Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate GFF3994 HP15_3934 acetyl-CoA carboxylase biotin carboxylase subunit
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__Marino:GFF3994 Length = 473 Score = 420 bits (1080), Expect = e-122 Identities = 216/467 (46%), Positives = 300/467 (64%), Gaps = 2/467 (0%) Query: 7 SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66 +I++LL+ANRGEIA R+ R+ LGI SVA+HS+ D ++ HV +AD A + P Y Sbjct: 2 AIRKLLIANRGEIAVRIARACSELGIRSVAIHSEADEYSLHVKKADEAYQIS-KDPLSGY 60 Query: 67 LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126 L I+ A+ +G A+HPGYGFLSENA+ A CE+ G+ F+GP A AI +MG K+ A+ Sbjct: 61 LNPHHIVNMAVETGCDALHPGYGFLSENAELAAICEQRGITFVGPSANAISSMGDKTQAR 120 Query: 127 ALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 AGVP+ PG G D+E +A IGYPV+LKA +GGGG+G++ + E EL + Sbjct: 121 QTALAAGVPVTPGSEGNLADVEDAVVQAADIGYPVMLKATSGGGGRGIRRCDNEKELRQN 180 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 EA AFG A + +EK +++PRH+E+Q+ AD HG+ ++L ERDCSIQRR+QK++E Sbjct: 181 FERVISEATKAFGSAEVFLEKCIIEPRHIEVQILADTHGNVVHLYERDCSIQRRNQKLIE 240 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 AP+P L R +G+ A R A+ GYV AGTVEFLLD G F+FMEMNTR+QVEH +T Sbjct: 241 LAPSPQLEESQREYIGDLAKRVAKQCGYVNAGTVEFLLDHDGSFYFMEMNTRVQVEHTIT 300 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E ITG+D++ QIR+A GE L L QE + G A + R+ AEDP+ FLP+ GR+ Y Sbjct: 301 EEITGVDIIKAQIRIAAGEPLGLKQEDISYRGFAAQFRINAEDPKNGFLPSFGRISRY-Y 359 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 +A GPG R D+ + G E+ P+YD M AKLI W +E R L + + G++T + Sbjct: 360 SAGGPGVRTDANMYTGYEIPPYYDSMCAKLIVWAMDWDELIARSRRALGDMGIYGVQTTI 419 Query: 427 AFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEA 473 + ++IL HP F AA+ +TGF+ R+ L + + PE A A A Sbjct: 420 PYYKQILEHPDFQAADFNTGFVERNPQLLEYSSKTRPESIATAIAAA 466 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: 674 Number of extensions: 30 Number of successful extensions: 3 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: 473 Length adjustment: 36 Effective length of query: 619 Effective length of database: 437 Effective search space: 270503 Effective search space used: 270503 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