Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate SMa2037 SMa2037 Oxidoreductase
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__Smeli:SMa2037 Length = 750 Score = 325 bits (834), Expect = 4e-93 Identities = 259/777 (33%), Positives = 371/777 (47%), Gaps = 62/777 (7%) Query: 10 TVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVI 69 +VG R DGV+KVTG+A+Y AD P LVGRILRSPHAHA I IDT A L GV Sbjct: 14 SVGTRPIRPDGVDKVTGRARYGADFNMPGQLVGRILRSPHAHAIIRKIDTLKAAQLPGVK 73 Query: 70 AVCTGAETP----VPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKALALIKV 125 AV T A+ P + I +N +AR K Y G VAAVAAID TA++AL LI+V Sbjct: 74 AVLTAADLPDLTDGDAAMYDILDN--CMARKKALYDGHAVAAVAAIDARTAKQALKLIEV 131 Query: 126 DYEVLPAYMTPKAAMKAGAIALHD-----------DKPNNILREVHAEFGDVAAAFAEAD 174 +YE+LP A A ++D D+P+N+ GDV A A AD Sbjct: 132 EYELLPHVTDVDQAFAPDAPLINDTIFTTGVDPKPDRPSNVSMRSQFGHGDVDAGMARAD 191 Query: 175 LIREKTYTFAEVNHVHMELNATLAEY--DPVRDMLTLNTTTQVPYYVHLKVAACLQMDSA 232 + E+T+ + + ++E +A +A D D L TQ + A L MD++ Sbjct: 192 FVVERTFKTEQTHQGYIEPHACVASVSSDGTAD---LWVCTQGHFVYRQHCAQLLGMDAS 248 Query: 233 RIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKM 292 ++RV +GGGFG +T + E +A L+RKA V+L+ TR+E F A T + + Sbjct: 249 KLRVTSSEIGGGFGGKTH-VWAEPVALALSRKAGRPVKLVMTRDEVFRASGPTSATSIDV 307 Query: 293 KIGLKKDGKIAALALEATQAGGAYAGYGIITILYTGAL-MHGLYHIPAIKHDAWRVYTNT 351 KIG KDG I A + G YAG GA+ Y + ++ + V N Sbjct: 308 KIGALKDGTIIAADATLRYSCGPYAG----AWAEVGAMTAFACYKLENVRTVGYEVLVNR 363 Query: 352 PPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGV 411 P A R A E+ + E+ +++G++ + R I Q Y G+ Sbjct: 364 PKTAAYRAPSAPMAAFAVESAIDELAKKVGMNPIDFR-IRNAAQEGTKASYGPVYGPIGI 422 Query: 412 PECLEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGG 471 LE VK K L + +G G+A + ++ G+ +L + DG Sbjct: 423 GPTLEAVK---NHPHMKAPLGRNQGRGMACGFWF-------NFGGQ--TCTDLNIGMDGT 470 Query: 472 ITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGN 531 ++L G D+G GS S VAAE LG+ S++R + AD++ ++ + SR TF Sbjct: 471 VSLAVGTVDVG-GSRASLSLVAAEELGIDYSQVRTVIADTSSLGYNDMTDGSRGTFSSSM 529 Query: 532 ASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQD---PGLSFQEVVKAAMVD 588 A+ISAA +L + AA+ D ED+ + G P LS +E+ A+ Sbjct: 530 ATISAARNAIKILRERAAQMWDIPVEDVTWEKGHAVAKGETHGNLPKLSLKEIAAASGTT 589 Query: 589 SGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAV 648 G I G +I G + +A + + VD TG + V Sbjct: 590 GGPIA------------GHSEIVADGAGVS----FATHICDIEVDPETGATKVLRYTVVQ 633 Query: 649 DVGKALNPLAVEGQTQGGVWMGMGQALSEETVYDN-GRMVHGNILDYRVPTIVESPDIEV 707 D GKA++P VEGQ QGG G+G AL+EE +Y N GR+ + LDYR+P + P I+ Sbjct: 634 DAGKAVHPTYVEGQYQGGAAQGIGWALNEEYIYGNDGRLQNAGFLDYRIPVCSDLPMIDT 693 Query: 708 IIVESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDA 764 I+E +PN P+G + E + L A+ AV AVGVR P+SP RI L+A Sbjct: 694 QILEIPNPNHPYGVRGVGETSIVPPLAAVANAVSNAVGVRMLHIPMSPPRILAALEA 750 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: 1269 Number of extensions: 64 Number of successful extensions: 10 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: 750 Length adjustment: 40 Effective length of query: 729 Effective length of database: 710 Effective search space: 517590 Effective search space used: 517590 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