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 RR42_RS26895 RR42_RS26895 3-methylcrotonyl-CoA carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Cup4G11:RR42_RS26895 Length = 674 Score = 351 bits (901), Expect = e-101 Identities = 190/457 (41%), Positives = 272/457 (59%), Gaps = 15/457 (3%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA RV + +G+ +AVYS+AD A H DEA +IG APA DSYL Sbjct: 2 FNKILIANRGEIACRVAATCRRLGIRTVAVYSDADADARHVALCDEAVHIGGAPARDSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 +HII+ A+ AIHPGYGFLSEN FAEA +AG+ FIGP + +R + K KR Sbjct: 62 RGDHIIEMAKATGAQAIHPGYGFLSENDGFAEACAEAGLVFIGPPASSIRAMGSKSAAKR 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L A VP PG G + A++IGYP+++KA++GGGG G+ V+ + Sbjct: 122 LMEAAAVPLVPGYHGEDQEPALLRREADRIGYPVLLKASAGGGGKGMRVVEASEGFEAAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A +FG + +EKY PRHIE Q+ D +GN V +ER+C++QRR+QK++EE Sbjct: 182 ASVQREASASFGDDRVLVEKYLTRPRHIEIQVFADTHGNCVYLFERDCSVQRRHQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P + E R +M E + + + Y GT E ++ FYF+E+N RLQVEHP T Sbjct: 242 APAPGMSEERRRAMGEAAVAAAQAVGYVGAGTVE-FIANQDGSFYFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E+I DLV+ Q+++AAGE LP Q+ L ++ G A+E R+ AE+ F S+G + Y Sbjct: 301 EMITGQDLVEWQLRVAAGEPLPLRQDQL--QIHGHALEARVYAENPDKGFLPSTGTLRYL 358 Query: 364 REP-----------TGP-GVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRA 411 R P GP GVR+DSG+ G + PYYD +++KLIV+G RE A+ +A Sbjct: 359 RTPAAVTFALGQDGNGPAGVRIDSGVREGDTISPYYDPMIAKLIVWGRDREEALARMAQA 418 Query: 412 LADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQ 448 LA+Y + G+ T I + ++ F+ T I + Sbjct: 419 LAEYHVVGLSTNIAFLQRLVTSQAFRTADLDTGLIER 455 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: 777 Number of extensions: 35 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: 674 Length adjustment: 37 Effective length of query: 472 Effective length of database: 637 Effective search space: 300664 Effective search space used: 300664 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