Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CCNA_02250 CCNA_02250 methylcrotonyl-CoA carboxylase biotin-containing subunit
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__Caulo:CCNA_02250 Length = 654 Score = 637 bits (1643), Expect = 0.0 Identities = 353/666 (53%), Positives = 436/666 (65%), Gaps = 27/666 (4%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 M S +LIANRGEIA RIIRTAR LG+RT+AVYS+AD +A V AD AI IG APA ESY Sbjct: 1 MLSSVLIANRGEIARRIIRTARELGVRTIAVYSEADANAPFVMEADAAILIGPAPAKESY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L I+ AAR +GA+AIHPGYGFLSENA+FA++V +AG++++GPPP+AIRAMGLKDAAK Sbjct: 61 LDPRKILAAARQMGAEAIHPGYGFLSENAEFAQSVIDAGLVWIGPPPSAIRAMGLKDAAK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 A+M ++GVP PGY GE+Q L A +IGYPVLIKA AGGGGKGMR+VER EDF A Sbjct: 121 AVMIKAGVPTTPGYLGEDQSVERLTVEAAKIGYPVLIKAVAGGGGKGMRKVERAEDFEAA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 L + RREA +AFGD VLLE+Y+T+PRHIE+QVFGD HGN+VHLFERDCSLQRRHQKVIE Sbjct: 181 LGSCRREASAAFGDDRVLLEKYVTRPRHIEVQVFGDSHGNVVHLFERDCSLQRRHQKVIE 240 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 EAPAPGM R A+ AAV+AAQA+ YVGAGTVEFIAD + GL D +FMEMNTRLQV Sbjct: 241 EAPAPGMDEATREAVCAAAVKAAQAVNYVGAGTVEFIADASEGLRADRIWFMEMNTRLQV 300 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EHPVTE +TG DLVEWQLRVASGEPLP +Q +I+++GWA EARLYAE+PA GFLP+TG+L Sbjct: 301 EHPVTEMVTGQDLVEWQLRVASGEPLPLEQDEITLDGWAMEARLYAENPATGFLPSTGKL 360 Query: 361 TELSFPEGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTV 420 PEG RVDS V +G +TP+YDP+IAKLI HG +R A RL +A + Sbjct: 361 KHFRLPEGDVRVDSAVEEGGEVTPFYDPMIAKLIAHGADREDAAQRLAEACALVEVWPVK 420 Query: 421 TNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAIFSTGALDPNRST 480 TN FL + DF G DTG I+ ++ LT + A+A L+ Sbjct: 421 TNAAFLAKCASHPDFVDGAVDTGFIEARLDELTERAFSDEPAMAAIGWRLDSFLEAEARR 480 Query: 481 DPW----SSLGSWQIWGDAHRMVVIEHADVRAT---VTLASRGRDQFA---VRAGASTLP 530 DPW S L +++ M + D +AT V L G + ++ A ST Sbjct: 481 DPWEGAPSKLLGFRMNAPRASMHLPMSTDGKATPLRVALIGGGTEDWSWDIRHADGST-- 538 Query: 531 VLVLDRFEGGARLEVAGQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDE 590 F+ RL K I+ +F GG F + G +D Sbjct: 539 ------FDEVTRLPTTYGKGPIQ---------VFEGGDVQEFDFVAKIGGAGEGGASDGA 583 Query: 591 LVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEG 650 +++PMPG + V V AG V+KGQ L+ +EAMKME ++A +G +A + G QVSEG Sbjct: 584 ILSPMPGKIVSVSVSAGQTVSKGQTLLTLEAMKMEHAMAAPFDGVVAELSAVAGGQVSEG 643 Query: 651 TVLVTL 656 VL L Sbjct: 644 VVLARL 649 Lambda K H 0.319 0.135 0.394 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: 1214 Number of extensions: 47 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 662 Length of database: 654 Length adjustment: 38 Effective length of query: 624 Effective length of database: 616 Effective search space: 384384 Effective search space used: 384384 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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