Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate CA265_RS15855 CA265_RS15855 2-isopropylmalate synthase
Query= BRENDA::Q58787 (491 letters) >FitnessBrowser__Pedo557:CA265_RS15855 Length = 386 Score = 283 bits (725), Expect = 6e-81 Identities = 166/374 (44%), Positives = 222/374 (59%), Gaps = 11/374 (2%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 V IFDTTLRDGEQ PG L N K+EIAK L+ LGVDVIEAG ++S G+ + ++K Sbjct: 8 VYIFDTTLRDGEQVPGCQLDTNQKVEIAKSLELLGVDVIEAGFPVSSPGDFNSVIELSKA 67 Query: 63 GLNAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALK 118 N IC+ RA DID A + +H + +S H+K+K T +E+LE A++ Sbjct: 68 VTNPIICALTRANKNDIDVAADALRYAKRPRIHTGIGSSDFHIKHKFNSTREEILERAVE 127 Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178 AV Y+K+ VE AEDA R+D+ FL K+ GA V + DT G P + Sbjct: 128 AVRYSKKFVEDVEFYAEDAGRADIEFLAKMVEAVIAAGATVVNIPDTNGYCLPDQYGSKI 187 Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234 + ENV +SVHCHND G+ATAN+ + + GA Q T+NGIGERAGN S+EEV Sbjct: 188 LFLKENVKNIDKAIISVHCHNDLGLATANSIAGLQNGARQVECTINGIGERAGNTSMEEV 247 Query: 235 VAALKI--LYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLI 292 V LK + G +T+I + YE+S +V M +PV PNKAIVG NAF+H +GIH DG + Sbjct: 248 VMILKTHKILGLNTQIDATRFYEMSHMVRNQMNMPVQPNKAIVGGNAFSHSSGIHQDGFL 307 Query: 293 KNTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGD 351 KN E YE IKPE VG I+L SGR ALK+ LD +G + + L+ +Y++ D Sbjct: 308 KNRENYEIIKPEDVGFPDATIVLTARSGRHALKHHLDRLGHKLEKDHLDIVYKQFLVLAD 367 Query: 352 LGKYISDADLLAIV 365 + I+D DL +V Sbjct: 368 SKQGINDQDLNQLV 381 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: 481 Number of extensions: 31 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: 386 Length adjustment: 32 Effective length of query: 459 Effective length of database: 354 Effective search space: 162486 Effective search space used: 162486 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