Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Echvi_0113 Echvi_0113 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__Cola:Echvi_0113 Length = 541 Score = 501 bits (1290), Expect = e-146 Identities = 254/527 (48%), Positives = 354/527 (67%), Gaps = 17/527 (3%) Query: 22 HQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSSFLEIGALAAYNV 81 H L L E+ + ++GGG ++ + +GKL R+RID L+D FLEIG AA + Sbjct: 11 HLELIQQLIEKTTRTKRGGGKQRIEKEHAKGKLTARERIDYLMDDPHDFLEIGTFAADGM 70 Query: 82 YDEE--VPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQEIARENRLPC 139 Y EE P+AG++ G+G+V+GR +++ANDATVK G +FP+T KK+LRAQEIA ENRLP Sbjct: 71 YQEEGGCPSAGVIMGLGKVSGRMCVVVANDATVKAGAWFPMTAKKNLRAQEIAMENRLPI 130 Query: 140 IYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCTAGGAYVPAMS 199 IYLVDS G +LP+Q+E+FPD++HFGR F N A+MSA GI Q+A +MGSC AGGAY+P MS Sbjct: 131 IYLVDSAGVFLPMQNEIFPDKEHFGRQFRNNAKMSAMGIVQVAAIMGSCVAGGAYLPIMS 190 Query: 200 DEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFANDDREALAIV 259 DE +IV G+IFL G LVKAA GE V E LGGA H ISGV D ++D E LA + Sbjct: 191 DEALIVDQTGSIFLAGSYLVKAAIGESVDNETLGGATTHCEISGVTDNKYDNDEECLAAI 250 Query: 260 RDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIARIVDGSRLHEF 319 + I LG + A ++ + + P P +++ P D + YD+ ++ +VD E+ Sbjct: 251 KRIFETLGAPETAGFDRKPAKAPAVAPEKVFERFPVDRAKPYDMHGILETLVDADSFDEY 310 Query: 320 KTRYGTTLVCGFAHIEGFPVGILAN--------------NGILFSESALKGAHFIELCCA 365 K +G TL+CG A I+G+ VGILAN G+++S+SA K A FI C Sbjct: 311 KPDFGQTLLCGTARIDGWAVGILANQRKMVKTKKGELQMGGVIYSDSADKAARFIMNCNQ 370 Query: 366 RNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMC 425 R +PL+F+Q+++GFMVG + E+GGI KDGAK+V A++ + VPKFTV+IG ++GAGNY MC Sbjct: 371 RKVPLLFIQDVSGFMVGSRAEHGGIIKDGAKMVNAMANSVVPKFTVMIGNAYGAGNYAMC 430 Query: 426 GRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKY 485 G+AY PR + WP A+++VM GT AA LL I+ +L+ G+ +T E++E+ + I KY Sbjct: 431 GKAYDPRLIVSWPTAQMAVMSGTSAAKTLLQIKVASLKKEGKVITSEDEEQLLKEITDKY 490 Query: 486 EQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGV 532 E+E PYYA+ARLW D VI P++TR +++ G+AAA AP++ RF V Sbjct: 491 EEELSPYYAAARLWVDEVISPLDTREIVSKGIAAADHAPIK-DRFNV 536 Lambda K H 0.322 0.139 0.423 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: 771 Number of extensions: 38 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: 535 Length of database: 541 Length adjustment: 35 Effective length of query: 500 Effective length of database: 506 Effective search space: 253000 Effective search space used: 253000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (24.6 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