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 HSERO_RS20550 HSERO_RS20550 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__HerbieS:HSERO_RS20550 Length = 462 Score = 380 bits (975), Expect = e-110 Identities = 194/458 (42%), Positives = 298/458 (65%), Gaps = 7/458 (1%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++L+ANRGEIA R+++A + +G+T +A S+AD ++ + ADE IG A A SYLN+ Sbjct: 7 KLLIANRGEIAVRIIRAAQALGITTVAACSDADTDSLAARMADEVQRIGPARADRSYLNV 66 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 + ++ AA + DA+HPGYGFLSENA FAEAV AG+ F+GP ++ +R++ DK + +R A Sbjct: 67 DALLKAARDSGADALHPGYGFLSENAAFAEAVNAAGLIFVGPQADTIRRMGDKAEARRTA 126 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 AGVP PGS G + + AL A++IGYP+++KA++GGGG GI + +L + Sbjct: 127 AAAGVPVVPGSAGELEDLATALACADEIGYPLLIKASAGGGGRGIRMARDATELAREFPL 186 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 + A AFG A +++E++ RHIE Q++GD V +EREC++QRR QK++EEAP Sbjct: 187 AQAEAQAAFGSAAVYLERFIRRARHIEVQILGDG-ERAVHLFERECSLQRRRQKVLEEAP 245 Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305 SPAL +R+++ + ++ + ++Y GT E F D S +F+F+E+N R+QVEHP TE+ Sbjct: 246 SPALTPAQRQALCDSAVRLAERLHYRGAGTLEYLFDDESGEFFFIEMNTRIQVEHPVTEM 305 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 I IDLV+ +++A GE L Q D+ R++G A+E RINAED NF G V + Sbjct: 306 ITGIDLVQAMLRIAGGEPLGLQQSDI--RMQGAALEMRINAEDPERNFFPCPGTVAELQW 363 Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 P G G+RV+S + +G +PPYYDSL++KL+V+G+ R AI A+ +I G+ TT+ Sbjct: 364 PQGEGIRVESHLYAGYRIPPYYDSLLAKLVVHGKDRAQAIARAQAAVLATRITGMATTLS 423 Query: 426 LYKWIMQDPDFQEGKFST----SYISQKTDQFVKYLRE 459 L++W++ D Q +F T ++++++TD K L E Sbjct: 424 LHQWLLADARVQSARFDTGALETWLAERTDTRAKQLEE 461 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: 480 Number of extensions: 18 Number of successful extensions: 3 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: 462 Length adjustment: 34 Effective length of query: 475 Effective length of database: 428 Effective search space: 203300 Effective search space used: 203300 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: 52 (24.6 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