Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Echvi_0113 Echvi_0113 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2192 (535 letters) >FitnessBrowser__Cola:Echvi_0113 Length = 541 Score = 476 bits (1226), Expect = e-139 Identities = 247/527 (46%), Positives = 346/527 (65%), Gaps = 20/527 (3%) Query: 25 HVEALRTLL---AQIRQGGGPKAQERHTSRGKLLPRERINRLLDPGSPFLEISPLAAHEV 81 H+E ++ L+ + ++GGG + E+ ++GKL RERI+ L+D FLEI AA + Sbjct: 11 HLELIQQLIEKTTRTKRGGGKQRIEKEHAKGKLTARERIDYLMDDPHDFLEIGTFAADGM 70 Query: 82 YGED--VPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPLTVKKHLRAQTIAQQNRLPC 139 Y E+ P+AGVI G+G+V G C++VANDATVK G+++P+T KK+LRAQ IA +NRLP Sbjct: 71 YQEEGGCPSAGVIMGLGKVSGRMCVVVANDATVKAGAWFPMTAKKNLRAQEIAMENRLPI 130 Query: 140 IYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQIAVVMGSCTAGGAYVPAMA 199 IYLVDS G LP Q+E+FPD+EHFGR F N A MSA GI Q+A +MGSC AGGAY+P M+ Sbjct: 131 IYLVDSAGVFLPMQNEIFPDKEHFGRQFRNNAKMSAMGIVQVAAIMGSCVAGGAYLPIMS 190 Query: 200 DEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCKISGVADHYADSDEHALALA 259 DEA++V Q +IFLAG LVKAA GE V E LGGA HC+ISGV D+ D+DE LA Sbjct: 191 DEALIVDQTGSIFLAGSYLVKAAIGESVDNETLGGATTHCEISGVTDNKYDNDEECLAAI 250 Query: 260 RRSVANLNWRKQGELQHRLPIAPLYSGEELYGVVSADAKQPFDVREVIARLVDGSVFDEF 319 +R L + + AP + E+++ D +P+D+ ++ LVD FDE+ Sbjct: 251 KRIFETLGAPETAGFDRKPAKAPAVAPEKVFERFPVDRAKPYDMHGILETLVDADSFDEY 310 Query: 320 KALFGTTLVCGFAHLHGYPIAILAN--------------NGILFAEAAQKGAHFIELACQ 365 K FG TL+CG A + G+ + ILAN G++++++A K A FI Q Sbjct: 311 KPDFGQTLLCGTARIDGWAVGILANQRKMVKTKKGELQMGGVIYSDSADKAARFIMNCNQ 370 Query: 366 RGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAGNYGMC 425 R +PLLF+Q+++GFMVG + E GGI K GAK+V A+A + VPKFTV+IG ++GAGNY MC Sbjct: 371 RKVPLLFIQDVSGFMVGSRAEHGGIIKDGAKMVNAMANSVVPKFTVMIGNAYGAGNYAMC 430 Query: 426 GRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQPILDQY 485 G+AYDPR + WP A++ VM AA L+Q+K ++ G ++E E ++ + I D+Y Sbjct: 431 GKAYDPRLIVSWPTAQMAVMSGTSAAKTLLQIKVASLKKEGKVITSEDEEQLLKEITDKY 490 Query: 486 EEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGV 532 EE+ PYY++ARLW D VI P TR+++ ++A+ +API+ RF V Sbjct: 491 EEELSPYYAAARLWVDEVISPLDTREIVSKGIAAADHAPIK-DRFNV 536 Lambda K H 0.321 0.137 0.411 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: 774 Number of extensions: 35 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: 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 (21.8 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