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 GFF4239 HP15_4179 methylcrotonyl-CoA carboxylase, alpha subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Marino:GFF4239 Length = 664 Score = 366 bits (940), Expect = e-105 Identities = 200/495 (40%), Positives = 290/495 (58%), Gaps = 6/495 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 FS++L+ANRGEIA R+++ MG+ +AVYSEAD A H ADEA++IG AP+ +SYL Sbjct: 2 FSKILIANRGEIACRIIQTAHRMGIRVVAVYSEADANARHVAMADEAFHIGPAPSSESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E II+ A+K+ AIHPGYGFLSEN FAE+ E I FIGP S + + K K Sbjct: 62 RAEKIIEIAKKSGAQAIHPGYGFLSENTGFAESCEANNIVFIGPPSSAIAAMGSKSAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 + AGVP PG G S++ AEK G+P+++KA +GGGG G+ V+N + D Sbjct: 122 IMEKAGVPLVPGYHGDDQSVETLRAEAEKCGFPLLLKAVAGGGGKGMRVVNNMGEFDDAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 KR A AFG D+ IE+Y PRH+E Q+ D+ G V ER+C++QRR+QK++EE Sbjct: 182 AAAKREAQNAFGNPDMLIERYLTQPRHVEIQVFCDQEGKGVYLAERDCSVQRRHQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P L E R++M E ++ + INY GT E + DV F+F+E+N RLQVEHP T Sbjct: 242 APAPGLSEETRKAMGEAAVRAAQAINYVGAGTVEFLY-DVDGSFFFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E++ DLV+ Q+K+A G+ LP Q + + RG A+E RI AED +F ++G + Y Sbjct: 301 EMVTGQDLVEWQLKVAWGDALPLEQSQV--KTRGHALEARIYAEDPDQDFLPATGNLRYL 358 Query: 364 REP-TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 P VRVD+G+ G + +YD +++KLIV+ E+R+ AI ++AL Y+I G+KT Sbjct: 359 STPDESAHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAINRMVQALEHYRIAGVKT 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFV--KYLREQEEIKAAIAAEIQSRGLLRTS 480 I + F+E + +T +I + L + + A ++ R Sbjct: 419 NIRFLHALADAQPFREAELTTGFIDDHRELLFPKSKLDTHKALVLAAGFVLEQRKSREVV 478 Query: 481 STDNKGKAQSKSGWK 495 STD ++ W+ Sbjct: 479 STDPWSPFGRQNSWR 493 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: 746 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: 664 Length adjustment: 36 Effective length of query: 473 Effective length of database: 628 Effective search space: 297044 Effective search space used: 297044 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