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 5210939 Shew_3365 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__PV4:5210939 Length = 450 Score = 363 bits (932), Expect = e-105 Identities = 192/449 (42%), Positives = 291/449 (64%), Gaps = 6/449 (1%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 M F +VLVANRGEIA R+++A +++G+ +A+YS ADK + H + AD+ IG APA + Sbjct: 1 MRRFDKVLVANRGEIALRIIRACRQLGIKTVALYSSADKDSGHLRLADQQICIGPAPAKE 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYLNI I+ AA+ A VDAIHPGYGFL+ENA+FA+ V +G FIGP ++ +R + DK+ Sbjct: 61 SYLNIAAILGAADLARVDAIHPGYGFLAENADFAQQVTDSGFHFIGPKADTIRLMGDKVS 120 Query: 121 GKRLANMAGVPTAPGSDGPVTSID-EALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179 AGVPT PGSDG + + ++L++A +IGYP+++KA +GGGG G+ V+++ QL Sbjct: 121 AIAAMKAAGVPTVPGSDGLLGDNEAQSLEIAAQIGYPLIIKATAGGGGKGMRVVEDEAQL 180 Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239 + ++ A AFG +++EKY PRHIE Q++ D G+ + ER+C++QR QK Sbjct: 181 LGAIALTRQEAEAAFGNGGVYLEKYLTRPRHIEVQVLCDHQGHCISLGERDCSLQRAQQK 240 Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299 +IE AP+P L E+R+ + E I+ + I Y GT E + D +FYF+E+N R+QVE Sbjct: 241 VIESAPAPGLTPEQRQQISESCIRACQAIGYRGAGTLEFLYQD--GEFYFMEMNTRIQVE 298 Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359 H +E++ +DL+ LQ+++A GE P + ++ + +G AIE RINAED +F S G Sbjct: 299 HTISEMVTGVDLLVLQLRVAQGE--PLALQESLIQPKGHAIECRINAEDPA-SFAPSPGR 355 Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419 + P G GVR +S + G++VPP YD++++KLI +G+ R AI AL + I G Sbjct: 356 IDRLVVPGGLGVRWESHLSPGAHVPPQYDAMIAKLIAWGDDRAQAIARMRTALDELTITG 415 Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQ 448 IKT + L + ++ DP Q+G+ S Y+ + Sbjct: 416 IKTNVPLLRALLADPQVQQGETSIHYLEE 444 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: 498 Number of extensions: 24 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: 450 Length adjustment: 34 Effective length of query: 475 Effective length of database: 416 Effective search space: 197600 Effective search space used: 197600 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: 51 (24.3 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