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 6937189 Sama_1359 3-methylcrotonyl-CoA carboxylase alpha subunit (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__SB2B:6937189 Length = 673 Score = 381 bits (979), Expect = e-110 Identities = 211/504 (41%), Positives = 300/504 (59%), Gaps = 6/504 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA RV++ ++MG+ +AVYS+AD+ A H ADE++Y+G++ SYL Sbjct: 2 FNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E IID A+K +AIHPGYGFLSENA FA A E +GI F+GP S+ + + K K Sbjct: 62 RGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAKL 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 + AGVP PG G S L A+KIGYP+++KAA GGGG G+ V+++ +L Sbjct: 122 IMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAAI 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + +R A +FG L +E+Y PRH+E Q+ D GN V +R+C+IQRR+QK++EE Sbjct: 182 DSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P L R+ M E + K I+Y GT E DV F+F+E+N RLQVEHP T Sbjct: 242 APAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLL-DVDMSFFFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E++ DLVK Q+ +AAG LP Q ++ ++ G A E RI AED N F +SG +T+ Sbjct: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEI--QIHGHAFEVRIYAEDPNNEFLPASGKLTFL 358 Query: 364 REP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 REP VR+DSG+ + YYD +++KLIV+ ESR A+ RAL DY++GG+K Sbjct: 359 REPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKH 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSST 482 IE I + P F + FST +I + D + R++ + +A Q R LR + + Sbjct: 419 NIEFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLAVLTQLR--LREAVS 476 Query: 483 DNKGKAQSKSGWKTYGIITQSSTR 506 + S W + SS R Sbjct: 477 QDVAGHDPFSPWSSLKGFRLSSPR 500 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: 761 Number of extensions: 30 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: 673 Length adjustment: 37 Effective length of query: 472 Effective length of database: 636 Effective search space: 300192 Effective search space used: 300192 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