Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate NP_346902.1 CA_C0261 homocitrate synthase subunit alpha NifV
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000008765.1:NP_346902.1 Length = 265 Score = 189 bits (481), Expect = 8e-53 Identities = 104/268 (38%), Positives = 157/268 (58%), Gaps = 5/268 (1%) Query: 1 MMVRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLIT 60 M V++ DTTLRDGEQ G++L +K EIAK LD++G+ IEAG A E++ I+ I Sbjct: 1 MEVKLVDTTLRDGEQKAGIALGVKEKTEIAKLLDDMGIFQIEAGVAAMGGQEKKSIEEIV 60 Query: 61 KEGLNAEICSFVRALPVDIDAALECDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120 + GL ++I SF R DI +++C VD +H+ VP S + +KY L+ +++ V+ K + Sbjct: 61 RLGLKSKISSFNRMKISDIQHSIDCKVDIIHISVPASNMQIKYNLKTSKEIVISNMKKCI 120 Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180 YA G V + EDA+R+D+ FL++L E K G RV DTVG+L P+K+ + Sbjct: 121 YYALGKGYEVTIGLEDASRADIEFLVELCKEAYKEGIRRVRYADTVGILYPRKTFYNINR 180 Query: 181 ITENVNLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALKI 240 I E V + V +H HNDFGMA N+ SA GA T+ GIGERAGN + + + Sbjct: 181 IIEEVPVEVEIHTHNDFGMAEVNSLSAAKAGANYIDTTIAGIGERAGNCDFVKFINIIG- 239 Query: 241 LYGYDTKIKMEKLYEVSRIVSRLMKLPV 268 T ++++ L +++ +MKL + Sbjct: 240 ----KTNLRIDDLKLKEKMIKNIMKLNI 263 Score = 23.9 bits (50), Expect = 0.007 Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 6/91 (6%) Query: 404 DITLIETAYGVGPVDAAINAVRKAISGVAD------IKLVEYRVEAIGGGTDALIEVVVK 457 ++ L++T G A I K + +A I +E V A+GG IE +V+ Sbjct: 2 EVKLVDTTLRDGEQKAGIALGVKEKTEIAKLLDDMGIFQIEAGVAAMGGQEKKSIEEIVR 61 Query: 458 LRKGTEIVEVRKSDADIIRASVDAVMEGINM 488 L ++I + I+ S+D ++ I++ Sbjct: 62 LGLKSKISSFNRMKISDIQHSIDCKVDIIHI 92 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: 332 Number of extensions: 21 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 491 Length of database: 265 Length adjustment: 29 Effective length of query: 462 Effective length of database: 236 Effective search space: 109032 Effective search space used: 109032 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: 49 (23.5 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