Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate 5210426 Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__PV4:5210426 Length = 1094 Score = 307 bits (786), Expect = 2e-87 Identities = 183/475 (38%), Positives = 278/475 (58%), Gaps = 12/475 (2%) Query: 6 RSIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADS 65 R R+L+ANRGEIA R+ ++ +GI S+A++++ D + H +AD AV L G + + Sbjct: 3 RVFNRILIANRGEIAIRIAQTCADMGIDSLAIYAEDDSQSLHTKKADQAVALKG-RGVKA 61 Query: 66 YLRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAA 125 YL +++IA A A G A+HPGYGFLSEN+ F++ C E G+ F+G A +D +G+K+ A Sbjct: 62 YLDIEQLIAVAKAHGCDAVHPGYGFLSENSSFSKRCHEEGICFIGSSAELLDLLGNKATA 121 Query: 126 KALMEEAGVPLVPGYHGEA--QDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAEL 183 + + PL G + ++++ F G G V++KA AGGGG+GM+ V R +L Sbjct: 122 RETALRSDTPLTGGINKPCSLEEVQAFFTSLGD-GAAVMIKALAGGGGRGMRPVSRYEDL 180 Query: 184 AEALSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQK 243 AEA + EA AFG + VE+ + RH+E+Q+ D G ++ ER+C++QRR+QK Sbjct: 181 AEAYRQCREEAIIAFGSGELYVEQLVQHARHIEVQILGDGTGAAVHAWERECTLQRRNQK 240 Query: 244 VVEEAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLL--DERGQFFFMEMNTRLQV 301 ++E AP+P L R + E+A++ A + Y G GT EFLL D+ +F+FME+N R+QV Sbjct: 241 LLEIAPSPSLDDATRMPIIESALQLASDVKYQGLGTFEFLLDADDHSKFYFMEINPRIQV 300 Query: 302 EHPVTEAITGLDLVAWQIRVARGEAL-PLTQEQVPL-NGHAIEVRLYAED--PEGDFLPA 357 EH +TE ITGL+LV QI + G+ L L+ + P+ G AI+ R+ E P+G PA Sbjct: 301 EHTITEEITGLNLVKLQILLGAGKTLAELSLTEAPIKRGCAIQARINLEQMLPDGSTKPA 360 Query: 358 SGRLMLYREAAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAET 417 SG + Y + G RVD + G +VSP YD + AK+IA GE A ++ L Sbjct: 361 SGVIKAY-QVPNGHNVRVDDYLYAGYKVSPSYDSLGAKIIAKGEDFSAALNKVYLSLKAL 419 Query: 418 SVGGLRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAE 472 ++ G+++N A L +L L T F+ H +LL A EHF+ A++ Sbjct: 420 NIDGVQSNKALLMNLLQREEVQHNRLSTRFVEAHMAELL-ADDDHHEHFFNIASD 473 Score = 49.3 bits (116), Expect = 9e-10 Identities = 25/61 (40%), Positives = 41/61 (67%), Gaps = 1/61 (1%) Query: 584 GLSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVV-KALYCSEGELVE 642 G+ +P G +V+V +E G V AG + V+EAMKME +++ HAG+V + L + GE+++ Sbjct: 489 GVKSPTAGVLVQVNIESGDEVFAGQEIAVIEAMKMEIPVKSEHAGIVTEVLTGNIGEVID 548 Query: 643 E 643 E Sbjct: 549 E 549 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: 1437 Number of extensions: 67 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 655 Length of database: 1094 Length adjustment: 42 Effective length of query: 613 Effective length of database: 1052 Effective search space: 644876 Effective search space used: 644876 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: 56 (26.2 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