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 PfGW456L13_2588 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2588 Length = 651 Score = 365 bits (938), Expect = e-105 Identities = 193/454 (42%), Positives = 282/454 (62%), Gaps = 4/454 (0%) Query: 2 PPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDS 61 P + +LVANRGEIA RV++ K +G+T +AV+S D+ A H++ AD +G + A+DS Sbjct: 4 PVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAVDS 63 Query: 62 YLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDG 121 YL I+ +I AA+ + AIHPGYGFLSENA FA A+E AG+ F+GP + + + K Sbjct: 64 YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAA 123 Query: 122 KRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMD 181 K L AGVP PG G ++ E+IGYP+++KA +GGGG G+ V++ QL + Sbjct: 124 KALMETAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183 Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241 +R A +FG + + +EKY + PRH+E Q+ D++GN + ER+C+IQRR+QK++ Sbjct: 184 ALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243 Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHP 301 EEAP+P L E R +M E ++ + I Y GT E D +F+F+E+N RLQVEHP Sbjct: 244 EEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEHP 302 Query: 302 TTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVT 361 TE I +DLV QI++A GE LP +Q+ + + G AIE R+ AED N+F ++G + Sbjct: 303 VTEAITGLDLVAWQIRVARGEALPMTQDQV--PLVGHAIEVRLYAEDPGNDFLPATGRLE 360 Query: 362 YYREPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420 YRE GPG RVDSG+E G + P+YD ++ KLI +GE RE A + L ++ IGG+ Sbjct: 361 LYRESAQGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420 Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454 KT I + I+ P F + T +I + +Q + Sbjct: 421 KTNINFLRRIIGHPAFATAELDTGFIPRYQEQLL 454 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: 748 Number of extensions: 29 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: 651 Length adjustment: 36 Effective length of query: 473 Effective length of database: 615 Effective search space: 290895 Effective search space used: 290895 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