Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_012410426.1 NPUN_RS20595 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000020025.1:WP_012410426.1 Length = 540 Score = 375 bits (964), Expect = e-108 Identities = 224/518 (43%), Positives = 314/518 (60%), Gaps = 30/518 (5%) Query: 11 PDEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRI 70 PD V IFDTTLRDGEQ+PG L EEKL IA +L +GVD IEAGFA AS G+ +A++ I Sbjct: 7 PDRVIIFDTTLRDGEQSPGATLNVEEKLAIAHQLALLGVDVIEAGFAVASPGDFQAVKTI 66 Query: 71 ARE---ELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEV 123 A + +CS+AR ++ D+ AA EA A +H ++ TS++H+K +L+ R EV Sbjct: 67 AEQVGIPGGPIICSLARAIRQDIHAAAEALKGAARPRIHTMISTSDIHLKYQLKKSRSEV 126 Query: 124 LERAREVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPE 183 L A E+V YA+ VE S D +RTE E+LYEV +A + AGA + DTVG P+ Sbjct: 127 LAIASEMVAYAKSFVDDVEFSPMDASRTEPEFLYEVLEAAIAAGATTINIPDTVGYCTPK 186 Query: 184 GMFLAVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGN 241 + ++ +RE V + VILS+H +D G+ATAN +AA+ G RQV T+NGIGERAGN Sbjct: 187 EIGTLIQGIREHVPNIDGVILSIHTQNDLGLATANALAAIEYGVRQVECTINGIGERAGN 246 Query: 242 AALEEVVVVLE-------ELYG--VD-----TGIRTERLTELSKLVERLTGVRVPPNKAV 287 AALEE+V+ L+ +G VD T I+T+ + + S LV +LTG+ + PNKA+ Sbjct: 247 AALEEIVMALQVRKPFFNPYFGRPVDADTPLTNIKTQEIYKTSSLVSQLTGMLIQPNKAI 306 Query: 288 VGENAFTHESGIHADGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVD 346 VG NAF HESGIH DGI+K TYE + +G E R VLGKH G + R +LK++G + Sbjct: 307 VGANAFAHESGIHQDGIIKHRQTYEIMEAAAIGLPENRIVLGKHSGRNAFRTRLKELGFE 366 Query: 347 VDDEQLLEILRRLKRLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPT 406 +++ L + R K + D+ K I++ DL AI D E ++E + G T PT Sbjct: 367 LNEADLNKAFNRFKDVADKKKEISDWDLEAIVRDETQIQVESGFQIEHVQVICGDCTCPT 426 Query: 407 ASI-VVKIDGTRKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITH 465 A+I +V DG AS G GPVDA +A+ R ++ I +L+E+ +++TGG DA+ Sbjct: 427 ATITIVTPDGKILTDASVGTGPVDAVYQAINRLVQ---IPNQLIEFSVQSVTGGIDALGT 483 Query: 466 VDVKLRDPETGDIVHSGSSREDIVVASLEAFIDGINSL 503 V V+L+ E I +S DIVVA+ A I+ +N L Sbjct: 484 VTVRLKHQER--IFSGQASDTDIVVAAAYAHINALNRL 519 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: 26 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: 540 Length adjustment: 35 Effective length of query: 474 Effective length of database: 505 Effective search space: 239370 Effective search space used: 239370 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