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 CA265_RS18365 CA265_RS18365 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Pedo557:CA265_RS18365 Length = 446 Score = 399 bits (1024), Expect = e-115 Identities = 206/443 (46%), Positives = 293/443 (66%), Gaps = 5/443 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA R+++ KEMG+ +AVYS AD+ ++H ++ADEA IG P+ DSYL Sbjct: 2 FKKILIANRGEIALRIIRTCKEMGIKTVAVYSTADRESLHVRFADEAVCIGPPPSKDSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 NI +II AAE + DAIHPGYGFLSENA+F+ + I FIG + E + + DK K Sbjct: 62 NIPNIISAAELTNADAIHPGYGFLSENAKFSNICREYNIKFIGATPEQINGMGDKASAKE 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 +AGVPT PGS+G +TS+ E + +A ++GYP+++KA +GGGG G+ V + + W Sbjct: 122 TMKIAGVPTIPGSEGLLTSVKEGIAIANEMGYPVILKATAGGGGRGMRVVWKDEDFENAW 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + ++ + AFG L++EKY +PRHIE Q+IGD++G ER+C+IQRR+QKL+EE Sbjct: 182 DSARQESGAAFGNDGLYLEKYIEDPRHIEIQIIGDQFGKACHLSERDCSIQRRHQKLVEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 +PSP + E R M E IK +NY GT E D R+FYF+E+N R+QVEHP T Sbjct: 242 SPSPFMTDELRVRMGEAAIKGAMAVNYEGAGTIE-FLVDKHRNFYFMEMNTRIQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E + DL+K QIK+AAG +P S ++ + AIE RINAED NNF S G +T + Sbjct: 301 EEVINFDLIKEQIKVAAG--IPISGKNYFPDMH--AIECRINAEDPANNFRPSPGKITNF 356 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 P G GVRVD+ + +G +P YDS+++KLI ++RE AI RAL ++ I G+KTT Sbjct: 357 HSPGGHGVRVDTHVYAGYSIPSNYDSMIAKLICVAQTREEAICTMERALGEFVIEGVKTT 416 Query: 424 IELYKWIMQDPDFQEGKFSTSYI 446 I + +M+DP+F+ G F+T ++ Sbjct: 417 IPFHLQLMKDPNFRAGNFTTKFM 439 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: 558 Number of extensions: 16 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: 446 Length adjustment: 33 Effective length of query: 476 Effective length of database: 413 Effective search space: 196588 Effective search space used: 196588 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