Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate SM_b20756 SM_b20756 propionyl-CoA carboxylase subunit alpha
Query= SwissProt::Q99MR8 (717 letters) >FitnessBrowser__Smeli:SM_b20756 Length = 670 Score = 504 bits (1298), Expect = e-147 Identities = 288/684 (42%), Positives = 402/684 (58%), Gaps = 29/684 (4%) Query: 42 GGSITKVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQ 101 G K+LIANRGEIACRVIRT K +G+ +VAVYS+ADR++MHV MADEA IGP+PS Q Sbjct: 2 GHMFKKILIANRGEIACRVIRTTKALGIPTVAVYSDADRDAMHVRMADEAVHIGPSPSSQ 61 Query: 102 SYLAMEKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKST 161 SY+ +E I+ + + A A+HPGYGFLSEN FAE +++G+ FIGPP AI MG K T Sbjct: 62 SYIVIENILAAIRRTGADAVHPGYGFLSENAAFAEALEKDGVTFIGPPVRAIEAMGDKIT 121 Query: 162 SKSIMAAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQ 221 SK + A AGV V G+ G + A +IG+PVMIKA GGGGKGMRI +ERE + Sbjct: 122 SKKLAAEAGVFTVPGHMGLIEDADEAARIAAEIGFPVMIKASAGGGGKGMRIAWNEREAR 181 Query: 222 EQLESARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKI 281 E +S+R EAK SF DD + IEKFV PRH+E+QV GD HGN +YL ER+CS+QRR+QK+ Sbjct: 182 EGFQSSRNEAKSSFGDDRIFIEKFVTEPRHIEIQVLGDKHGNILYLGERECSIQRRNQKV 241 Query: 282 IEEAPAPGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHP 341 IEEAP+P ++ + RR +GE AV AKAV Y AGTVEFI+D+ NFYF+EMNTRLQVEHP Sbjct: 242 IEEAPSPFLDEKTRRAMGEQAVALAKAVGYHSAGTVEFIVDAGRNFYFLEMNTRLQVEHP 301 Query: 342 VTEMITGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHL 401 VTE++TG DLVE +R+AAG K+ +Q+++ L G A E+R+YAEDP F+P G L Sbjct: 302 VTELVTGLDLVEQMIRVAAGAKLAFAQKDVKLDGWAIESRLYAEDPYRTFLPSIGRLTRY 361 Query: 402 STPSADMST-----RIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNI 456 P R +TGV +G E+S++YDPMIAKL W DR +A+ + L + + Sbjct: 362 RPPEEGTQADGTVIRNDTGVFEGGEISMYYDPMIAKLCTWGPDRLTAVRAMADALDAFEV 421 Query: 457 VGLRSNVDFLLRLSGHPEFEAGNVHTDFIPQHHKDLLPSHSTIAKESVCQAALGLILKEK 516 G+ N+ FL + F G + T +I + + +A + L + Sbjct: 422 EGIGHNLPFLAAVMQQERFHEGRLTTAYIAE---EFAGGFHGVALDDASARKLAAVAATV 478 Query: 517 EMTSAFKLHTQDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIAVTYNRDGSYDMQIDN 576 T Q++ S S + G + +T G +I + + DG+Y D Sbjct: 479 NQT------LQERASRISGTIGNHRRVVGHEWVTSLDG-HEIQVTCEVSADGTYVRFADG 531 Query: 577 KSFRVLGD---------LSSEDGCTYLKSSINGVARKSKFILLDNTVHLFSMEGSIEVGI 627 S V D + ++ +K + G + ++ +D + S E+ Sbjct: 532 TSVSVATDWAPGRTRAAFNIDNQPMSVKVELAGPGIRLRWRGIDVVARVRSPR-IAELAR 590 Query: 628 PVPKYLSPVSAEGAQGGTIAPMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAPKD 687 +PK L P +++ + PM G + + VKAG+ V+AG ++ V+ AMKME+ ++A K Sbjct: 591 LMPKKLPPDTSK----MLLCPMPGVVTSITVKAGETVEAGQAIAVVEAMKMENILRAEKR 646 Query: 688 GRIKKVFFSEGAQANRHAPLVEFE 711 +K+V GA ++EFE Sbjct: 647 AIVKRVAIEAGASLAVDELIMEFE 670 Lambda K H 0.318 0.133 0.382 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: 1024 Number of extensions: 34 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: 717 Length of database: 670 Length adjustment: 39 Effective length of query: 678 Effective length of database: 631 Effective search space: 427818 Effective search space used: 427818 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