of database: 360 Effective search space: 130680 Effective search space used: 130680 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_011382706.1 AMB_RS01315 (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.5184.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-206 669.7 0.0 6.7e-206 669.5 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011382706.1 AMB_RS01315 4-hydroxybenzoate 3- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011382706.1 AMB_RS01315 4-hydroxybenzoate 3-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 669.5 0.0 6.7e-206 6.7e-206 1 390 [] 1 389 [. 1 389 [. 1.00 Alignments for each domain: == domain 1 score: 669.5 bits; conditional E-value: 6.7e-206 TIGR02360 1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreg 69 m++qvaiigaGpsGl+lgqll kaGida+ile +++dyvlgriraGvleq+ vdll+eagv+erl++eg lcl|NCBI__GCF_000009985.1:WP_011382706.1 1 MRVQVAIIGAGPSGLILGQLLAKAGIDALILEAQTPDYVLGRIRAGVLEQVCVDLLDEAGVGERLHAEG 69 9******************************************************************** PP TIGR02360 70 lvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpk 138 l+h+G+e+ ++g+++r+dl+ ltggk+v+vyGqte+trdl+ear +a lktvyea+ev + d+++d+p+ lcl|NCBI__GCF_000009985.1:WP_011382706.1 70 LPHQGIELLVDGTRHRIDLAGLTGGKQVTVYGQTELTRDLMEARTRAALKTVYEAKEVMVSDFDTDHPR 138 ********************************************************************* PP TIGR02360 139 vtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserG 207 v++ kdg +++++cdfiaGcdG+hGv+r+s+p+++l++fe+vypfGwlG+ls+tppv++eliy++serG lcl|NCBI__GCF_000009985.1:WP_011382706.1 139 VSYLKDGVRHEVECDFIAGCDGYHGVCRASVPKDALRTFERVYPFGWLGLLSDTPPVNHELIYAKSERG 207 ********************************************************************* PP TIGR02360 208 falcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepm 276 falcs+rs trsryy+qv+l++kvedwsd+rfw el++rld +a + lvtgps+eksiaplrsfvaepm lcl|NCBI__GCF_000009985.1:WP_011382706.1 208 FALCSQRSLTRSRYYLQVPLSEKVEDWSDERFWGELRQRLDGRANDALVTGPSLEKSIAPLRSFVAEPM 276 ********************************************************************* PP TIGR02360 277 ryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfsww 345 r+GrlflaGdaahivpptGakGlnlaasdv +l +al+e+y ++ +g++rys+++l+r+wkaerfsww lcl|NCBI__GCF_000009985.1:WP_011382706.1 277 RFGRLFLAGDAAHIVPPTGAKGLNLAASDVRTLGHALIEFYG-GSLEGIDRYSERCLRRIWKAERFSWW 344 ****************************************96.7899********************** PP TIGR02360 346 ltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlpy 390 +t+llhrfpd+ f+++ +ael+y+++s a+++t+aenyvGlp+ lcl|NCBI__GCF_000009985.1:WP_011382706.1 345 MTNLLHRFPDTPPFEQRALEAELDYVVHSLAGRTTIAENYVGLPF 389 ********************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (390 nodes) Target sequences: 1 (391 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: 8.41 // [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