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 N515DRAFT_0927 N515DRAFT_0927 3-methylcrotonyl-CoA carboxylase alpha subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Dyella79:N515DRAFT_0927 Length = 665 Score = 336 bits (862), Expect = 1e-96 Identities = 190/452 (42%), Positives = 261/452 (57%), Gaps = 4/452 (0%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F RVL+ANRGEIA RV++ + +G+ IAVYSEAD A H + ADEA+ IG DSYL Sbjct: 2 FERVLIANRGEIACRVIRTCRRLGIRTIAVYSEADADAQHVRLADEAWPIGGPRPADSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E I++ A ++ AIHPGYGFLSEN FA A +AGI FIGP + + K K Sbjct: 62 RGETILEVARRSGAQAIHPGYGFLSENTAFARACTEAGIAFIGPRPASIDAMGSKAAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L VP PG G D A G+P+M+KAA+GGGG G+ V + + D Sbjct: 122 LMEKHAVPLVPGYHGDNQDADFLAGQARSTGFPLMIKAAAGGGGKGMRIVRAEREFADAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A AFG + +E+Y +PRHIEFQ+ GD +GN + EREC+ QRR QK++EE Sbjct: 182 ASAQREAANAFGDTRVILERYVEHPRHIEFQVFGDTHGNVIHLNERECSAQRRYQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 PSP L R +M + + ++Y GT E +F+F+E+N RLQVEHP T Sbjct: 242 TPSPFLTPARRAAMGAAAVAAARAVDYVGAGTVEFIVGQ-DGEFFFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E +DLV+ Q+++AAGE LP QED++ +G AIE R+ AED NF SG + Sbjct: 301 EETLGLDLVEWQLRVAAGEALPLRQEDVH--AQGHAIEVRLYAEDPEQNFLPGSGKLLRL 358 Query: 364 REP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 R P T VR+D G+ G V +YD +++KLIV+ R A+Q AL +I G K+ Sbjct: 359 RLPETSRHVRLDGGVIEGDTVTIFYDPMIAKLIVHDRDRAQALQRLREALMACEIAGPKS 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454 I + +++ P EG+ T Y+ + D+F+ Sbjct: 419 NIAFLERLVRHPVVVEGRIDTGYLDRHLDEFL 450 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: 710 Number of extensions: 19 Number of successful extensions: 5 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