Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate GFF2606 PGA1_c26470 2-isopropylmalate synthase LeuA
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__Phaeo:GFF2606 Length = 523 Score = 349 bits (895), Expect = e-100 Identities = 206/506 (40%), Positives = 297/506 (58%), Gaps = 18/506 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D V IFDTTLRDGEQ+PG +T +EKL IA LD++GVD IEAGF ASEG+ KA+ IA Sbjct: 8 DRVLIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFKAVSEIA 67 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 ++ +C +AR D+D EA A +H + TS +H + + ++E+ E+ Sbjct: 68 ERSKNSRICGLARANFKDIDRCAEAVKRAAQPRIHTFIGTSPLH-RAIPNLTKDEMAEKI 126 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 + V +AR+ V+ S D TRTE +YL V + ++AGA + DTVG AP Sbjct: 127 HDTVTHARNLVDNVQWSPMDATRTEWDYLCRVIEIAIKAGATTINIPDTVGYTAPVESAD 186 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 +K+L E V +DVI + HCH+D GMATAN++AAV GARQ+ T+NG+GERAGN ALE Sbjct: 187 LIKRLIETVPGADDVIFATHCHNDLGMATANSLAAVAGGARQIECTINGLGERAGNTALE 246 Query: 246 EVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EVV+ L+ ++ TGI T+++ +S+ V ++G V PNKA+VG+NAF HESGIH D Sbjct: 247 EVVMALKVRNDIMPFTTGIDTQKIMHISRRVSTVSGFVVQPNKAIVGKNAFAHESGIHQD 306 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G+LK++ T+E + PE VG LGKH G + +R KL Q+G +V D QL ++ R K Sbjct: 307 GMLKNKETFEIMRPEDVGIAGTSLPLGKHSGRAALRDKLSQLGFEVGDNQLKDLFVRFKE 366 Query: 362 LGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAA 421 L DR K + + D+ A+ + +++ V G A++ ++++G Sbjct: 367 LADRKKEVFDDDIIALMR--TSGDEDDHLKLVSMKVVCGTGGPAEATLEMEVEGKDVSET 424 Query: 422 STGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHS 481 + G GPVDA +A+ + + L Y+ A+T GTDA V V+L E G I Sbjct: 425 AEGDGPVDAAFRAIRKIHPNSA---HLQLYQVHAVTEGTDAQATVSVRLE--ENGVIATG 479 Query: 482 GSSREDIVVASLEAFIDGINSLMARK 507 S+ D VVAS A+I +N L+ R+ Sbjct: 480 ESANTDTVVASAAAYIGALNRLIIRR 505 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: 686 Number of extensions: 43 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: 523 Length adjustment: 35 Effective length of query: 474 Effective length of database: 488 Effective search space: 231312 Effective search space used: 231312 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