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 Ac3H11_1927 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1927 Length = 670 Score = 308 bits (790), Expect = 3e-88 Identities = 186/492 (37%), Positives = 277/492 (56%), Gaps = 18/492 (3%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++L+ANR EIA R++ MG+ +AVYS+ D A+H + A +A +G A + D+YL Sbjct: 3 KILIANRSEIARRIIHTAHRMGIETVAVYSDPDASALHVREATQAVALGGAASADTYLRT 62 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 + ++ AA DA+HPGYGFLSENA+FA+AV AG+T+IGP +R + K K LA Sbjct: 63 DKLLAAARATGADAVHPGYGFLSENADFAQAVVDAGLTWIGPPPAAIRALGSKAGAKALA 122 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 VP PG G S + A +IG P+MVKA +GGGG G+ V + QL Sbjct: 123 VAHCVPCLPGYAGDDQSDERFAAEAARIGTPLMVKAVAGGGGRGMRLVTDLAQLPAALAS 182 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 + A FG DL IE+ + PRH+E Q+ D +G + ER+C++QRR+QK+IEEAP Sbjct: 183 ARSEALAGFGCGDLLIERALLQPRHVEVQIFADAHGACIHLGERDCSVQRRHQKIIEEAP 242 Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305 SPA+ RE M + + Y GT E F DFY +E+N RLQVEHP TE Sbjct: 243 SPAVDAALRERMGACAVALAQAAGYVGAGTVE--FLLDGPDFYLMEMNTRLQVEHPVTEA 300 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 + +DLV+ QI++A GE LP +Q+ ++ ++G AIE R+ AEDA +F +G V + Sbjct: 301 LTGLDLVEWQIRVARGEPLPLTQDQVH--LQGHAIEVRLCAEDA--HFRPHTGRVLQFSA 356 Query: 366 P-------TGPG-VRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKI 417 P PG +R D +E G+ V P+YD+++ KLIV+ +R AI A +RAL ++ Sbjct: 357 PPATAFERAAPGALRFDHALEEGAEVTPHYDAMLGKLIVHAPTRAEAIAALVRALHSTRV 416 Query: 418 GGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLL 477 G+ T +Q P F G ++++ Q ++ L E+K + + + ++ Sbjct: 417 LGLPTNRAFLAACLQHPVFGAGHALVPFLAEHAAQ-LQGLLSNIELKVLVQSAV---AVI 472 Query: 478 RTSSTDNKGKAQ 489 +S++ AQ Sbjct: 473 FSSNSSGAASAQ 484 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: 724 Number of extensions: 29 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: 670 Length adjustment: 36 Effective length of query: 473 Effective length of database: 634 Effective search space: 299882 Effective search space used: 299882 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