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_043746657.1 AMB_RS13620 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::Q2QMG2 (737 letters) >NCBI__GCF_000009985.1:WP_043746657.1 Length = 447 Score = 436 bits (1120), Expect = e-126 Identities = 231/444 (52%), Positives = 300/444 (67%), Gaps = 4/444 (0%) Query: 40 EKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARESYLN 99 EKVL+ANRGEIA R+ R R +GI TVAV+S AD A+HVR ADEAV +GPP AR+SYLN Sbjct: 3 EKVLIANRGEIALRIHRACREMGIRTVAVHSTADNDAMHVRLADEAVCIGPPSARDSYLN 62 Query: 100 ASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSASKRI 159 +AI+ AA TGA AIHPGYGFLSE+ADFAQ+ + G FIGP P IR MGDK +K+ Sbjct: 63 KAAILSAASITGADAIHPGYGFLSENADFAQMVEEHGFVFIGPTPDHIRMMGDKITAKQA 122 Query: 160 MGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFVDSVL 219 + AG+P+VPG G+ E A IGYPVLIK T GGGGKGM++ + E+ V+S Sbjct: 123 VKDAGIPVVPGSDGSVDTEETALEVAASIGYPVLIKATAGGGGKGMKVARNAEELVESWK 182 Query: 220 SAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKIIEEA 279 A+ EA A+FG + +EKY+ +PRHIE+QI D +G V+HL ERDCSLQR+HQK++EEA Sbjct: 183 LARNEAKAAFGNADVYMEKYLGKPRHIEMQILADNYGAVVHLGERDCSLQRKHQKVLEEA 242 Query: 280 PAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEHPVTE 339 P+P + A R+ IG+ A A +GY +AGT+EF+ + +GEFYF+EMNTRLQVEHP+TE Sbjct: 243 PSPALNADQRARIGKIACDAIAKLGYRNAGTIEFLYE--NGEFYFIEMNTRLQVEHPITE 300 Query: 340 MIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHHYRPV 399 I G DLV QIRIA G L +Q V GHA E R+ AE+ P F P G + Y Sbjct: 301 AITGIDLVREQIRIAAGAPLGYTQADVRFAGHALECRVNAED-PVTFTPCPGRIEGYH-A 358 Query: 400 PSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIAGLPTNVG 459 P VRV++G+ G + HYD MIAKL+V+G +RN AL++LK +L + I G+ T + Sbjct: 359 PGGLGVRVDSGLYAGYRIPPHYDSMIAKLIVFGNTRNEALMRLKRALGEYVIEGVKTTLP 418 Query: 460 FLQELAGHSAFEKGLVDTHFIERY 483 L + F G D H++E++ Sbjct: 419 LHNRLVQDADFVNGDYDIHWLEKF 442 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: 765 Number of extensions: 35 Number of successful extensions: 4 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: 737 Length of database: 447 Length adjustment: 36 Effective length of query: 701 Effective length of database: 411 Effective search space: 288111 Effective search space used: 288111 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: 53 (25.0 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