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_011383117.1 AMB_RS03465 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_000009985.1:WP_011383117.1 Length = 665 Score = 364 bits (935), Expect = e-105 Identities = 196/446 (43%), Positives = 277/446 (62%), Gaps = 5/446 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV++ K +G+ +AVYSEAD A+H ADEA IG A A +SYL Sbjct: 2 FDKILIANRGEIACRVMRTAKRLGIRTVAVYSEADANAMHVAMADEAVLIGPAAAAESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 + I++AA++ AIHPGYGFLSENA FAEA KAG+ FIGP + + K + KR Sbjct: 62 KGDVILEAAKRTGAQAIHPGYGFLSENAGFAEACAKAGVVFIGPPVGAIHAMGSKAESKR 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L AGVP PG G +++E + A IGYP++VKA++GGGG G+ V L + Sbjct: 122 LMEAAGVPLVPGYHGKGQTLEELTREAAIIGYPVLVKASAGGGGKGMRVVSEASGLAEAV 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 KR A AFG L +E Y PRH+E Q+ D +GN V +ER+C+IQRR+QK+IEE Sbjct: 182 ASAKREAKAAFGDDSLLLETYLGRPRHVEIQVFCDTHGNGVYLFERDCSIQRRHQKVIEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+PAL E R +M E + + ++Y GT E + D F+F+E+N RLQVEHP T Sbjct: 242 APAPALADETRRAMGEAAVAAAQAVDYVGAGTVEFLYQD--GRFFFIEMNTRLQVEHPVT 299 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E+I +DLV+ Q+ +A+G LP +QE L++ +G A E R+ AED +F + G + + Sbjct: 300 EMITGLDLVEWQLLVASGGKLPLAQEQLSR--KGHAFEARLYAEDPSRDFLPAIGKLVHL 357 Query: 364 REPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 P+ VRVD+G+ G V P+YD +++KLIV+ E R+ A++ RALADY++ G+ T Sbjct: 358 APPSENRHVRVDTGVRQGDQVTPFYDPMIAKLIVWDEDRDSALRRLRRALADYQVAGVTT 417 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQ 448 + I P F + T +I + Sbjct: 418 NVSFLGAIAAHPAFAALEIDTGFIER 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: 755 Number of extensions: 32 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: 665 Length adjustment: 36 Effective length of query: 473 Effective length of database: 629 Effective search space: 297517 Effective search space used: 297517 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