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_035704420.1 BA79_RS18225 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_000691145.1:WP_035704420.1 Length = 449 Score = 396 bits (1017), Expect = e-114 Identities = 206/449 (45%), Positives = 297/449 (66%), Gaps = 4/449 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F +VL+ANRGEIA RV++ K +G+ +AVYSEAD++A+H K AD AYYIG A +SYL Sbjct: 2 FEQVLIANRGEIARRVIRTCKRLGIKTVAVYSEADQHALHVKEADSAYYIGGAKVSESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 N+E II A++ + DAIHPGYG LSENA FAE GITFIGPS++V++++ +K++ ++ Sbjct: 62 NMEAIIKVAKQTNADAIHPGYGLLSENAAFAERCRSEGITFIGPSAQVIQQMGNKIEARK 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 AG+P PG P+ DE + A +GYPIM+KA+SGGGG+G+ V N ++L + Sbjct: 122 TMEQAGIPIVPGVSAPLHDADEGVHKAHTLGYPIMLKASSGGGGIGMQLVRNDEELHRAF 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 E N++ A F L++EK + RHIE Q++ D +G+ V +ER+C++QRR+QK++EE Sbjct: 182 EGNQKRAQSFFQDGTLYMEKVIEHARHIEIQVLFDSFGHGVHLFERDCSLQRRHQKIVEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+ L+ R+ M + +K K I Y GT E D ++ FYFLE+N RLQVEHP T Sbjct: 242 APAVCLEETVRQQMGQMAVKAAKAIGYENAGTIE-CLVDQNQQFYFLEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E I IDLV+ Q+K+AA E L FSQED+++ G AIE RI AED + F S G +T Sbjct: 301 EEITGIDLVEEQLKIAALEPLSFSQEDIHQ--IGHAIEVRIYAEDPV-TFYPSPGTITRL 357 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 P P +R +S + SGS + P+YD +++K+IVYG++R+ AI+ AL Y+I GIKT Sbjct: 358 STPDAPYIRHESSVTSGSVITPFYDPMIAKMIVYGDTRKLAIERLKAALQAYEIEGIKTN 417 Query: 424 IELYKWIMQDPDFQEGKFSTSYISQKTDQ 452 + L K + + F G +T Y+ +K ++ Sbjct: 418 VPLLKEMAESTAFLHGSITTDYLMKKREE 446 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: 507 Number of extensions: 19 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: 449 Length adjustment: 34 Effective length of query: 475 Effective length of database: 415 Effective search space: 197125 Effective search space used: 197125 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