Align (R)-citramalate synthase CimA; LiCMS; EC 2.3.3.21 (characterized)
to candidate WP_020565007.1 A3OW_RS0118785 2-isopropylmalate synthase
Query= SwissProt::Q8F3Q1 (516 letters) >NCBI__GCF_000372865.1:WP_020565007.1 Length = 514 Score = 503 bits (1294), Expect = e-147 Identities = 252/504 (50%), Positives = 340/504 (67%), Gaps = 5/504 (0%) Query: 8 LEILDVTLRDGEQTRGVSFSTSEKLNIAKFLLQKLNVDRVEIASARVSKGELETVQKIME 67 ++++D TLRDGEQT+GVSF+ +EK+NIAK LLQ L VDR+E+ASARVS GE E V I + Sbjct: 8 IQLMDTTLRDGEQTQGVSFTPAEKVNIAKALLQSLRVDRIEVASARVSAGEKEAVTNINQ 67 Query: 68 WAATEQLTERIEILGFVDGNKTVDWIKDSGAKVLNLLTKGSLHHLEKQLGKTPKEFFTDV 127 WA E +E+LGFVD ++VDWI ++G V+NLLTKGS H +QLGKT ++ D+ Sbjct: 68 WAKQEGFDGCVEVLGFVDHTRSVDWILETGGSVINLLTKGSEKHCREQLGKTREQHTADI 127 Query: 128 SFVIEYAIKSGLKINVYLEDWSNGFRNSPDYVKSLVEHLSKEHIERIFLPDTLGVLSPEE 187 ++YA+ LK+NVYLEDWSNG++NSPDYV +L++ L + I LPDTLGV+SP+E Sbjct: 128 LQTVDYALSRSLKVNVYLEDWSNGYQNSPDYVYALMDSLKEAGISHFMLPDTLGVMSPDE 187 Query: 188 TFQGVDSLIQKYPDIHFEFHGHNDYDLSVANSLQAIRAGVKGLHASINGLGERAGNTPLE 247 F + + YP + F+FH HNDY L+ AN + A+RAG +H ++N LGERAGN L Sbjct: 188 VFTSFSDMCRCYPALQFDFHPHNDYGLATANVMAAVRAGATAVHCTVNCLGERAGNASLA 247 Query: 248 ALVTTIHDKSNSKTNINEIAITEASRLVEVFSGKRISANRPIVGEDVFTQTAGVHADGDK 307 + + DK N + +I+E I S +VE FSGKR++AN PIVG DVFTQTAG+HADGD Sbjct: 248 EVAVVLRDKMNMQLSIDETHIVRLSNMVENFSGKRVAANAPIVGSDVFTQTAGIHADGDH 307 Query: 308 KGNLYANPILPERFGRKRSYALGKLAGKASISENVKQLGMVLSEVVLQKVLERVIELGDQ 367 KG LY + + PERF R RSYALGK++GKAS+ +N++ L + LSE +KVL R++ LGD Sbjct: 308 KGGLYKSRLSPERFSRSRSYALGKMSGKASLKKNLELLEIDLSEENQKKVLARIVSLGDS 367 Query: 368 NKLVTPEDLPFIIADVSGRTGEKVLTIKSCNIHSGIGIRPHAQIELEYQGKIHKEISEGD 427 + +T +DLPFIIADV + + + +C I SG+ + A + L+ G H G+ Sbjct: 368 KQTITTDDLPFIIADVLESKNYQHIKLLNCFITSGLHLESTASLRLDVNGAKHVISGAGN 427 Query: 428 GGYDAFMNALTKITNRLGISIPKLIDYEVRIPPGGKTDALVETRITWNKSLDLEEDQTFK 487 GG+DAF++A+ K ++P L DYEVRIP GG TDAL E ITWN +L K Sbjct: 428 GGFDAFIDAVNKAMKEHDYTVPPLADYEVRIPKGGHTDALTECVITWNCGSELR-----K 482 Query: 488 TMGVHPDQTVAAVHATEKMLNQIL 511 T GVH +Q AA+ AT K++N L Sbjct: 483 TRGVHANQVFAAIMATLKIINMQL 506 Lambda K H 0.315 0.134 0.379 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: 723 Number of extensions: 23 Number of successful extensions: 2 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: 516 Length of database: 514 Length adjustment: 35 Effective length of query: 481 Effective length of database: 479 Effective search space: 230399 Effective search space used: 230399 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 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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