Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate Ga0059261_0531 Ga0059261_0531 4-hydroxybenzoate 3-monooxygenase
Query= reanno::Cup4G11:RR42_RS21940 (389 letters) >FitnessBrowser__Korea:Ga0059261_0531 Length = 389 Score = 459 bits (1181), Expect = e-134 Identities = 226/387 (58%), Positives = 281/387 (72%) Query: 1 MRTQVAIIGAGPAGLLLGQLLAKAGIDAVIVEQRSPDYILGRIRAGILESVTADALERAG 60 MRTQVAI+GAGP+GLLLG LL +AG+D VIVE++S Y+LGRIRAG+LE+VT D + R G Sbjct: 1 MRTQVAIVGAGPSGLLLGHLLLQAGVDCVIVERQSASYVLGRIRAGVLETVTTDLMTRLG 60 Query: 61 VAQRLQHDGLVHHGIELSYGGERHRIDFHALIGRSVTVYGQTEVTRDLMAARQAGNAVTI 120 + R+ +GL+ G L+ RID AL GR V VYGQTE+TRDLM A + + Sbjct: 61 IDARMNAEGLIEQGFNLATSDRVIRIDIAALTGRHVMVYGQTELTRDLMDAARDRGLEIV 120 Query: 121 YDAQDVSVHDFDTATPMVRYRKGGQQYELRCDFIAGCDGFHGVTRRSVPEPSRRIFERVY 180 Y+A+DV++HD ++ P V Y K G+ + C FIAGCDGFHG +RR++P + R +ER Y Sbjct: 121 YEAKDVALHDVESGAPYVTYAKDGKAQRIDCAFIAGCDGFHGPSRRAIPASAAREYEREY 180 Query: 181 PFGWLGVLADTPPVANELIYASHERGFALCSMRSLTRSRYYVQVSADERVEDWSDQRFWD 240 PFGWLG+LAD PP ELIYA+ ++GFAL SMRS TRSRYY+QV +RVEDWS++R WD Sbjct: 181 PFGWLGILADVPPCHPELIYANTDQGFALASMRSATRSRYYIQVPLTDRVEDWSEERLWD 240 Query: 241 ELRSRLDTSAAEALVTGASIEKSIAPLRSFVCEPMRFGNLFLAGDAAHIVPPTGAKGLNL 300 EL +R D ++ + G ++E SIAPLRS+V E MR G LFLAGD+AHIVPPTGAKGLNL Sbjct: 241 ELAARFDPLSSAGVTRGPALEMSIAPLRSYVFETMRHGRLFLAGDSAHIVPPTGAKGLNL 300 Query: 301 AASDVLYLADGLIARYLRDDASELDAYSQKCLRRVWKAERFSWWMTSLLHRFPDADDFAL 360 AASDV YL+ LIA + R D L Y K L R+WKAERFSW++T L+HRFPD F Sbjct: 301 AASDVAYLSTALIAFFARGDEEGLAGYQAKALARIWKAERFSWYLTKLMHRFPDDGSFEH 360 Query: 361 RIQQAELDYLAGSRAAQMSLAENYVGL 387 R+Q AELDYLA S A Q +AENYVGL Sbjct: 361 RMQAAELDYLAHSEAMQRVIAENYVGL 387 Lambda K H 0.323 0.137 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: 422 Number of extensions: 16 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: 389 Length of database: 389 Length adjustment: 30 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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 Ga0059261_0531 Ga0059261_0531 (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.11077.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-190 617.9 0.0 3.7e-190 617.7 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0531 Ga0059261_0531 4-hydroxybenzoate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0531 Ga0059261_0531 4-hydroxybenzoate 3-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 617.7 0.0 3.7e-190 3.7e-190 1 389 [. 1 388 [. 1 389 [] 1.00 Alignments for each domain: == domain 1 score: 617.7 bits; conditional E-value: 3.7e-190 TIGR02360 1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreg 69 m+tqvai+gaGpsGlllg+ll +aG+d vi+er+s+ yvlgriraGvle++t dl+ ++g+d r+++eg lcl|FitnessBrowser__Korea:Ga0059261_0531 1 MRTQVAIVGAGPSGLLLGHLLLQAGVDCVIVERQSASYVLGRIRAGVLETVTTDLMTRLGIDARMNAEG 69 9******************************************************************** PP TIGR02360 70 lvheGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpk 138 l+ +G+++a++++ +r+d+++ltg ++v+vyGqte+trdl++a+ +gl++vyea++v lhd+es +p+ lcl|FitnessBrowser__Korea:Ga0059261_0531 70 LIEQGFNLATSDRVIRIDIAALTG-RHVMVYGQTELTRDLMDAARDRGLEIVYEAKDVALHDVESGAPY 137 ***********************9.******************************************** PP TIGR02360 139 vtfekdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserG 207 vt+ kdg+ +r+dc fiaGcdGfhG sr++ipa++ +e+e+ ypfGwlGil+++pp++ eliy+n ++G lcl|FitnessBrowser__Korea:Ga0059261_0531 138 VTYAKDGKAQRIDCAFIAGCDGFHGPSRRAIPASAAREYEREYPFGWLGILADVPPCHPELIYANTDQG 206 ********************************************************************* PP TIGR02360 208 falcslrsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepm 276 fal+s+rs+trsryy+qv+ltd+vedws++r+w+el +r+d+ +++ + +gp++e siaplrs+v e m lcl|FitnessBrowser__Korea:Ga0059261_0531 207 FALASMRSATRSRYYIQVPLTDRVEDWSEERLWDELAARFDPLSSAGVTRGPALEMSIAPLRSYVFETM 275 ********************************************************************* PP TIGR02360 277 ryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfsww 345 r+GrlflaGd+ahivpptGakGlnlaasdvayl++al++++ +d++gl +y akalar+wkaerfsw+ lcl|FitnessBrowser__Korea:Ga0059261_0531 276 RHGRLFLAGDSAHIVPPTGAKGLNLAASDVAYLSTALIAFFARGDEEGLAGYQAKALARIWKAERFSWY 344 ********************************************************************* PP TIGR02360 346 ltsllhrfpdedefdkkiqqaeleylleseaaqktlaenyvGlp 389 lt+l+hrfpd+ +f++++q ael+yl++sea q+++aenyvGl lcl|FitnessBrowser__Korea:Ga0059261_0531 345 LTKLMHRFPDDGSFEHRMQAAELDYLAHSEAMQRVIAENYVGLQ 388 ******************************************95 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.20 // [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