Align p-hydroxybenzoate hydroxylase; PHBH; PHBHase; 4-hydroxybenzoate 3-monooxygenase; EC 1.14.13.2 (characterized)
to candidate Ac3H11_3418 P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
Query= SwissProt::P00438 (394 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3418 Length = 400 Score = 494 bits (1273), Expect = e-144 Identities = 236/390 (60%), Positives = 296/390 (75%) Query: 1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAG 60 MKTQV IIG GPSGL+L QLLH GI ++LERQ+ +YVLGRIRAGVLE G L+REA Sbjct: 11 MKTQVCIIGGGPSGLMLSQLLHLKGIATIVLERQSREYVLGRIRAGVLEHGFAALMREAQ 70 Query: 61 VDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATT 120 RM ++G +H+G IA GQ R+DL + SGG +V VYGQTE+TRDL EAR+ Sbjct: 71 CGERMDKEGEIHDGFIIAHDGQMDRVDLHKYSGGSSVVVYGQTELTRDLYEARDRMKGVV 130 Query: 121 VYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERV 180 ++ A +V+ H+L+ PYVT+ E +R+DCD++ G DGFHG+SR+SIP + LK +E+V Sbjct: 131 IHNAEDVQPHNLKSANPYVTYRNGDEVVRIDCDFVIGADGFHGVSRKSIPRDVLKEYEKV 190 Query: 181 YPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFW 240 YPFGWLG+L+ T PVS ELIYA H RGFALCS RS SRYY+QVPLT+ VEDWSDE FW Sbjct: 191 YPFGWLGVLSRTKPVSPELIYAKHERGFALCSLRSQVLSRYYIQVPLTDNVEDWSDEAFW 250 Query: 241 TELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLN 300 ELK RLPAEVA+KL+TG S+EKSIAPLRSFV EPM++G LFLAGDAAHIVPPTGA+GLN Sbjct: 251 AELKRRLPAEVADKLITGASIEKSIAPLRSFVAEPMRYGNLFLAGDAAHIVPPTGARGLN 310 Query: 301 LAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFS 360 AASD+ L+ ++ Y+ G L++YS L R+WKA+RFSWWMT++LH FPD+ A+ Sbjct: 311 SAASDIYYLHHAMVAHYQNGDSTGLDKYSEKALARVWKAQRFSWWMTTMLHTFPDSIAYD 370 Query: 361 QRIQQTELEYYLGSEAGLATIAENYVGLPY 390 Q++Q T+L Y SE L ++AENYVGLP+ Sbjct: 371 QKLQDTDLAYLFSSEKALGSLAENYVGLPF 400 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: 519 Number of extensions: 12 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: 394 Length of database: 400 Length adjustment: 31 Effective length of query: 363 Effective length of database: 369 Effective search space: 133947 Effective search space used: 133947 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 Ac3H11_3418 (P-hydroxybenzoate hydroxylase (EC 1.14.13.2))
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.31357.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-210 685.1 0.0 1.4e-210 684.9 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 P-hydroxybenzoate hydroxylase (E Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 P-hydroxybenzoate hydroxylase (EC 1.14.13.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 684.9 0.0 1.4e-210 1.4e-210 1 390 [] 11 400 .] 11 400 .] 1.00 Alignments for each domain: == domain 1 score: 684.9 bits; conditional E-value: 1.4e-210 TIGR02360 1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvd 62 mktqv+iig+GpsGl+l+qllh +Gi++++ler+sr+yvlgriraGvle+g+++l++ea+++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 11 MKTQVCIIGGGPSGLMLSQLLHLKGIATIVLERQSREYVLGRIRAGVLEHGFAALMREAQCG 72 9************************************************************* PP TIGR02360 63 erldreglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyea 124 er+d+eg +h+G+ ia++g++ rvdl+k +gg+sv+vyGqte+trdlyear+++ + ++++a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 73 ERMDKEGEIHDGFIIAHDGQMDRVDLHKYSGGSSVVVYGQTELTRDLYEARDRMKGVVIHNA 134 ************************************************************** PP TIGR02360 125 devrlhdlesdrpkvtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwl 186 ++v++h+l+s +p+vt+++ +e +r+dcdf++G+dGfhGvsrksip+++lke+ekvypfGwl lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 135 EDVQPHNLKSANPYVTYRNGDEVVRIDCDFVIGADGFHGVSRKSIPRDVLKEYEKVYPFGWL 196 ************************************************************** PP TIGR02360 187 GilsetppvsdeliysnserGfalcslrsetrsryyvqvsltdkvedwsddrfweelkrrld 248 G+ls+t+pvs eliy+++erGfalcslrs+++sryy+qv+ltd+vedwsd++fw+elkrrl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 197 GVLSRTKPVSPELIYAKHERGFALCSLRSQVLSRYYIQVPLTDNVEDWSDEAFWAELKRRLP 258 ************************************************************** PP TIGR02360 249 eeaaeklvtgpsieksiaplrsfvaepmryGrlflaGdaahivpptGakGlnlaasdvayly 310 e+a+kl+tg sieksiaplrsfvaepmryG lflaGdaahivpptGa+Gln+aasd++yl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 259 AEVADKLITGASIEKSIAPLRSFVAEPMRYGNLFLAGDAAHIVPPTGARGLNSAASDIYYLH 320 ************************************************************** PP TIGR02360 311 ealleaykekdsaglerysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleyll 372 +a++++y+++ds+gl++ys+kalarvwka+rfsww+t++lh fpd ++d+k+q ++l+yl+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 321 HAMVAHYQNGDSTGLDKYSEKALARVWKAQRFSWWMTTMLHTFPDSIAYDQKLQDTDLAYLF 382 ************************************************************** PP TIGR02360 373 eseaaqktlaenyvGlpy 390 +se a+ +laenyvGlp+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3418 383 SSEKALGSLAENYVGLPF 400 *****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (390 nodes) Target sequences: 1 (400 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: 00:00:00.02 # Mc/sec: 7.41 // [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