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 5210790 Shew_3218 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)
Query= SwissProt::Q2QMG2 (737 letters) >FitnessBrowser__PV4:5210790 Length = 1516 Score = 298 bits (762), Expect = 2e-84 Identities = 181/460 (39%), Positives = 259/460 (56%), Gaps = 15/460 (3%) Query: 39 VEKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALH---VRAADEAVRLGPPPARE 95 ++KVLV RG A +++R A I V V SD D ++ + D+ V +G + E Sbjct: 940 IDKVLVHARGCTAVKLIRKAHDNNIKVVLVASDPDMTSVPADMLNENDKLVCIGGNTSDE 999 Query: 96 SYLNASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSA 155 SYLNA +++ A A+HPG GFLSES FA LC G+ F+GP ++ MG+KS Sbjct: 1000 SYLNAYSVLKVAEYEQVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNKSN 1059 Query: 156 SKRIMGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFV 215 + + + VP+VPG HG + E AN+IGYPVL+K GGGGKG+++VQRPED + Sbjct: 1060 AIKTSQSQNVPVVPGSHGILTNAEQAVNVANEIGYPVLLKAVQGGGGKGIQVVQRPEDMI 1119 Query: 216 DSVLSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKI 275 EAAA+FG L +EKY+T RHIEVQ+ D+ GN L RDCS+QR +QK+ Sbjct: 1120 SLFQKTSTEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGNTKVLGLRDCSVQRNNQKV 1179 Query: 276 IEEAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEH 335 IEE+ + + + + + E + A Y AGTVEFI + + E YFMEMNTRLQVEH Sbjct: 1180 IEESGSTMLPEELKQQVMEYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEH 1239 Query: 336 PVTEMIVGQDLVEWQIRIANGECL-PLSQEQVPLNGHAFEARIYAE------NVPRGFLP 388 PVTE G D+V IA G + L +++ G+A E R+ AE N LP Sbjct: 1240 PVTEATSGIDIVSAGFDIAAGRSIEDLEPQEI---GYAIEVRVTAEKAALDSNGVLQLLP 1296 Query: 389 ATGTLHHYRPVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSN 448 G + +P + + + EG VS +YD +IA+++ GESR + KL + L+N Sbjct: 1297 HPGMITEC-VIPERDDIEIISIAGEGKEVSPYYDSLIAQIICRGESREDVINKLHDYLAN 1355 Query: 449 -FQIAGLPTNVGFLQELAGHSAFEKGLVDTHFIERYQNDL 487 I G+ TN+ L + F +G+ DT+++ R+ +L Sbjct: 1356 QVVIKGIATNIPLLTRILKDGTFNEGVYDTNYLPRFMAEL 1395 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: 1874 Number of extensions: 67 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: 1516 Length adjustment: 45 Effective length of query: 692 Effective length of database: 1471 Effective search space: 1017932 Effective search space used: 1017932 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 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