Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_015739102.1 ADEG_RS05565 homocitrate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000024605.1:WP_015739102.1 Length = 381 Score = 325 bits (832), Expect = 2e-93 Identities = 175/370 (47%), Positives = 239/370 (64%), Gaps = 1/370 (0%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 +RI DTTLRDGEQT GV + +KL IAK LDE+GV IEAG + E E IK I + Sbjct: 10 IRIVDTTLRDGEQTAGVVFSNLEKLRIAKMLDEIGVHQIEAGIPVMGGDEAEAIKQICRA 69 Query: 63 GLNAEICSFVRALPVDIDAALECDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAVEY 122 GL A I + R + D++A+L C VD+V + + TS IH+++KLR T + V+E ++AV + Sbjct: 70 GLKASIMGWNRPVIKDLEASLACGVDAVAISISTSDIHIEHKLRATREWVVEKMVEAVHF 129 Query: 123 AKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKKIT 182 AK+HGL V ++AEDA+RSD+ FLI ++ GADR+ CDTVGVL P + E K++ Sbjct: 130 AKKHGLYVSVNAEDASRSDMEFLIAFARAAKEAGADRLRYCDTVGVLDPFTTYENIKRLV 189 Query: 183 ENVNLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALKILY 242 V LP+ +H HNDFGMATAN + VL GA VTV G+GERAGNA+LEEVV ALK ++ Sbjct: 190 SEVGLPIEMHTHNDFGMATANALAGVLAGADWIGVTVCGLGERAGNAALEEVVMALKHIF 249 Query: 243 GYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIKNTETYEPIK 302 G D K E E++ VS +P K IVG N FAHE+GIH DG +KN +TYE + Sbjct: 250 GVDLGFKTELFREIAEYVSHAAHRELPAWKPIVGSNMFAHESGIHADGALKNPKTYEAFQ 309 Query: 303 PEMVGNRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG-DLGKYISDADL 361 PE VG R+I++GKHSG AL+ K GI++S + + V++ L + + D +L Sbjct: 310 PEEVGLTRQIVIGKHSGTAALRAKFAEYGISLSKHEAELLLPEVRKAAVSLKRPLFDKEL 369 Query: 362 LAIVREVTGK 371 ++I E+ G+ Sbjct: 370 VSIYEELFGR 379 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: 478 Number of extensions: 15 Number of successful extensions: 1 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: 381 Length adjustment: 32 Effective length of query: 459 Effective length of database: 349 Effective search space: 160191 Effective search space used: 160191 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