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 RR42_RS29420 RR42_RS29420 3-methylcrotonyl-CoA carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Cup4G11:RR42_RS29420 Length = 666 Score = 360 bits (923), Expect = e-103 Identities = 200/467 (42%), Positives = 282/467 (60%), Gaps = 5/467 (1%) Query: 3 PFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSY 62 PF ++L+ANRGEIA RV+++ +G +AVYS AD A H + A +A YIG+A SY Sbjct: 6 PFQKILIANRGEIALRVMRSATALGYRTVAVYSSADAGARHVEEAGQAVYIGQAQPAQSY 65 Query: 63 LNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGK 122 L I+ II+AA ++ DA+HPGYGFL+ENA FA A +AG+ FIGPS+E + + +K K Sbjct: 66 LRIDAIIEAARRSGADAVHPGYGFLAENAAFARACREAGLVFIGPSAESIVAMGNKAGAK 125 Query: 123 RLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182 RL A VP PG G AE+IG+P+M+KA +GGGG G+ V + ++ Sbjct: 126 RLMMAADVPCIPGYQGEDQDEARLCAEAERIGFPVMIKATAGGGGRGMRLVPHARAFPEL 185 Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242 + A AFG ++ +E+ V PRHIE Q++ D+YGN + ER+C++QRR+QKLIE Sbjct: 186 LRSARSEAQGAFGDPEVILERAVVEPRHIEIQILADRYGNAIHLGERDCSVQRRHQKLIE 245 Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302 EAPSPA+ E R M + K I Y GT E D ++YF+E+N RLQVEHP Sbjct: 246 EAPSPAVSAELRARMGATAVAAVKAIGYEGAGTLEFLL-DRDGNYYFMEMNTRLQVEHPV 304 Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362 TE I +DLV LQ+++AAGE LP QED+ R G AIE R+ AEDA F SG + Sbjct: 305 TEAITGLDLVALQLRIAAGEPLPLRQEDV--RFSGHAIEVRLCAEDADQGFMPQSGEIAL 362 Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 ++ P P +RV+ + SG+ +PPYYDS+++KLI YG +R+ A + + L D G+ T Sbjct: 363 WQAP--PALRVEHALGSGAAIPPYYDSMIAKLISYGGTRDEARRKLSQGLEDLVALGVTT 420 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAA 469 + P F G+ +T++I Q D ++ + AA+AA Sbjct: 421 NQVFLGRCLAHPAFAAGEATTAFIGQHQDALLQPDAALRQRAAALAA 467 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: 722 Number of extensions: 33 Number of successful extensions: 5 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: 666 Length adjustment: 36 Effective length of query: 473 Effective length of database: 630 Effective search space: 297990 Effective search space used: 297990 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