Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_018123428.1 B149_RS0101700 2-isopropylmalate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000375485.1:WP_018123428.1 Length = 512 Score = 361 bits (926), Expect = e-104 Identities = 207/503 (41%), Positives = 316/503 (62%), Gaps = 19/503 (3%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 + IFDTTLRDGEQ+PG ++ ++K+ +A++L+ LGVD+IEAG I S+G+ E +K I + Sbjct: 5 IMIFDTTLRDGEQSPGATMNIDEKIRMARQLETLGVDIIEAGFPIASQGDFESVKSIAES 64 Query: 63 GLNAEICSFVRALPVDIDAALECDVDS----VHLVVPTSPIHMKYKLRKTEDEVLETALK 118 N ++ R++ DID E ++ +H + TSPIHM+YKL KT D+V+E A Sbjct: 65 VTNLQVAGLCRSVTKDIDRCWEAVKNAPEGRIHTFLATSPIHMEYKLGKTPDQVVEMAEA 124 Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178 AV++A ++ VE SAEDA+RSD +FL+++FN K GA + V DTVG P + E+ Sbjct: 125 AVKHAAKYTSNVEFSAEDASRSDWDFLVRVFNTAIKAGARTLNVPDTVGYTQPHEFYEMI 184 Query: 179 KKITENVNLP----VSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234 + + E + + +SVHCHND G+A AN+ +A+ GA Q TV+GIGERAGNA+LEEV Sbjct: 185 RFLMEKLEMKSDTVISVHCHNDLGLAVANSLAAIRAGARQVECTVSGIGERAGNAALEEV 244 Query: 235 VAAL---KILYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291 V AL K LY D + E+LY R +S+++ P+PP KAIVG NAFAHE+G+H DG+ Sbjct: 245 VMALNTRKDLYDIDCDVVTEQLYPSCRRLSQIIGQPIPPYKAIVGTNAFAHESGVHQDGV 304 Query: 292 IKNTETYEPIKPEMVGNR-RRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350 IKN +TYE + E +G + I++GKHSG A+K K++ +G + D+Q+ ++ VKE Sbjct: 305 IKNRQTYEIMTAESIGRQGTEIVIGKHSGSHAIKRKVEELGYTLQDDQVEAMFSAVKELA 364 Query: 351 DLGKYISDADLLAIVREVTGKLVEEKIKLDELTVVSG-NKITPIASVKLHY--KGEDITL 407 D + I D D+ A+V E + +K +L +++V SG ++ P A+V + + +G D+ + Sbjct: 365 DKKERIHDEDVEALVLEKVYRR-RDKFRLRDMSVFSGTGEVPPHAAVVMEFGDEGGDVEV 423 Query: 408 IE-TAYGVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVE 466 + TA+G G +DA +++ I A ++ Y V A+ GTDAL V V++ Sbjct: 424 RKNTAFGRGTIDAVFSSIYDLIGYRASLE--SYTVNAVTSGTDALAGVAVRITHDGFKAV 481 Query: 467 VRKSDADIIRASVDAVMEGINML 489 R +D D++RAS A++ +N L Sbjct: 482 GRANDEDVVRASALALVNALNRL 504 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: 614 Number of extensions: 27 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: 491 Length of database: 512 Length adjustment: 34 Effective length of query: 457 Effective length of database: 478 Effective search space: 218446 Effective search space used: 218446 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