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 GFF1016 PGA1_c10330 methylcrotonoyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Phaeo:GFF1016 Length = 645 Score = 340 bits (873), Expect = 7e-98 Identities = 193/450 (42%), Positives = 274/450 (60%), Gaps = 11/450 (2%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV++ + MG+ +AVYS+AD A H + ADEA +IG + DSYL Sbjct: 2 FDKILIANRGEIACRVMETARAMGVRTVAVYSDADVTAKHVQMADEAVHIGGSAPADSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 + II A+++ AIHPGYGFLSEN F +AVE AG++FIGPS++ +RK+ K K Sbjct: 62 KGDVIIRVAQESGAQAIHPGYGFLSENPAFVDAVEAAGLSFIGPSADAIRKMGLKDAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L AGVP PG G + AEKIGYP+++KA +GGGG G+ V+ + D Sbjct: 122 LMEKAGVPVVPGYHGANQDAEFLAGEAEKIGYPVLIKAVAGGGGKGMRLVEAPAEFSDAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVV-AWERECTIQRRNQKLIE 242 + + A AFG D+ IEKY PRHIE Q+ GD G + V +ER+C++QRR+QK+IE Sbjct: 182 KSAQGEATTAFGNPDVLIEKYIQQPRHIEVQVFGD--GTHAVHLFERDCSLQRRHQKVIE 239 Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAF--SDVSR--DFYFLELNKRLQV 298 EAP+P + E RE+M E ++ + I Y GT E SD R F+F+E+N RLQV Sbjct: 240 EAPAPGMTAEMREAMGEAGVRAAEAIGYKGAGTVEFIVDGSDGLRTDGFWFMEMNTRLQV 299 Query: 299 EHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSG 358 EHP TELI +DLV+ Q+++A+GE LP Q+DL + G A E R+ AED F ++G Sbjct: 300 EHPVTELITGVDLVEWQLRVASGESLPAQQDDLT--ITGHAFEARLYAEDVPKGFLPATG 357 Query: 359 FVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418 +T+ P R DSG+ +G + P+YD ++SK+IV+G +R A+ RAL ++ Sbjct: 358 TLTHLSFPA--ECRADSGVRAGDTISPWYDPMISKVIVHGATRSVALSKLRRALERTEVA 415 Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQ 448 G T + + F G+ T I++ Sbjct: 416 GTVTNLAFLGALASHQGFGRGEVDTGLIAR 445 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: 738 Number of extensions: 40 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: 645 Length adjustment: 36 Effective length of query: 473 Effective length of database: 609 Effective search space: 288057 Effective search space used: 288057 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