Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_041246148.1 GURA_RS18920 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000016745.1:WP_041246148.1 Length = 511 Score = 381 bits (979), Expect = e-110 Identities = 215/505 (42%), Positives = 320/505 (63%), Gaps = 19/505 (3%) Query: 14 VRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIARE 73 ++IFDTTLRDGEQ+PG ++ +EKLR+A++L ++ VD IEAGF ASEG+ +A+++IA+ Sbjct: 6 IKIFDTTLRDGEQSPGASMNIDEKLRLAKQLQKLNVDVIEAGFPIASEGDFEAVKKIAQT 65 Query: 74 ELDAEVCSMARMVKGDVDAAVEA-----EADAVHIVVPTSEVHVKKKLRMDREEVLERAR 128 E+ + R D+D A EA E +H + TS++H+K KL+M ++VLE A Sbjct: 66 IKGPEIAGLCRSSFKDIDRAWEALQYAGERGRIHTFIATSDIHMKYKLKMTPKQVLESAV 125 Query: 129 EVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLA 188 + V+ AR + VE S ED RT+L++L EV A ++AGA + DTVG P F Sbjct: 126 KAVKRARTYTPNVEFSCEDAVRTDLKFLAEVVGAVIDAGATVVNIPDTVGYTIPFEYFNI 185 Query: 189 VKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEE 246 +K L++ V E ++SVHCH+D G++ AN++AAV+AGA QV T+NGIGERAGN +LEE Sbjct: 186 IKYLKDNVANVEKAVISVHCHNDLGLSVANSIAAVQAGAGQVECTINGIGERAGNCSLEE 245 Query: 247 VVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303 V+ L +++ T + TE+LT S+L+ +TG+ V PNKA+VG NAF HE+GIH G Sbjct: 246 FVMTLKTRQDILPFKTNVVTEQLTPASRLLTTVTGIVVQPNKAIVGANAFAHEAGIHQHG 305 Query: 304 ILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362 ++ D++TYE + PE VG VLGKH G +K+L+++G D+DDE+L R K L Sbjct: 306 MMMDKTTYEIMTPESVGLKASALVLGKHSGRHAFKKRLEELGYDLDDEKLNRAFDRFKAL 365 Query: 363 GDRGKRITEADLRAI-AEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAA 421 D K + + DL AI A++VL AE ++ T G + TA++ ++IDG + A Sbjct: 366 ADLKKEVFDEDLDAIVADEVL--TAEEKYKLSHITVTCGSFAVATATVQMEIDGIQVRTA 423 Query: 422 STGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHS 481 G GPVDAT+KA+++ K + +L++Y ++TGGTDA V V+L D ++ Sbjct: 424 ELGDGPVDATLKAIKKLTKTKA---KLLQYNVGSITGGTDAQGEVTVRLTD-GARTVIGR 479 Query: 482 GSSREDIVVASLEAFIDGINSLMAR 506 G+S DI+ AS +A+I +N L+ R Sbjct: 480 GAS-TDIIEASAKAYIHALNRLLFR 503 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: 622 Number of extensions: 36 Number of successful extensions: 8 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: 511 Length adjustment: 34 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 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 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