Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_013840433.1 DESRU_RS01880 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000215085.1:WP_013840433.1 Length = 505 Score = 405 bits (1042), Expect = e-117 Identities = 238/505 (47%), Positives = 320/505 (63%), Gaps = 18/505 (3%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 +V + DTTLRDGEQ+PGVSL EKL+IA ++ LG DIIEAG ITS G+ ++ + Sbjct: 4 RVYIFDTTLRDGEQSPGVSLNMNEKLQIARQLARLGVDIIEAGFPITSPGDFAAVQAVAR 63 Query: 62 EGLRAEICSFARAVREDIDAAISCDVDS----VHLVVPTSDLHLEHKLRKTREEVLEQAV 117 E + ARA +DID A +D+ +H+ + TSD+HL++KLRK RE+VL AV Sbjct: 64 EVKGVTVAGLARANFKDIDRAWEALLDAEQARIHVFIATSDIHLKYKLRKDREQVLAAAV 123 Query: 118 DCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEF 177 + +YA + VE SAED++RSD+D+L +F E I+AGA I DTVG TPE F Sbjct: 124 EAVKYAKKYTSDVEFSAEDASRSDVDYLCRVFGEVIKAGATVINVPDTVGYTTPEEYARF 183 Query: 178 YRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEE 232 + + E A LSVHCH+D G+AVANSLA + AGA +V TINGIGERAGNAALEE Sbjct: 184 IQTIMEKTPGMEKAVLSVHCHDDLGMAVANSLAAVGAGARQVEGTINGIGERAGNAALEE 243 Query: 233 VVVAL---KSLYDVDTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADG 289 VV+ L K Y + T N ++ TSR+++ +TG+ + PNKA+VG+NAFAHESGIH DG Sbjct: 244 VVMGLYTRKDRYGLTTGFNTREIFRTSRLISSLTGMPVHPNKAVVGKNAFAHESGIHQDG 303 Query: 290 VLKKAETYEPITPEMVGHGRG-FVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTL 348 VLK+ TYE + PE+VG G V+GKH G HA R RL ELG ++ D++L F R K L Sbjct: 304 VLKERTTYEIMNPELVGITAGNLVLGKHSGRHAFRNRLTELGYELNDEELNLAFGRFKAL 363 Query: 349 GDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTASVKLRVDDREVLEAG 408 D K +TD DLQA+ ED + + + V L+ + I SG V PTA++ LR D+ +A Sbjct: 364 ADKKKEITDHDLQALVEDEIRHVPETYV-LEYLHISSGTTVVPTATLGLRAGDKLKEDAA 422 Query: 409 TGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGD--RIISARS 466 G GPVDA + K TL Y ++AIT G DAL DV +KLR D ++ + R Sbjct: 423 CGDGPVDAIYNTVDKITG--VSCTLVNYAINAITAGKDALGDVTVKLRKADQEKVYTGRG 480 Query: 467 TQPDIIMASVEAFLSGVNRLLANEK 491 DI+ AS +A+++ VN+L+ + K Sbjct: 481 VSTDILEASAKAYVNAVNKLMYDNK 505 Lambda K H 0.317 0.135 0.373 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: 652 Number of extensions: 37 Number of successful extensions: 9 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: 496 Length of database: 505 Length adjustment: 34 Effective length of query: 462 Effective length of database: 471 Effective search space: 217602 Effective search space used: 217602 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: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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