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 AZOBR_RS22285 AZOBR_RS22285 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__azobra:AZOBR_RS22285 Length = 667 Score = 354 bits (909), Expect = e-102 Identities = 203/495 (41%), Positives = 286/495 (57%), Gaps = 8/495 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV++ + MG+ +AVYSEAD A+H + ADEA IG AP +SYL Sbjct: 2 FDKILIANRGEIACRVIRTARRMGIRTVAVYSEADARAMHVEMADEAVCIGPAPVGESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 + I++ A++ AIHPGYGFLSENA FA A +AG+ FIGP E +R + K + KR Sbjct: 62 RGDAILEVAKRTGAQAIHPGYGFLSENAGFAAACAEAGVVFIGPPIEAIRVMGSKAESKR 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 + + A VP PG G ++ AE+IGYP++VKA++GGGG G+ V + D Sbjct: 122 VMSQADVPLVPGFHGEAQDLETLSAEAERIGYPVLVKASAGGGGKGMRVVRAAGEFADAV 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 KR A AFG + +EKY PRH+E Q+ D +GN V +ER+C+IQRR+QK+IEE Sbjct: 182 AGAKREAKAAFGDDSVLLEKYLGRPRHVEIQVFCDTHGNGVYLFERDCSIQRRHQKVIEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+PAL + R M E + K +NY GT E + D FYF+E+N RLQVEHP T Sbjct: 242 APAPALPDDLRRRMGEAAVAAAKAVNYVGAGTVEFLYED--GGFYFIEMNTRLQVEHPVT 299 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E I DLV+ Q+++AAG LP Q+ L + RG A E R+ AED F + G + Sbjct: 300 EKITGQDLVEWQLRVAAGGVLPLMQDQLTR--RGHAFEARLYAEDPQREFLPAIGKLVRL 357 Query: 364 REPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 R P VRVD+G+ G V +YD +++KLIV+ E R+ A++ ALA Y++ G+ T Sbjct: 358 RPPAENEHVRVDTGVREGDEVTMFYDPMIAKLIVWDEDRDAALRRLRVALAAYEVVGVTT 417 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSST 482 + I P F+ + T +I + + + AIAA LLR ++ Sbjct: 418 NVAFLGAIAGHPAFRAVEIDTGFIERHRADLLPPPAPVPDRGLAIAA---LSVLLRRNAD 474 Query: 483 DNKGKAQSKSGWKTY 497 K + + W + Sbjct: 475 TRKARRAASDPWSPW 489 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: 756 Number of extensions: 35 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: 667 Length adjustment: 36 Effective length of query: 473 Effective length of database: 631 Effective search space: 298463 Effective search space used: 298463 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 Apr 09 2024. 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