Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate Echvi_3833 Echvi_3833 Isopropylmalate/homocitrate/citramalate synthases
Query= BRENDA::Q58787 (491 letters) >FitnessBrowser__Cola:Echvi_3833 Length = 390 Score = 288 bits (737), Expect = 2e-82 Identities = 172/376 (45%), Positives = 226/376 (60%), Gaps = 13/376 (3%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 V IFDTTLRDGEQ PG L K+EIA++L+ LGVDVIEAG I+S G+ + + I+K Sbjct: 6 VLIFDTTLRDGEQVPGCKLNTPQKIEIARQLESLGVDVIEAGFPISSPGDFKSVVEISKS 65 Query: 63 GLNAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALK 118 IC R + DI+ A E +H + TSP H+KYK + T D++LE A+ Sbjct: 66 VSEPIICGLSRGVAKDIEVAAEALKYAKRPRIHTGIGTSPSHIKYKFKSTPDQILERAVA 125 Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178 AV++AK VE AEDA R+D +L ++ K GA + + DT G P + Sbjct: 126 AVKHAKSFVEDVEFYAEDAGRTDNEYLARICEAVVKAGATVLNIPDTTGYCLPDEYGAKI 185 Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234 K + +NV N+ +S HCHND G+ATAN+ SAV+ GA Q T+NGIGERAGN SLEEV Sbjct: 186 KYLMDNVKGIENVIISAHCHNDLGLATANSISAVMNGARQIECTINGIGERAGNTSLEEV 245 Query: 235 VAALK---ILYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291 +K L Y+ KI L +SR+VS M + V PNKAIVG NAFAH +GIH DG+ Sbjct: 246 AMIMKQHPRLNVYN-KINSRLLNPISRLVSERMGMHVQPNKAIVGSNAFAHSSGIHQDGV 304 Query: 292 IKNTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350 IKN ETYE I PE VG I+L SGR AL ++L +G ++ QL+ IY+ E Sbjct: 305 IKNRETYEIIDPEEVGVTESMIVLTARSGRAALAFRLHKIGYTITKLQLDDIYQLFLEHA 364 Query: 351 DLGKYISDADLLAIVR 366 D+ K I+D DL I++ Sbjct: 365 DMKKEITDEDLHEIMK 380 Lambda K H 0.316 0.136 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: 459 Number of extensions: 25 Number of successful extensions: 5 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: 491 Length of database: 390 Length adjustment: 32 Effective length of query: 459 Effective length of database: 358 Effective search space: 164322 Effective search space used: 164322 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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