Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 3609096 Dshi_2485 pyruvate carboxylase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >FitnessBrowser__Dino:3609096 Length = 1145 Score = 361 bits (926), Expect = e-103 Identities = 198/446 (44%), Positives = 278/446 (62%), Gaps = 9/446 (2%) Query: 9 LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLG-GSKAADSYLQI 67 +L+ANRGEIA RVMR A +G TVAV++ D+ H +AD +G G +YL I Sbjct: 7 ILIANRGEIAIRVMRAANELGKKTVAVYAEEDKLCLHRFKADEAYKIGEGLGPVAAYLSI 66 Query: 68 DKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALM 127 D++I AK SGA AIHPGYG LSEN F A G+ F+GP A + A+G K++A+ + Sbjct: 67 DEIIRVAKLSGADAIHPGYGLLSENPDFVDACVANGIAFIGPRAETMRALGDKASARRVA 126 Query: 128 ETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187 AGVP++P D++ R AE IG+P++LKA+ GGGG+GM+ + D ++A+ + Sbjct: 127 IEAGVPVIPATEVLGDDMDKVRAEAEAIGFPLMLKASWGGGGRGMRPIFDPDEVADKVRE 186 Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247 +REA+++FG+ +EK + + RHVE+Q+ D GN +L ERDCS+QRR+QKVVE AP Sbjct: 187 GRREAEAAFGNGEGYLEKMITRARHVEVQILGDSMGNIYHLWERDCSVQRRNQKVVERAP 246 Query: 248 APGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDA-RGEFFFMEMNTRLQVEHPVTEA 306 AP L++ R+ + E + + Y AGTVEFL+D GEFFF+E+N R+QVEH VTE Sbjct: 247 APYLSSSQREQLCELGRKICAHVNYECAGTVEFLMDMDTGEFFFIEVNPRVQVEHTVTEE 306 Query: 307 ITGLDLVAWQIRVAQGEPL-----PITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLAL 361 +TG+D+V QI +A+G+ L +Q V L GHAI+ R+ EDP N+F+P GR+ Sbjct: 307 VTGIDIVRAQILIAEGKSLVEATGMASQYDVQLNGHAIQCRITTEDPQNNFIPDYGRITA 366 Query: 362 YRESAKGPGRRVDSGVE-EGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGL 420 YR A G G R+D G G I+ +YD +L K+ AW E A R+ L EF I G+ Sbjct: 367 YR-GATGMGIRLDGGTAYSGAVITRYYDSLLEKVTAWAPTPEAAIARMDRALREFRIRGV 425 Query: 421 KTNIGFLRRIVAHPAFAAAELDTGFI 446 TNI F+ ++ HP F + T FI Sbjct: 426 STNIAFVENLLKHPTFLNNQYTTKFI 451 Score = 44.3 bits (103), Expect = 3e-08 Identities = 24/67 (35%), Positives = 33/67 (49%) Query: 582 LAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEG 641 + APM G + V V G V G L+ +EAMKME I A + V+KA++ + Sbjct: 1079 VGAPMPGVVASVAVQAGASVKEGDLLLTIEAMKMETGIHAERDAVVKAVHVTPAAQIDAK 1138 Query: 642 SALVAFE 648 LV E Sbjct: 1139 DLLVELE 1145 Lambda K H 0.319 0.134 0.389 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: 1597 Number of extensions: 70 Number of successful extensions: 7 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: 649 Length of database: 1145 Length adjustment: 42 Effective length of query: 607 Effective length of database: 1103 Effective search space: 669521 Effective search space used: 669521 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 (21.7 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