Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate N515DRAFT_0574 N515DRAFT_0574 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__Dyella79:N515DRAFT_0574 Length = 535 Score = 334 bits (856), Expect = 5e-96 Identities = 200/466 (42%), Positives = 278/466 (59%), Gaps = 23/466 (4%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D VRIFDTTLRDGEQ PG + KLR+A L+ +GVD +EAGF AS + A+ IA Sbjct: 20 DRVRIFDTTLRDGEQAPGFGMDRRAKLRMAHALEALGVDVMEAGFPQASPDDFAAVADIA 79 Query: 72 REELDAEVCSMARMVKGDVDAA----VEAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 + + VC++AR D+D A A+ +H+ + TS +H + KL M +++V++ A Sbjct: 80 KAVRHSTVCALARCQAADIDTAGRALEAAQHSRIHVFLSTSPLHREHKLGMSKQQVIDTA 139 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 VE AR VE S ED RTE +YL EVF A + AGA + DTVG + P + Sbjct: 140 IAAVERARALCHEVEFSAEDAMRTEPDYLAEVFSAAIAAGATTVNAPDTVGYVTPAEIAE 199 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 LR+ V E V+ S HCHDD GMA AN++AAV AGARQ+ T+NGIGERAGNA+LE Sbjct: 200 RFAYLRKHVKGAERVVFSSHCHDDLGMAVANSLAAVSAGARQIECTINGIGERAGNASLE 259 Query: 246 EVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EVV+ L +GVD+ I RL + S+L+ +LTG VP NKA+VG+NAF HESGIH Sbjct: 260 EVVMALRVRGPYFGVDSRIDARRLVQTSRLLTQLTGQAVPRNKAIVGDNAFAHESGIHQH 319 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G+LK TYE + P+ VG E + VLGKH G +R +L+ +G ++ + +I R K Sbjct: 320 GMLKHRGTYEIMRPQDVGMGETKLVLGKHSGRHALRSRLQALGHTPEEAAMDDIFARFKA 379 Query: 362 LGDRGKRITEADLRAIA--EDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKI---DGT 416 L D+ + I + DL A+A +D R +++ + + G +AS V++ DG Sbjct: 380 LADKKREIHDEDLEALALGQDPDAAGPWRIVQLNSSSHLGG-----SASASVRLAHDDGR 434 Query: 417 RKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDA 462 A+ G GPVDA ++A+ERA G D EL +++ A++ G DA Sbjct: 435 EIGEAAIGDGPVDAVLRAMERA---TGTDLELTQFQVRAVSEGGDA 477 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: 615 Number of extensions: 39 Number of successful extensions: 6 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: 535 Length adjustment: 35 Effective length of query: 474 Effective length of database: 500 Effective search space: 237000 Effective search space used: 237000 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 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