Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_057507601.1 ABB28_RS05090 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Smeli:SM_b21124 (662 letters) >NCBI__GCF_001431535.1:WP_057507601.1 Length = 660 Score = 657 bits (1696), Expect = 0.0 Identities = 369/665 (55%), Positives = 458/665 (68%), Gaps = 21/665 (3%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 MF+K+LIANRGEIACR+I T RRLGI TVAVYSDAD A HV LADEAI IG APAAESY Sbjct: 1 MFTKILIANRGEIACRVIATCRRLGIATVAVYSDADRTARHVRLADEAIAIGPAPAAESY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L + I++AAR GAQAIHPGYGFLSENA FAEA A AG++F+GPP +AIRAMG K AAK Sbjct: 61 LRADVILEAARRSGAQAIHPGYGFLSENAAFAEACAAAGVVFIGPPASAIRAMGDKSAAK 120 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 ALM+++GVP+ PGYHG++QD FL +A IGYPVLIKA AGGGGKGMRRV+ F A Sbjct: 121 ALMQQAGVPLTPGYHGDDQDPQFLRGQADAIGYPVLIKASAGGGGKGMRRVDDSAAFIEA 180 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 L + +REA SAFG+ VL+E+Y+ +PRHIE+QVFGD HGN+VHLFERDCS+QRRHQKV+E Sbjct: 181 LASCQREARSAFGNDHVLVEKYVLRPRHIEIQVFGDGHGNVVHLFERDCSVQRRHQKVLE 240 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPD-HFYFMEMNTRLQ 299 EAPAPGMTAE R AMG AAV AA+A+GYVGAGTVEFIA PD FYFMEMNTRLQ Sbjct: 241 EAPAPGMTAERRAAMGKAAVDAARAVGYVGAGTVEFIAS------PDGDFYFMEMNTRLQ 294 Query: 300 VEHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGR 359 VEHPVTE ITG DLV WQLRVA+G+PLPK+Q ++++ G A EARLYAED +GFLP+ G Sbjct: 295 VEHPVTEFITGTDLVAWQLRVAAGQPLPKRQDELAIGGHALEARLYAEDADKGFLPSIGT 354 Query: 360 LTELSFPEGTS--RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIG 417 L L P ++ RVD+GV QGDTITP+YDP+IAKLIV +R AAL R+Q AL +C++ Sbjct: 355 LRHLRLPPESAHVRVDTGVEQGDTITPFYDPMIAKLIVWDVDRDAALRRMQQALADCQVV 414 Query: 418 GTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEAL----ALAAIFST-- 471 G TN FL RL F DT LI+RE + L AP A G+ AL A+ A+ +T Sbjct: 415 GVTTNAGFLRRLVGTDSFAQAKLDTALIEREQDALAAPAA-GEAALWTLAAIGAVVTTAR 473 Query: 472 GALDPNRSTDPWSSLGSWQIWGDAHRMVVIEHADVRATVTLASRGRDQFAVRAGASTLPV 531 A+D PW + W+I A R++ ++ + + ++ + ++ + V+ A Sbjct: 474 AAVDARDPRSPWQAQDGWRIGASASRLLPLQQGERQHSLRVQTQ-PGGWQVQRDAEPAQ- 531 Query: 532 LVLDRFEGGARLEVA--GQKRLIRFSRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADD 589 V RF G +L+VA GQ+ + RD + LF F V D + + + Sbjct: 532 QVSGRFADG-QLDVALDGQRWRVGVQRDDGQVYLFTAQGQQRFSVHDPVGESEQATADAG 590 Query: 590 ELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVAEGAQVSE 649 L+APMPG + V G V++G LVV+EAMKME TL+A +GT+ G QV + Sbjct: 591 SLLAPMPGRIVATLVEPGSKVSRGTPLVVLEAMKMEHTLAAPADGTVHGYRAKAGEQVGD 650 Query: 650 GTVLV 654 G VLV Sbjct: 651 GAVLV 655 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: 1298 Number of extensions: 65 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 662 Length of database: 660 Length adjustment: 38 Effective length of query: 624 Effective length of database: 622 Effective search space: 388128 Effective search space used: 388128 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 24 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