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 WP_057507423.1 ABB28_RS04140 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_001431535.1:WP_057507423.1 Length = 455 Score = 370 bits (949), Expect = e-107 Identities = 201/445 (45%), Positives = 282/445 (63%), Gaps = 6/445 (1%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++++ANRGEIA R+L+A +G+ +AV+S D+ H ADE+ IG A + DSYLNI Sbjct: 4 KIVIANRGEIALRILRACHTLGIRTVAVHSTVDRNLKHVAMADESVCIGPAASTDSYLNI 63 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 +I AAE AIHPGYGFLSENA FAE VE++G FIGP ++ +R + DK++ R Sbjct: 64 PALIAAAEVTDAQAIHPGYGFLSENANFAERVEESGFIFIGPKADTIRLMGDKVEAIRAM 123 Query: 126 NMAGVPTAPGSDGPV-TSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWE 184 AGVP PGS GP+ I K+A +IGYP+++KA+ GGGG G+ V + L E Sbjct: 124 KAAGVPCVPGSGGPLGDDIVANTKIAREIGYPVIIKASGGGGGRGMRVVHAEASLKTSIE 183 Query: 185 RNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEA 244 K A AFG ++++EKY NPRH+E Q++ D GN + ER+C++QRR+QK++EEA Sbjct: 184 TTKSEAKAAFGNGEVYMEKYLENPRHVEIQVLADGQGNAIHLGERDCSMQRRHQKVVEEA 243 Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304 P+P + E RE + + ++ I Y GTFE + D FYF+E+N R+QVEHP TE Sbjct: 244 PAPGITDEAREQIGKVCVEACIRIGYRGAGTFEFLYED--GRFYFIEMNTRIQVEHPVTE 301 Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364 ++ IDLV Q+K+AAG+ L Q D+ + G AIE RINAED+ F S G ++ + Sbjct: 302 MVTGIDLVVEQLKIAAGQKLSIKQSDI--VLTGHAIECRINAEDS-ETFVPSPGQISAFH 358 Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424 P GPGVRVD+ I +G VP YDS++ KLIV+G RE AI AL++ + GIKT + Sbjct: 359 APGGPGVRVDTHIYAGYRVPSNYDSMIGKLIVHGPDRETAIARMRVALSEMVVDGIKTNV 418 Query: 425 ELYKWIMQDPDFQEGKFSTSYISQK 449 L + IM+D FQ G + Y+ ++ Sbjct: 419 ALQQRIMRDKGFQAGGQNIHYLEKR 443 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: 560 Number of extensions: 28 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: 455 Length adjustment: 34 Effective length of query: 475 Effective length of database: 421 Effective search space: 199975 Effective search space used: 199975 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 24 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