Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate AO356_05295 AO356_05295 4-hydroxybenzoate 3-monooxygenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2914 (396 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05295 Length = 396 Score = 775 bits (2000), Expect = 0.0 Identities = 383/396 (96%), Positives = 389/396 (98%) Query: 1 MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60 MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTP+YVL RIRAGVLEQGMVELLR Sbjct: 1 MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPDYVLGRIRAGVLEQGMVELLR 60 Query: 61 QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120 QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG Sbjct: 61 QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120 Query: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180 ARTLYLASNAQPHDMQT+ PFVTFEHEG+T RLDCDYIAGCDGFHGVARQSIPAEKLKVF Sbjct: 121 ARTLYLASNAQPHDMQTEHPFVTFEHEGQTLRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180 Query: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240 ERVYPFGWLGVLADTPPVHEELVYARH RGFALCSMRSKTRTRYYLQVPAEEQVADWPDE Sbjct: 181 ERVYPFGWLGVLADTPPVHEELVYARHARGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240 Query: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300 RFW ELKNRLP DLA ALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK Sbjct: 241 RFWHELKNRLPTDLAEALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300 Query: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDDDA 360 GLNLAASDVSTLFNILLKVYRDGRV+LLE+YSAICLRRVWKAERFSWWMTSMLHRFDDDA Sbjct: 301 GLNLAASDVSTLFNILLKVYRDGRVDLLEQYSAICLRRVWKAERFSWWMTSMLHRFDDDA 360 Query: 361 FNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 396 FNQRISEAELEYF+DSEAGRKTIAENYVGLPYEAIE Sbjct: 361 FNQRISEAELEYFLDSEAGRKTIAENYVGLPYEAIE 396 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: 681 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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 AO356_05295 AO356_05295 (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.820947.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-209 681.2 0.0 2.2e-209 681.0 0.0 1.0 1 FitnessBrowser__pseudo5_N2C3_1:AO356_05295 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo5_N2C3_1:AO356_05295 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 681.0 0.0 2.2e-209 2.2e-209 1 390 [] 4 392 .. 4 392 .. 1.00 Alignments for each domain: == domain 1 score: 681.0 bits; conditional E-value: 2.2e-209 TIGR02360 1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldr 67 +ktqvaiigaGpsGlllgqllh+aGid+viler+++dyvlgriraGvleqg+v+ll++agv++r+d+ FitnessBrowser__pseudo5_N2C3_1:AO356_05295 4 LKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPDYVLGRIRAGVLEQGMVELLRQAGVGQRMDA 70 69***************************************************************** PP TIGR02360 68 eglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdles 134 egl+h+G+e+ ++++v++dlk ltggk+v+vyGqtevtrdl+ areaag++t+y a + ++hd+++ FitnessBrowser__pseudo5_N2C3_1:AO356_05295 71 EGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAGARTLYLASNAQPHDMQT 137 ******************************************************************* PP TIGR02360 135 drpkvtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliy 201 ++p vtfe++g++ rldcd+iaGcdGfhGv+r+sipaeklk+fe+vypfGwlG+l++tppv++el+y FitnessBrowser__pseudo5_N2C3_1:AO356_05295 138 EHPFVTFEHEGQTLRLDCDYIAGCDGFHGVARQSIPAEKLKVFERVYPFGWLGVLADTPPVHEELVY 204 ******************************************************************* PP TIGR02360 202 snserGfalcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiapl 268 ++++rGfalcs+rs+tr+ryy+qv+ +++v dw+d+rfw+elk+rl+++ ae lvtgpsieksiapl FitnessBrowser__pseudo5_N2C3_1:AO356_05295 205 ARHARGFALCSMRSKTRTRYYLQVPAEEQVADWPDERFWHELKNRLPTDLAEALVTGPSIEKSIAPL 271 ******************************************************************* PP TIGR02360 269 rsfvaepmryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalar 335 rsfv+epm+yGr+fl+GdaahivpptGakGlnlaasdv++l++ ll+ y++++ + le+ysa +l+r FitnessBrowser__pseudo5_N2C3_1:AO356_05295 272 RSFVVEPMQYGRMFLVGDAAHIVPPTGAKGLNLAASDVSTLFNILLKVYRDGRVDLLEQYSAICLRR 338 ******************************************************************* PP TIGR02360 336 vwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlpy 390 vwkaerfsww+ts+lhrf+d d+f+++i +aeley+l+sea++kt+aenyvGlpy FitnessBrowser__pseudo5_N2C3_1:AO356_05295 339 VWKAERFSWWMTSMLHRFDD-DAFNQRISEAELEYFLDSEAGRKTIAENYVGLPY 392 ******************76.79*******************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (390 nodes) Target sequences: 1 (396 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: 00:00:00.00 # Mc/sec: 17.77 // [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