Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate Pf1N1B4_703 P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2914 (396 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 Length = 397 Score = 698 bits (1802), Expect = 0.0 Identities = 345/397 (86%), Positives = 369/397 (92%), Gaps = 1/397 (0%) Query: 1 MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60 MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDT+ILERQTP+YVL RIRAGVLEQGMVELLR Sbjct: 1 MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTLILERQTPDYVLGRIRAGVLEQGMVELLR 60 Query: 61 QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120 QAGVGQRMDAEGL H GFEL L+ RRVHIDL+ LTGGK VM+YGQTEVTRDLMAAR AG Sbjct: 61 QAGVGQRMDAEGLVHAGFELALDGRRVHIDLQALTGGKTVMIYGQTEVTRDLMAARRDAG 120 Query: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180 A+T+Y ASN PH M+T PFVTF+ +GET+RLDCDYIAGCDGFHGVARQSIPA+ LKVF Sbjct: 121 AQTIYAASNVVPHGMKTAEPFVTFDKDGETYRLDCDYIAGCDGFHGVARQSIPADCLKVF 180 Query: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240 ERVYPFGWLG+LADTPPVHEELVYARH RGFALCSMRS TRTRYYLQVPA+++V DW D+ Sbjct: 181 ERVYPFGWLGILADTPPVHEELVYARHERGFALCSMRSPTRTRYYLQVPAQDKVEDWSDQ 240 Query: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300 RFW ELK+RLPA LA LVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK Sbjct: 241 RFWDELKSRLPAALADTLVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300 Query: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDD-D 359 GLNLAASDVSTLFNILLKVYR+GRV+LLEKYS +CLRRVWKAERFSWWMTSMLHRFD+ D Sbjct: 301 GLNLAASDVSTLFNILLKVYREGRVDLLEKYSEVCLRRVWKAERFSWWMTSMLHRFDEHD 360 Query: 360 AFNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 396 AF+QRISE+EL YFVDSEAGRKTIAENYVGLPYEAIE Sbjct: 361 AFSQRISESELAYFVDSEAGRKTIAENYVGLPYEAIE 397 Lambda K H 0.321 0.137 0.415 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: 648 Number of extensions: 15 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: 396 Length of database: 397 Length adjustment: 31 Effective length of query: 365 Effective length of database: 366 Effective search space: 133590 Effective search space used: 133590 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate Pf1N1B4_703 (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.21183.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-210 684.5 0.0 2.2e-210 684.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 P-hydroxybenzoate hydroxylase (E Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 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 ! 684.3 0.0 2.2e-210 2.2e-210 1 390 [] 4 393 .. 4 393 .. 1.00 Alignments for each domain: == domain 1 score: 684.3 bits; conditional E-value: 2.2e-210 TIGR02360 1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderl 65 +ktqvaiigaGpsGlllgqllh+aGid++iler+++dyvlgriraGvleqg+v+ll++agv++r+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 4 LKTQVAIIGAGPSGLLLGQLLHNAGIDTLILERQTPDYVLGRIRAGVLEQGMVELLRQAGVGQRM 68 69*************************************************************** PP TIGR02360 66 dreglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlh 130 d+eglvh+G+e+a +g++v++dl++ltggk+v++yGqtevtrdl+ ar ag++t+y a +v +h lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 69 DAEGLVHAGFELALDGRRVHIDLQALTGGKTVMIYGQTEVTRDLMAARRDAGAQTIYAASNVVPH 133 ***************************************************************** PP TIGR02360 131 dlesdrpkvtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppv 195 +++ +p vtf kdge++rldcd+iaGcdGfhGv+r+sipa+ lk+fe+vypfGwlGil++tppv lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 134 GMKTAEPFVTFDKDGETYRLDCDYIAGCDGFHGVARQSIPADCLKVFERVYPFGWLGILADTPPV 198 ***************************************************************** PP TIGR02360 196 sdeliysnserGfalcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgps 260 ++el+y+++erGfalcs+rs tr+ryy+qv+ +dkvedwsd+rfw+elk+rl+ a++lvtgps lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 199 HEELVYARHERGFALCSMRSPTRTRYYLQVPAQDKVEDWSDQRFWDELKSRLPAALADTLVTGPS 263 ***************************************************************** PP TIGR02360 261 ieksiaplrsfvaepmryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsagl 325 ieksiaplrsfv+epm+yGr+fl+GdaahivpptGakGlnlaasdv++l++ ll+ y+e++ + l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 264 IEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAKGLNLAASDVSTLFNILLKVYREGRVDLL 328 ***************************************************************** PP TIGR02360 326 erysakalarvwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlpy 390 e+ys+ +l+rvwkaerfsww+ts+lhrf+++d+f+++i ++el+y+++sea++kt+aenyvGlpy lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_703 329 EKYSEVCLRRVWKAERFSWWMTSMLHRFDEHDAFSQRISESELAYFVDSEAGRKTIAENYVGLPY 393 ****************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (390 nodes) Target sequences: 1 (397 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: 00:00:00.01 # Mc/sec: 12.20 // [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