Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011840591.1 RSPH17029_RS03905 pyruvate carboxylase
Query= reanno::SB2B:6937189 (673 letters) >NCBI__GCF_000015985.1:WP_011840591.1 Length = 1154 Score = 384 bits (985), Expect = e-110 Identities = 201/451 (44%), Positives = 298/451 (66%), Gaps = 13/451 (2%) Query: 2 FNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGES-APASSY 60 F K+LIANRGEIA RV+R A +MG KTVAVY++ D+ + H ADE++ +GE +P +Y Sbjct: 4 FRKILIANRGEIAIRVMRAANEMGKKTVAVYAEEDKLSLHRFKADEAYRIGEGLSPVGAY 63 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L II +A+ GA+AIHPGYG LSEN F AC+A+GIAF+GP ++ + A+G K++A+ Sbjct: 64 LSIPEIIRVAQMSGADAIHPGYGLLSENPDFVEACDAAGIAFIGPKAETMRALGDKASAR 123 Query: 121 LIMEKAGVPLVPGYH--GDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELK 178 + AGVP++P GDD + + +A +IGYPL++KA++GGGG+GMR + SE+EL Sbjct: 124 RVAMAAGVPVIPATEVLGDDMEE--IKRQAAEIGYPLMLKASWGGGGRGMRPITSEAELA 181 Query: 179 AAIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKV 238 + RREA ++FGN + +E+ +++ RHVEVQ+ D G +L +RDC++QRR+QKV Sbjct: 182 DKVREGRREAEAAFGNGEGYLEKMIQRARHVEVQILGDKYGAIYHLYERDCTVQRRNQKV 241 Query: 239 VEEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDM-SFFFMEMNTRLQVEH 297 VE APAP L + R ++ E ++Y AGTVEFL+D+D F+F+E+N R+QVEH Sbjct: 242 VERAPAPYLTEEQRTEICELGRRICAHVNYECAGTVEFLMDMDSEKFYFIEVNPRVQVEH 301 Query: 298 PVTEMVTGQDLVKWQLLVAAGAQLP-----LEQHEIQIHGHAFEVRIYAEDPNNEFLPAS 352 VTE VTG D+V+ Q+ +A GA L Q +I++ GHA + R+ EDP N F+P Sbjct: 302 TVTEEVTGIDIVQSQIRIAEGATLAEATGCPSQDDIKLSGHALQCRVTTEDPQNNFIPDY 361 Query: 353 GKLTFLREPEPSRHVRIDSGVR-ENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDY 411 G+LT R +R+D G VI+ YYD ++ K+ W + +A+AR+ RAL ++ Sbjct: 362 GRLTAYRS-ATGMGIRLDGGTAYAGGVITRYYDSLLVKVTAWAPTPEKAIARMDRALREF 420 Query: 412 RVGGLKHNIEFLSNIAEHPAFAQANFSTDFI 442 R+ G+ NI F+ N+ +HP+F +++T FI Sbjct: 421 RIRGVATNIAFVENLLKHPSFLDYSYTTKFI 451 Score = 43.5 bits (101), Expect = 6e-08 Identities = 37/132 (28%), Positives = 59/132 (44%), Gaps = 15/132 (11%) Query: 544 ELKCEIN-GHKMKVTVSL-----EDGGLTVFLS-SGSYHFREVLGQVLEETASSEDKLK- 595 E+ EI+ G +++ +S +DG VF +G V + ++ ++ K + Sbjct: 1022 EISAEIDPGKTLEIRLSAVGETSDDGDAKVFFELNGQPRVIRVANRAVKAKTATRPKAQD 1081 Query: 596 -------APMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGE 648 APM G+V + V+ G KV G L+ +EAMKME + A V PG Sbjct: 1082 GNPAHVGAPMPGSVASVAVSTGQKVKPGDLLVTIEAMKMETGLHADRAATVKAVHVGPGA 1141 Query: 649 LVSDGTLLLALE 660 + LL+ LE Sbjct: 1142 QIEAKDLLVELE 1153 Lambda K H 0.317 0.134 0.380 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: 1714 Number of extensions: 69 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: 673 Length of database: 1154 Length adjustment: 43 Effective length of query: 630 Effective length of database: 1111 Effective search space: 699930 Effective search space used: 699930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Apr 10 2024. 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