Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate Echvi_3962 Echvi_3962 Acetyl/propionyl-CoA carboxylase, alpha subunit
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__Cola:Echvi_3962 Length = 499 Score = 469 bits (1207), Expect = e-136 Identities = 237/465 (50%), Positives = 324/465 (69%), Gaps = 6/465 (1%) Query: 8 IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67 I+++LVANRGEIA R+MR+ R +G+ SVAV+S++D++A HV AD + LG A SYL Sbjct: 4 IRKILVANRGEIALRIMRTIREMGLKSVAVYSEVDKNAPHVLYADESYCLGPAPSHKSYL 63 Query: 68 RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127 G+RII A A GA AIHPGYGFLSEN FA+ +AGL+F+GP +I+ MG K AAK Sbjct: 64 LGERIIEACQALGADAIHPGYGFLSENTAFAKKVADAGLIFIGPSPESIEIMGDKLAAKK 123 Query: 128 LMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187 + +P+VPG D++ ++ A IGYP+L+KA+AGGGGKGM++V+ E E E + Sbjct: 124 AVSHYDIPMVPGTDHAILDIQEAKKTAVEIGYPILIKASAGGGGKGMRIVQDEGEFEEQM 183 Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247 A EA++AFGD + +EKY+ PRH+EIQ+ AD+HG+ L+L ER+CS+QRRHQKV+EE Sbjct: 184 KRAVSEAQSAFGDGAVFIEKYITSPRHIEIQILADQHGNYLHLFERECSVQRRHQKVIEE 243 Query: 248 APAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTE 307 AP+ + E+R+AMG+AA+ A+A Y GAGTVEF++DE F+F+EMNTRLQVEHPVTE Sbjct: 244 APSAVVNQEMRKAMGQAAIDVAKACQYYGAGTVEFIVDEALNFYFLEMNTRLQVEHPVTE 303 Query: 308 AITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREA 367 ITG DLV QI +A G+AL Q+ + + GHAIE R+YAEDP +FLP G+L YR Sbjct: 304 MITGKDLVREQIFIAEGQALSFAQDDLTILGHAIETRVYAEDPTNNFLPDIGKLATYR-L 362 Query: 368 AAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLA 427 GPG RVD G REG E+ +YDPM+AKL+ + E R +A Q+++ + + + G+ T L+ Sbjct: 363 PQGPGIRVDDGFREGMEIPIYYDPMIAKLVTFEEDRPKAIQKMVRAIDDYHITGISTTLS 422 Query: 428 FLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAE 472 F R ++ HPAF + E DT F+ +H AP L E+F + E Sbjct: 423 FARFVMLHPAFQSGEFDTKFVEKHF-----APSKLAENFSEEEEE 462 Lambda K H 0.319 0.135 0.397 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: 716 Number of extensions: 30 Number of successful extensions: 2 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: 655 Length of database: 499 Length adjustment: 36 Effective length of query: 619 Effective length of database: 463 Effective search space: 286597 Effective search space used: 286597 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: 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