Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate WP_012275835.1 SHAL_RS03620 ATP-grasp domain-containing protein
Query= SwissProt::Q2QMG2 (737 letters) >NCBI__GCF_000019185.1:WP_012275835.1 Length = 1517 Score = 303 bits (775), Expect = 6e-86 Identities = 192/510 (37%), Positives = 278/510 (54%), Gaps = 20/510 (3%) Query: 39 VEKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALH---VRAADEAVRLGPPPARE 95 +EKVLV RG A +++R A I V V SD D ++ ++ D+ V +G + E Sbjct: 940 IEKVLVHARGCTAVKLIRKAHDNNIKVVLVASDPDMTSVPADMLKDNDKLVCIGGNTSDE 999 Query: 96 SYLNASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSA 155 SYLNA +++ A A+HPG GFLSES FA LC G+ F+GP ++ MG+KS Sbjct: 1000 SYLNAYSVLKVAEYENVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNKSN 1059 Query: 156 SKRIMGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFV 215 + + A VP+VPG HG + E A++IGYPVL+K GGGGKG+++V+RP D + Sbjct: 1060 AIKTSQAQNVPVVPGSHGILTNAEQAVNVASEIGYPVLLKAVQGGGGKGIQVVERPGDMI 1119 Query: 216 DSVLSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKI 275 EAAA+FG L +EKY+T RHIEVQ+ DQ GN L RDCS+QR +QK+ Sbjct: 1120 SLFQKTSTEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDQFGNTKVLGLRDCSVQRNNQKV 1179 Query: 276 IEEAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEH 335 +EE+ + + + + + E A Y AGTVEFI + + E YFMEMNTRLQVEH Sbjct: 1180 VEESGSTMLPDELKQRVMEYTRLLGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEH 1239 Query: 336 PVTEMIVGQDLVEWQIRIANGECLPLSQEQVPLN-GHAFEARIYAENVPRG------FLP 388 PVTE G D+V IA G + E P N G+A E R+ AE LP Sbjct: 1240 PVTEATSGIDIVSAGFDIAAGRSI---AELEPQNIGYAMEVRVTAEKAALDSHGVLQLLP 1296 Query: 389 ATGTLHHYRPVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSN 448 G + Y+ +P + + + EG VS +YD +IA+++ GESR +VKL + L+N Sbjct: 1297 YPGLITEYQ-MPERDDIEIISIAGEGKEVSPYYDSLIAQIICRGESREDVIVKLHDYLAN 1355 Query: 449 -FQIAGLPTNVGFLQELAGHSAFEKGLVDTHFIERYQNDLLSTSTQALSGSHEAEELGAI 507 I G+ TN+ L + F +G+ DT+++ R+ + L S AE +G Sbjct: 1356 QVVIKGIATNIPLLTRILKDGTFNEGVYDTNYLPRFMAE-LDVSEMIAEMEAAAETVGVD 1414 Query: 508 LAAACICKKDHVSSEVSLHDKKLSMWYAHP 537 A+ + + S+E+ + + ++Y P Sbjct: 1415 TASLRVGE----SNELKVMAQGAGIFYTSP 1440 Lambda K H 0.317 0.133 0.389 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: 1862 Number of extensions: 70 Number of successful extensions: 4 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: 737 Length of database: 1517 Length adjustment: 45 Effective length of query: 692 Effective length of database: 1472 Effective search space: 1018624 Effective search space used: 1018624 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: 58 (26.9 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