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_086510401.1 BZY95_RS13285 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_002151265.1:WP_086510401.1 Length = 681 Score = 345 bits (885), Expect = 3e-99 Identities = 193/455 (42%), Positives = 280/455 (61%), Gaps = 15/455 (3%) Query: 3 PFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSY 62 PF +LVANRGEIA RV++ + MG+ +AVYS+AD A H + ADEA +G A A +SY Sbjct: 10 PFDTLLVANRGEIACRVMRTARAMGLRTVAVYSDADANARHVREADEAVRLGPAAARESY 69 Query: 63 LNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGK 122 L +E +++AA++ AIHPGYGFLSEN F +A++ AGITF+GP + + + DK K Sbjct: 70 LKVEAVVEAAKRTGAGAIHPGYGFLSENGAFVQALDAAGITFVGPPASAIAAMGDKSAAK 129 Query: 123 -RLANMAGVPTAPGSDGPVTSIDEAL--KLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179 R+AN AGVP PG G D+AL A+KIGYP+++KA++GGGG G+ V+ +Q Sbjct: 130 ARMAN-AGVPLVPGYHG--DDQDDALLKSEADKIGYPVLLKASAGGGGKGMRVVEAPEQF 186 Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239 + +R + AFG + IEKY PRH+E Q+ D +GN V +ER+C++QRR+QK Sbjct: 187 QAALDGCRRESQAAFGDTRMLIEKYLTQPRHVEVQVFCDSHGNGVYLFERDCSVQRRHQK 246 Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299 ++EEAP+P + E R M E ++ K I Y GT E D FYF+E+N RLQVE Sbjct: 247 VLEEAPAPGMTAELRREMGEAAVRAAKEIGYVGAGTVEFLL-DKDGSFYFMEMNTRLQVE 305 Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSG- 358 HP TE+I DLV+ Q+++A GE LP QE+L + G + E R+ AED +F ++G Sbjct: 306 HPVTEMITGQDLVEWQLRVAMGETLPLQQEELT--ITGHSFEARLYAEDPEQDFLPATGR 363 Query: 359 FVTYYREPTGPG-----VRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALA 413 + + G G VR+DSG+E+G V +YD +++KLIV+G+ R+ A+ RALA Sbjct: 364 LERFAMDLKGAGLDPRQVRLDSGVETGDVVSMHYDPMLAKLIVHGDDRDQALSTLNRALA 423 Query: 414 DYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQ 448 + G+ T + + P F+ + T +I + Sbjct: 424 ALDVQGVVTNRAFLQRLATHPAFRNAELDTRFIEK 458 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: 739 Number of extensions: 35 Number of successful extensions: 4 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: 681 Length adjustment: 37 Effective length of query: 472 Effective length of database: 644 Effective search space: 303968 Effective search space used: 303968 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 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