Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF4239 HP15_4179 methylcrotonyl-CoA carboxylase, alpha subunit
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__Marino:GFF4239 Length = 664 Score = 716 bits (1849), Expect = 0.0 Identities = 376/672 (55%), Positives = 484/672 (72%), Gaps = 15/672 (2%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF+K+LIANRGEIACR+I+TA MGI+ VAVYS+AD +ARHVA+ADE+F++G + + SY Sbjct: 1 MFSKILIANRGEIACRIIQTAHRMGIRVVAVYSEADANARHVAMADEAFHIGPAPSSESY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 LR E II+IAKK GA+AIHPGYGFLSEN FA +CEA+ I F+GP S AI AMGSKSAAK Sbjct: 61 LRAEKIIEIAKKSGAQAIHPGYGFLSENTGFAESCEANNIVFIGPPSSAIAAMGSKSAAK 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 IMEKAGVPLVPGYHGDDQS TL AEA+K G+PLL+KA GGGGKGMR+V + E A Sbjct: 121 AIMEKAGVPLVPGYHGDDQSVETLRAEAEKCGFPLLLKAVAGGGGKGMRVVNNMGEFDDA 180 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 + +A+REA ++FGN +L+ERYL QPRHVE+QVF D +G VYL++RDCS+QRRHQKV+E Sbjct: 181 LAAAKREAQNAFGNPDMLIERYLTQPRHVEIQVFCDQEGKGVYLAERDCSVQRRHQKVLE 240 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 EAPAPGL + RK MGEAAV AA+AI+Y GAGTVEFL DVD SFFFMEMNTRLQVEHPVT Sbjct: 241 EAPAPGLSEETRKAMGEAAVRAAQAINYVGAGTVEFLYDVDGSFFFMEMNTRLQVEHPVT 300 Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 EMVTGQDLV+WQL VA G LPLEQ +++ GHA E RIYAEDP+ +FLPA+G L +L Sbjct: 301 EMVTGQDLVEWQLKVAWGDALPLEQSQVKTRGHALEARIYAEDPDQDFLPATGNLRYLST 360 Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420 P+ S HVR+D+GV E D IS +YDPMIAKLIVWDE+R +A+ R+ +AL YR+ G+K NI Sbjct: 361 PDESAHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAINRMVQALEHYRIAGVKTNI 420 Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLA---VLTQLRLREAVSQ 477 FL +A+ F +A +T FI + + L S+ + A VLA VL Q + RE VS Sbjct: 421 RFLHALADAQPFREAELTTGFIDDHRELLFPKSKLDTHKALVLAAGFVLEQRKSREVVST 480 Query: 478 DVAGHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLCLNDKLIELS 537 DP+SP+ +R++S + L + ++ E + RYQ+ + D + L+ Sbjct: 481 -----DPWSPFGRQNSWRMNSEFAQPLQ-LQVGEEIHDLKVLERDDRYQVFVGDSVYNLT 534 Query: 538 GSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYH---FREVLGQVLEETASSEDKL 594 ++D L+ INGH++ + +L + L +F +++ ++E G EE A E L Sbjct: 535 ARLDDDYLQAVINGHRISIHGNLHNDQLVLFYEGDTFNCTVYKESYG--FEEMA-GEGSL 591 Query: 595 KAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGELVSDGT 654 APMNG +V GDKV+AGQ L++MEAMKME+ I+AP DGVV+E FFA G+ VS+G Sbjct: 592 AAPMNGAIVAVQAKVGDKVTAGQSLVIMEAMKMEHAIKAPADGVVTEIFFAEGDQVSEGA 651 Query: 655 LLLALEMADAAA 666 L+A+E+ + A Sbjct: 652 ELIAIEVNEEEA 663 Lambda K H 0.317 0.134 0.380 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: 1139 Number of extensions: 59 Number of successful extensions: 5 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: 673 Length of database: 664 Length adjustment: 38 Effective length of query: 635 Effective length of database: 626 Effective search space: 397510 Effective search space used: 397510 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 (21.7 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