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_011386591.1 AMB_RS21445 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_000009985.1:WP_011386591.1 Length = 663 Score = 378 bits (970), Expect = e-109 Identities = 196/447 (43%), Positives = 288/447 (64%), Gaps = 3/447 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA RV+K K+MG+ +AVYS+ADK A+H ADEA +IG A + SYL Sbjct: 2 FTKILIANRGEIACRVIKTAKKMGIKTVAVYSDADKDALHVSMADEAVHIGPAASAQSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 I+ I+DA ++ A+HPGYGFLSE EF EA+ KAGI FIGP + + + DK++ K+ Sbjct: 62 VIDKIVDACKQTGAQAVHPGYGFLSEKREFQEALGKAGIAFIGPDAHAIFAMGDKIESKK 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 LA AGV T PG G + DEA+K+A +IGYP+M+KA++GGGG G+ N + + + Sbjct: 122 LAREAGVNTVPGYLGVIKDADEAVKIAREIGYPVMLKASAGGGGKGMRLAWNDAEAHEGF 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 A +FG +F+EK+ PRHIE Q++ D G + EREC+IQRR+QK+IEE Sbjct: 182 TSATNEAKTSFGDDRVFVEKFIEQPRHIEIQVLADGQGTTLYLGERECSIQRRHQKVIEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 APSP L E R++M E +++NY + GT E + +FYFLE+N RLQVEHP T Sbjct: 242 APSPFLTPETRKAMGEQACALARIVNYKSAGTVEFIVGGATGEFYFLEMNTRLQVEHPVT 301 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E+I +DLV+ I++A+GE L +Q+D+ ++ G ++E R+ AED NF S+G +T Y Sbjct: 302 EMITGLDLVEQMIRVASGEKLSITQDDV--KLNGWSMEARVYAEDPFRNFLPSTGRLTRY 359 Query: 364 REPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 + P VRVD+G+ G + +YD +++KLI YG +R+ AI +AL +Y I G+ Sbjct: 360 QPPAESAHVRVDTGVYEGGEISMFYDPMIAKLITYGPTRDAAIAHMRQALDEYYIRGLSH 419 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQK 449 I + F +G +T++I+++ Sbjct: 420 NIPFLASLFSKERFVKGALTTNFIAEE 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: 797 Number of extensions: 33 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: 663 Length adjustment: 36 Effective length of query: 473 Effective length of database: 627 Effective search space: 296571 Effective search space used: 296571 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: 53 (25.0 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