Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate BPHYT_RS23275 BPHYT_RS23275 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__BFirm:BPHYT_RS23275 Length = 692 Score = 347 bits (890), Expect = e-100 Identities = 198/523 (37%), Positives = 288/523 (55%), Gaps = 30/523 (5%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA RV K +G+ ++AVYS+AD A H DEA +IG + A +SYL Sbjct: 2 FNKILIANRGEIACRVAATCKRLGIASVAVYSDADANAKHVAACDEAVHIGGSTAAESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 +E II+AA A+HPGYGFLSEN +FA A E AGI FIGP E + + K K Sbjct: 62 RVERIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L + A VP PG G + A+ IGYP+++KA++GGGG G+ V+ + Sbjct: 122 LMHTAAVPLVPGYHGDDQDAQLLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFEAAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 KR A +FG + IEKY PRH+E Q+ D++G V ++R+C++QRR+QK++EE Sbjct: 182 ASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P L E + M + + + +NY GT E + DFYF+E+N RLQVEHP T Sbjct: 242 APAPGLAAEIKREMGDAAVAAARAVNYVGAGTVEFIMTGTG-DFYFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E++ DLV+ Q+++AAGE LP +QE L ++ G AIE RI AE F S+G + + Sbjct: 301 EMVTGQDLVEWQLRVAAGEALPLTQEQL--KIDGHAIEARIYAEHPARGFLPSTGTLKHL 358 Query: 364 REPTG---------------------PGVRVDSGIESGSYVPPYYDSLVSKLIVYGESRE 402 R P G VR+DSG+ G + P+YD +++KLIV+G +RE Sbjct: 359 RMPEGVEFTLDAAGSGAAGLGESGRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATRE 418 Query: 403 YAIQAGIRALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLRE--Q 460 A+ RAL ++ G T +E + I+ F G T I + D ++ + Sbjct: 419 EALARMSRALHACEVVGPHTNVEFLQSIVASEPFATGDLDTGLIERHHDALFAPRKKPFK 478 Query: 461 EEIKAAIAAEIQSRGLLRTSSTDNKGKAQSKSGWKTYGIITQS 503 E + A AA ++ G + + S W+ G TQ+ Sbjct: 479 EALALACAALLKREG----GTAHGASPWDALSHWRLNGGYTQT 517 Lambda K H 0.317 0.135 0.385 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: 788 Number of extensions: 37 Number of successful extensions: 4 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: 509 Length of database: 692 Length adjustment: 37 Effective length of query: 472 Effective length of database: 655 Effective search space: 309160 Effective search space used: 309160 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 (21.6 bits) S2: 53 (25.0 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