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 GFF2598 HP15_2542 methylcrotonoyl-coenzyme A carboxylase 1 (alpha)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Marino:GFF2598 Length = 656 Score = 369 bits (946), Expect = e-106 Identities = 193/443 (43%), Positives = 279/443 (62%), Gaps = 3/443 (0%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++L+ANRGEIA RV++ K +G +AVYSEAD A+H + ADEA IG A SYLN Sbjct: 4 KLLIANRGEIAVRVIRTAKALGYRTVAVYSEADAKAMHVELADEAVCIGPAQVSASYLNS 63 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 + I++AA K D IHPGYGFLSENA FA A + AG+ F+GP + + + K K Sbjct: 64 DAILEAARKTGADCIHPGYGFLSENAAFANACKDAGLVFVGPPASAIELMGSKRRSKIAM 123 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 AGVP PG +G + DE + A+ IGYP+M+KA++GGGG G+ V+++ +L D +R Sbjct: 124 QEAGVPVVPGYEGNNANDDELIAAAKDIGYPLMIKASAGGGGRGMRLVESESELADNIKR 183 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 + + QAFG +L +EK + PRH+E Q+ D++GN V ER+C++QRR+QK++EEAP Sbjct: 184 ARSESKQAFGDDELILEKAVIEPRHVEIQVFADRHGNAVYLGERDCSVQRRHQKVVEEAP 243 Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305 SP + E R++M E +K NY GT E D R+FYFLE+N RLQVEHP TEL Sbjct: 244 SPFVTPELRQAMGEAAVKAALACNYEGAGTVE-FLVDKHRNFYFLEMNTRLQVEHPVTEL 302 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 I DLV Q+ +A G LP SQ+D++ + G AIE R+ AED + FT +G + + Sbjct: 303 ITGQDLVAWQLNVAEGRPLPLSQDDIH--LNGHAIEVRLYAEDPAHGFTPQTGSLYAFEP 360 Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 G G+R D+G+ SG + P+YD +++K+I +G++R+ A + IR+L D + G+ T Sbjct: 361 AEGEGLRFDTGVRSGDAITPHYDPMLAKVIAWGQNRDEARRRLIRSLEDTTVFGVTTNRH 420 Query: 426 LYKWIMQDPDFQEGKFSTSYISQ 448 I+ D F G +T+++ Q Sbjct: 421 FLSRIIADETFGAGGATTAFLQQ 443 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: 682 Number of extensions: 26 Number of successful extensions: 3 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: 656 Length adjustment: 36 Effective length of query: 473 Effective length of database: 620 Effective search space: 293260 Effective search space used: 293260 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