Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_028487006.1 B076_RS0108940 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000483485.1:WP_028487006.1 Length = 513 Score = 363 bits (931), Expect = e-104 Identities = 209/512 (40%), Positives = 312/512 (60%), Gaps = 21/512 (4%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D + IFDTTLRDGEQ+PG ++T EEK+RIA++L+++ VD IEAGF AASEG+ ++++ +A Sbjct: 3 DHLVIFDTTLRDGEQSPGASMTKEEKVRIAKQLEKLQVDVIEAGFPAASEGDFESVKAVA 62 Query: 72 REELDAEVCSMARMVKGDV----DAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 D+ +C +AR V+ D+ +A A + +H + TS +H++KKLRM ++V+ERA Sbjct: 63 SVIKDSTICGLARAVESDIVRAGEAIKPANSGRIHTFIATSPIHMEKKLRMTPDQVVERA 122 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 ++ AR+ VE S ED R+++++L V +A ++AGA + DTVG P Sbjct: 123 VWAIKKARNFTDDVEFSPEDAGRSDVDFLCRVIEAAIDAGATTINIPDTVGYNVPHQFGQ 182 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 K L ER+ + I S HCH+D G+A AN++AAVR GARQ+ T+NG+GERAGN ALE Sbjct: 183 LFKSLIERIPNSDKAIFSAHCHNDLGLAAANSLAAVRNGARQIECTINGLGERAGNTALE 242 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EVV+ + ++++ VDT I T + S+LV +TG V PNKA+VG NAF+HESGIH D Sbjct: 243 EVVMAVKTRQDIFDVDTRINTREILASSRLVSNITGFAVQPNKAIVGANAFSHESGIHQD 302 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQ-LLEILRRLK 360 G+LK TYE + E VG + VLGKH G + R +L+++G+ + EQ L + K Sbjct: 303 GVLKHRETYEIMRAEDVGWTTNKMVLGKHSGRNAFRSRLEELGITFETEQELNDAFVGFK 362 Query: 361 RLGDRGKRITEADLRAIAEDVLGRPAERD---IEVEDFTTVTGKRTIPTASIVVKIDGTR 417 L DR I + DL+A+ D + E + + +T TG++ P A + + ++G Sbjct: 363 ELADRKHEIYDEDLQALVTDNSAQRVENETYRLVSLKVSTETGEK--PHAEVTLWMNGNE 420 Query: 418 KEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGD 477 A + G G VDAT KA+E+ L G+ EL Y +T GTD++ V+L G Sbjct: 421 VTAVADGGGVVDATFKAIEK-LVHSGVTLEL--YSVSNVTNGTDSMGETTVRLE--LAGR 475 Query: 478 IVHSGSSREDIVVASLEAFIDGINSLMARKRS 509 IV+ + DIV AS A+I+ +N L + ++ Sbjct: 476 IVNGQGADTDIVTASARAYINALNKLQSSTKA 507 Lambda K H 0.315 0.134 0.367 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: 609 Number of extensions: 37 Number of successful extensions: 7 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: 509 Length of database: 513 Length adjustment: 35 Effective length of query: 474 Effective length of database: 478 Effective search space: 226572 Effective search space used: 226572 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 (21.6 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