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 GFF3827 PS417_19595 3-methylcrotonyl-CoA carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__WCS417:GFF3827 Length = 627 Score = 370 bits (951), Expect = e-107 Identities = 199/468 (42%), Positives = 286/468 (61%), Gaps = 5/468 (1%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 MP FS++L+ANRGEIA R+ + + +G +AVYS+AD A+H + ADEA +IG AP Sbjct: 1 MPAFSKILIANRGEIACRIQRTAQALGYRTVAVYSDADAQALHVQMADEAVHIGPAPVQQ 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYLNI+ I++AA DAI PGYGFLSEN +FA A ++AG+TFIGPS E + + K Sbjct: 61 SYLNIDAILNAARVTSADAIPPGYGFLSENPDFARACQQAGLTFIGPSPEAIELMGSKRL 120 Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180 K AGVP G G + A+ IGYP+M+KA++GGGG G+ V + ++L+ Sbjct: 121 SKLAMLDAGVPCIAGYQGSAQDDSTLQREADAIGYPLMIKASAGGGGRGMRLVQHPEELL 180 Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240 D + A AFG +L +E+ ++PRH+E QL GD +G+ + ER+C+IQRR+QK+ Sbjct: 181 DNLHTARSEAKNAFGSGELILEQALIDPRHVEIQLFGDSHGHLIYLGERDCSIQRRHQKI 240 Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300 IEEAP P + E R++M E + G+ +NY GT E D + FYFLE+N RLQVEH Sbjct: 241 IEEAPCPVMTPELRQAMGEAALNAGRAVNYVGAGTVEFLL-DRNGRFYFLEMNTRLQVEH 299 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360 P TELI +DLV Q+++AAG+ LP +Q D++ + G A+E R+ AED F +G V Sbjct: 300 PVTELITGLDLVDWQLQIAAGQPLPLTQPDVS--LNGHAMEVRLYAEDPAQGFLPQTGEV 357 Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420 R GVR+D G+ G + P+YD ++ K+I YG +RE A + +RA+ D + G+ Sbjct: 358 --LRWDPAAGVRIDHGVTEGQRISPFYDPMLGKIIAYGATREEARRKLLRAVEDTVLLGV 415 Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIA 468 T L +++ PDF G FST +I++ + E + A A Sbjct: 416 TTNQPLLVDLLKHPDFVGGDFSTGFIAEHFSEIRPLTPSAEHLALAAA 463 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: 743 Number of extensions: 28 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: 627 Length adjustment: 36 Effective length of query: 473 Effective length of database: 591 Effective search space: 279543 Effective search space used: 279543 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