Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_013645641.1 METBO_RS10235 2-isopropylmalate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000191585.1:WP_013645641.1 Length = 391 Score = 360 bits (924), Expect = e-104 Identities = 175/368 (47%), Positives = 252/368 (68%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 + ++DTTLRDGEQTPGV L +KL+IAKKLDE+G+ IEAG + SK E++ + I E Sbjct: 20 ITVYDTTLRDGEQTPGVCLRTPEKLKIAKKLDEVGIHQIEAGFPVVSKEEKKSVTAIVNE 79 Query: 63 GLNAEICSFVRALPVDIDAALECDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAVEY 122 LNA+I R DID A++CDVD + + TS +H+K+K++ + +E+L + ++E+ Sbjct: 80 DLNAQILCLSRTKKSDIDTAIDCDVDGIITFMSTSDLHLKHKIKMSREEILNVCMNSIEH 139 Query: 123 AKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKKIT 182 AK+HGL V SAEDATR+D++FL K++ + + G DRV + DTVG ++P L K++ Sbjct: 140 AKDHGLFVAFSAEDATRTDLDFLKKMYKKADDYGVDRVHIADTVGAISPYGMDYLVKQLR 199 Query: 183 ENVNLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALKILY 242 +N +++HCHNDFGMA AN+ + +L GA TVNGIGERAGNA+LEE+V LK +Y Sbjct: 200 STINAEIALHCHNDFGMALANSIAGLLAGANAVSTTVNGIGERAGNAALEELVMTLKFIY 259 Query: 243 GYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIKNTETYEPIK 302 G D + K E+S++V L + +P NK IVG N F HE+GIHVD +I+ TYEP Sbjct: 260 GVDLGFDVSKFCELSKLVESLTHMDIPYNKPIVGKNIFRHESGIHVDAVIEEPLTYEPFL 319 Query: 303 PEMVGNRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGDLGKYISDADLL 362 PE++G+RR+I+LGKHSG +A++ KL+ GI+V+ ++L KI E+VK + G YI+D Sbjct: 320 PELIGHRRQIVLGKHSGCRAVRAKLNECGIDVTKDELCKIVEQVKSKREEGNYINDELFN 379 Query: 363 AIVREVTG 370 +IV V G Sbjct: 380 SIVASVRG 387 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: 547 Number of extensions: 23 Number of successful extensions: 2 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: 391 Length adjustment: 32 Effective length of query: 459 Effective length of database: 359 Effective search space: 164781 Effective search space used: 164781 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 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