Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011779394.1 MVAN_RS10860 pyruvate carboxylase
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >NCBI__GCF_000015305.1:WP_011779394.1 Length = 1145 Score = 352 bits (904), Expect = e-101 Identities = 196/448 (43%), Positives = 279/448 (62%), Gaps = 6/448 (1%) Query: 3 APALTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGG-SKAA 61 A ++ +LVANRGEIA R R A MG+ TVAV+ DR++ H +AD +G Sbjct: 2 AGQISKVLVANRGEIAIRAFRAAYEMGIATVAVYPYEDRNSLHRLKADESYQIGEIGHPV 61 Query: 62 DSYLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKS 121 +YL + +++ A +G A++PGYGFLSEN A A +AG+ F+GP A+ ++ G+K+ Sbjct: 62 RAYLSVAEIMRVAVEAGCDAVYPGYGFLSENPELAAACADAGITFVGPSANVLELTGNKA 121 Query: 122 AAKTLMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQL 181 A AG+P++ A ++ AA+ + +P+ +KA +GGGG+GM+ V D + L Sbjct: 122 RAIQAARAAGLPVLTSSAPSAS-VDELVAAADGMEFPLFVKAVSGGGGRGMRRVTDRAAL 180 Query: 182 AEALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQK 241 AEA+ +A REA+S+FGD + +E+ +L PRH+E+Q+ AD G+ ++L ERDCS+QRRHQK Sbjct: 181 AEAVEAASREAESAFGDPNVYLEQAVLNPRHIEVQILADTAGHVMHLFERDCSVQRRHQK 240 Query: 242 VVEEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEH 301 V+E APAP L +LR+ + + AV A+ I Y AGTVEFLLD RG F+E N R+QVEH Sbjct: 241 VIELAPAPNLPDELRQKICDDAVAFAKEIDYSCAGTVEFLLDERGHHVFIECNPRIQVEH 300 Query: 302 PVTEAITGLDLVAWQIRVAQGEPLP---ITQAQVPLLGHAIEVRLYAEDPGNDFLPATGR 358 VTE IT +DLV+ Q+R+A GE L ++Q + + G A++ R+ EDP N F P TGR Sbjct: 301 TVTEEITDVDLVSSQLRIASGETLADLGLSQETLVIRGAALQCRITTEDPANGFRPDTGR 360 Query: 359 LALYRESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIG 418 + YR S G G R+D G G EI +D ML KL G D A R L EF + Sbjct: 361 ITAYR-SPGGAGIRLDGGAHLGAEIGAHFDSMLVKLTCRGRDFATAVARAHRALAEFRVR 419 Query: 419 GLKTNIGFLRRIVAHPAFAAAELDTGFI 446 G+ TNI FL+ ++ P F A ++T FI Sbjct: 420 GVSTNIPFLQAVIDDPDFRAGRVNTSFI 447 Score = 46.2 bits (108), Expect = 8e-09 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 1/76 (1%) Query: 570 AAAEASHSHQGGLVAPMNGSIVRVLVGVGQTVEAGAQLVVLEAMKMEHSIRAPKAGVIKA 629 AA +A ++ + AP G +V V + G V+AG + +EAMKME I APK+G + Sbjct: 1056 AAEKADRTNPDHVAAPFAG-VVTVNIAEGDKVDAGQTIATIEAMKMEAGITAPKSGTVAR 1114 Query: 630 LYCQEGEMVSEGSALV 645 + V G LV Sbjct: 1115 VAVSATAQVEGGDLLV 1130 Score = 32.7 bits (73), Expect = 9e-05 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 3/54 (5%) Query: 557 EGDLHRIDLYDPLAAAEASHSHQGGLVAPMNGSIVRVLVGVGQTVEAGAQLVVL 610 EGD ++D +A EA + G+ AP +G++ RV V VE G LVV+ Sbjct: 1082 EGD--KVDAGQTIATIEAMKM-EAGITAPKSGTVARVAVSATAQVEGGDLLVVI 1132 Lambda K H 0.319 0.134 0.390 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: 1591 Number of extensions: 87 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 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 24 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