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 GFF3328 PS417_17030 3-methylcrotonyl-CoA carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >lcl|FitnessBrowser__WCS417:GFF3328 PS417_17030 3-methylcrotonyl-CoA carboxylase Length = 641 Score = 367 bits (942), Expect = e-106 Identities = 193/455 (42%), Positives = 282/455 (61%), Gaps = 4/455 (0%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 M + +LVANRGEIA RV++ K MG+T +AV+S D+ A H++ AD +G + A D Sbjct: 1 MSTLTTLLVANRGEIACRVMRTAKAMGLTTVAVHSAIDRDARHSREADIRVDLGGSKATD 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYL I+ +I AA+ + AIHPGYGFLSENA FA A+E AG+ F+GP + + + K Sbjct: 61 SYLQIDKLIAAAQASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSA 120 Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180 K L AGVP PG G ++ E+IGYP+++KA +GGGG G+ V++ QL Sbjct: 121 AKALMETAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLA 180 Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240 + +R A +FG + +EKY + PRH+E Q+ D++G+ + ER+C+IQRR+QK+ Sbjct: 181 EALASAQREALSSFGNGQMLVEKYLLKPRHVEIQVFADQHGHCLYLNERDCSIQRRHQKV 240 Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300 +EEAP+P L E+R++M E ++ + I Y GT E D +F+F+E+N RLQVEH Sbjct: 241 VEEAPAPGLSGEQRKAMGEAAVRAAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEH 299 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360 P TE I +DLV QI++A GE LP +QE + + G AIE R+ AED N+F ++G + Sbjct: 300 PVTEAITGLDLVAWQIRVAQGEALPITQEQV--PLTGHAIEVRLYAEDPTNDFLPATGRL 357 Query: 361 TYYREPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419 YRE GPG RVDSG+E G V P+YD ++ KLI +GE RE A + L ++ IGG Sbjct: 358 ALYRESAPGPGRRVDSGVEQGDSVSPFYDPMLGKLIAWGEDREQAQLRLLAMLDEFAIGG 417 Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454 +KT + + I+ P F + T +I + ++ + Sbjct: 418 LKTNLGFLRRIIGHPAFAAAELDTGFIPRYQEELL 452 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: 729 Number of extensions: 35 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: 641 Length adjustment: 36 Effective length of query: 473 Effective length of database: 605 Effective search space: 286165 Effective search space used: 286165 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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