Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate GFF1600 PGA1_c16220 molybdopterin binding domain-containing protein
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__Phaeo:GFF1600 Length = 756 Score = 333 bits (855), Expect = 2e-95 Identities = 266/778 (34%), Positives = 378/778 (48%), Gaps = 58/778 (7%) Query: 11 VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIA 70 VG R DG++KVTGKA++ AD AP L G ILRSPHAHARI IDTS AEAL V A Sbjct: 13 VGTRPNRPDGLDKVTGKARFGADATAPGMLFGAILRSPHAHARIKQIDTSKAEALADVKA 72 Query: 71 VCTGAETPVPFGVLPIAENEY------PLARDKVRYRGDPVAAVAAIDEVTAEKALALIK 124 + T A+ P E E +A D Y G +AAVAA + A AL LI+ Sbjct: 73 IVTRADFSDAIKPAPGLEGEQWNVLENVMAGDTALYDGHAIAAVAATSALAARDALKLIE 132 Query: 125 VDYEVLPAYMTPKAAMKAGAIALHDDKPN---------NILREVHAEFGDVAAAFAEADL 175 V+YEVLP AM A + + + N++R + GDV A FA+ADL Sbjct: 133 VEYEVLPHVTDVDKAMAQDAPVIREGAADYSVPEGMHPNVVRYHESGHGDVEAGFAKADL 192 Query: 176 IREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIR 235 + E+ + + ++E +A LA+ L TQ +YV AA L ++++++R Sbjct: 193 VVEEHFVTEATHQGYIEPHACLAQLGQ-DGKGELWCCTQGHWYVQKNCAALLGIETSQLR 251 Query: 236 VIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIG 295 V +GGGFG +T + E +A L+RK+ V+L+ +R E F A T + +KIG Sbjct: 252 VTASEIGGGFGGKTT-VFIEPVALALSRKSNRPVKLVMSRPEVFRATGPTASTSMDIKIG 310 Query: 296 LKKDGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCG 355 + DG I A GGA+ G + L H+ + +D + +N P Sbjct: 311 MTADGIITAAQGTFRLQGGAFPGAPADMTAMCAFAPYDLQHVQQVGYD---IMSNRPKQA 367 Query: 356 AMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECL 415 A R G+ A E+++ E+ +L +D + +R N + + Y + G+ E L Sbjct: 368 AYRAPGSPMAAYAVESVIDELCRKLDLDPVDVRLKNAAREGTRAS-YGPKFERIGLVETL 426 Query: 416 EKVKAASGWEERKGKLPKGRGLGIALSH-FVSGTSTPKHWTGEPHATVNLKLDFDGGITL 474 + KA + L G+G GI+ F G T +V+L L DG + Sbjct: 427 DAAKAHPHY---SAPLKSGQGRGISCGFWFNHGGET----------SVSLSLSEDGTCQI 473 Query: 475 LTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASI 534 G DIG GS + +AAEVLG+ IRV AD+A ++ S+ SRVT+ G A+I Sbjct: 474 SVGTPDIG-GSRASMALMAAEVLGIPYESIRVTIADTATLGYNDVSHGSRVTYASGLATI 532 Query: 535 SAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQ----DPGLSFQEVVKAAMVDSG 590 AAE+ L K AA K E+ ++ D + SG DP L E+ + G Sbjct: 533 KAAEDAVAKLSKRAAAKWGIPEDAVKWEDGHAVPSGPNAGNFDP-LPLAEITRDMGQTGG 591 Query: 591 TITVKGTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDV 650 I+ G + E GA G +A +V+A VD TGK + V D Sbjct: 592 PIS--GHFEATPE------------GA--GVSFATHIVDAEVDPETGKTAVTRYTVIQDA 635 Query: 651 GKALNPLAVEGQTQGGVWMGMGQALSEETVY-DNGRMVHGNILDYRVPTIVESPDIEVII 709 GKA++P VEGQ QGG G+G AL+EE +Y ++GR+ + LDYR+P + P I+ +I Sbjct: 636 GKAIHPTYVEGQFQGGAAQGIGWALNEEYIYGEDGRLQNAVFLDYRIPVASDLPMIDTVI 695 Query: 710 VESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDAKEA 767 VE +P PFG + E + L AI AV A GVR P+SP RI LD + A Sbjct: 696 VEVPNPGHPFGVRGVGETSICPPLAAIANAVSAAAGVRLHALPMSPPRILAALDQQRA 753 Lambda K H 0.317 0.134 0.386 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: 1266 Number of extensions: 61 Number of successful extensions: 8 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: 769 Length of database: 756 Length adjustment: 40 Effective length of query: 729 Effective length of database: 716 Effective search space: 521964 Effective search space used: 521964 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
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