Align 4-hydroxybenzoyl-CoA reductase, α subunit (EC 1.3.7.9) (characterized)
to candidate RR42_RS26495 RR42_RS26495 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-14376 (794 letters) >FitnessBrowser__Cup4G11:RR42_RS26495 Length = 802 Score = 280 bits (715), Expect = 3e-79 Identities = 241/817 (29%), Positives = 355/817 (43%), Gaps = 59/817 (7%) Query: 15 NAAPRGVGARLPLIDGVEKVTGTARYTADLPAQGALVGKLLRSPYAHAELLEVDISEALK 74 N +GVGAR+ + + G R+ AD+ G LRSP AHA LL + K Sbjct: 8 NQGGQGVGARVARKEDARHLHGKGRFVADIAMPGLQEVAFLRSPMAHARLLALH-----K 62 Query: 75 LPGVRGIVTGNDCDTPYGVIPIAQNEFP---------LARGRIRYVGEPVAAVAAVDEAT 125 G+ V G D D + +A + FP LA G++R+VGEP+A A A Sbjct: 63 PQGLEHAVIGRD-DMHGALDIVADSAFPSYQPSAQPPLAAGKVRFVGEPIAMAFAPTRAQ 121 Query: 126 TDAALALIRLKVRELPAYFDAADARKAD-VVLLHDNKKGN--IEREVHNEFGDAAAGFAA 182 + I ++ ELPA D AR+A +H++ K N + F + Sbjct: 122 AEDIAERIVAELDELPALTDVDGARQASGTTRVHEHWKNNHFLTLTADKNFDTLSK---T 178 Query: 183 ADLICEETFECAEVHHAMMEPNASLAAWDNERGHLTLWSVTQVPYYVHESLARCMKLDAA 242 A ++ + A ME A LA WD++ L ++S TQVP+ + L+ C+ L+ Sbjct: 179 ASVVVSRKIDLARQCMVPMEGKAVLAYWDHQFDQLIVYSATQVPHMIRTVLSHCLGLEQE 238 Query: 243 YIRVIKPFVGGGFGHRVETLNFEIIAGLLARAARGTVRLLQTREEAFLTHRGRPQTYVRM 302 +RVI P VGG FG++ E+ LA R R ++ R E + + + Sbjct: 239 KVRVISPDVGGAFGYKCVLQQEELCIAWLAMTYRKPFRFIEDRREHLTAGANSREHHYEV 298 Query: 303 KLGLTRDGRMTACEAEVVQRGGAYGGYGLVTILYAGALLNGLYDLPAVKYDGYR-----V 357 GR+ A +A + GGAY + L G + L A +DGYR V Sbjct: 299 TAYADARGRLLALDARIAIDGGAYSVWPFTIGLEPGQAIGNLPGPYA--FDGYRCITECV 356 Query: 358 YTNTPPCGAMRGHGTVNIRFAFESLLDMMAAELGLDAFAVRRRNLLK---APTETINGLK 414 TN P RG + FA E L+D +A E+ + + +R NL++ P + Sbjct: 357 ATNKPGFVPYRGVARTGVCFAMELLMDALAREVKREPWEIRCENLVQPESMPYVNVTNKH 416 Query: 415 VMSYGLPECLDWVEQ---ASGWRERAARLEANSDGPIRRGIGIACSHFVSGSA------- 464 P + Q +G RER R N R +G+ + SA Sbjct: 417 FDGGDYPASVRKAAQMIGLAGIRER-QRQRLNDPSAGSRYLGVGFGTYTEQSAHGTSVFA 475 Query: 465 ---KPVHFTGQPHATIALRVDFDAGITILTGASDIGQGSSTIITQVVAEILGVEYRRLRL 521 PV G AT+ R+ D G+ + G GQG T Q+ EILG++ R+++ Sbjct: 476 AWGTPV-IPGFDSATV--RITPDGGLEVRVGVHSHGQGMETTFAQIANEILGIDVSRVKV 532 Query: 522 IATDSALTPKDNGSYSSRVTFMVGNAAADAARNLKAVLVAAAAKRLQVAEADVDWLGEAA 581 + D+ +TP G+Y+SR M G A + A + L L+ A LQ E + G + Sbjct: 533 VHGDTGVTPFSTGTYASRSLVMSGGAVSRACKALVPRLLKIGAHMLQRPEGEATLAG-GS 591 Query: 582 AVVGDASRQIPFHDIVEEALVDVGMLTVKGTFTCPPEFQGGKQRGGAVGSTMGFSYAAQA 641 GDA+ +P +I ++ L T G K T F+Y+ A Sbjct: 592 VKAGDAA--VPISEIANAWYINPQRLPANVDPTGLETTMGYKPS----VDTGSFTYSTHA 645 Query: 642 VEVSVDTELGKVTVEKVWSAIDCGFAINPMSVEGQVQGAIWMGMGQAISEETVYE-NGRH 700 V VDT+ G V + DCG +NPM VEGQ G + G+G A+ EE Y+ NG+ Sbjct: 646 ALVEVDTDSGHVEILDYVVVEDCGTMVNPMVVEGQTYGGVAQGIGTAMFEEMRYDGNGQP 705 Query: 701 KAVSLLDYRVPTIIESPDIAVHIVESLDPNGPFGAKEASEGPLAGVMSAIAAAIEDATGT 760 A +L DY +P E P I +H E+ P+ FGAK EG +AI A+ DA G+ Sbjct: 706 LASTLADYMLPGPTEIPSIRIHHFETPSPHTEFGAKGMGEGGAIAPPAAIFNAVNDALGS 765 Query: 761 ---RIRATPFTPDRVFDALNRKPRPGAHVAAAAKGAA 794 + TP TP +V +AL R + A + AA Sbjct: 766 FGVELLETPLTPRKVLEALARAEQAREPQATPTREAA 802 Lambda K H 0.319 0.135 0.397 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: 1464 Number of extensions: 83 Number of successful extensions: 9 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: 794 Length of database: 802 Length adjustment: 41 Effective length of query: 753 Effective length of database: 761 Effective search space: 573033 Effective search space used: 573033 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 (21.8 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