Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_012991460.1 THAL_RS02075 homocitrate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000025605.1:WP_012991460.1 Length = 316 Score = 204 bits (520), Expect = 3e-57 Identities = 121/318 (38%), Positives = 181/318 (56%), Gaps = 2/318 (0%) Query: 1 MMVRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLIT 60 M V I DTTLR+G Q+P + L+ ++ + L L IE G + ERE I+ +T Sbjct: 1 MRVYITDTTLREGIQSPSLELSLEERYALFNHLVSLNFYEIEVGVPAKGEEEREYIRKLT 60 Query: 61 KEGLNAEICSFVRALPVDIDAALECDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120 K + + RA DI+ +L C+V V + P S I ++ KLRK+ + + A + V Sbjct: 61 KGEHADRVIVWNRANIKDIEYSLSCNVKKVEVAFPVSDIMIEKKLRKSREYLKGLAKEIV 120 Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180 KE GL + + EDA+R+D NFL++ + GADRV + DTVGV+ P ++ K Sbjct: 121 PCCKEKGLYLSVGLEDASRADYNFLLEFVELVKTHGADRVRLSDTVGVMNPLSVAKVVKD 180 Query: 181 ITENVNLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVAALKI 240 ++ + V VH HNDFGMATAN AV+ GA + ++ G+GER G EEVV L++ Sbjct: 181 LSNITD--VEVHFHNDFGMATANAVVAVMSGAKFVNSSLLGLGERCGITPTEEVVIYLEV 238 Query: 241 LYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIKNTETYEP 300 + G +T I + KLYE R + + V NK I+G NAF +++ IH+DGL K+ +TY P Sbjct: 239 ILGINTGIDIRKLYEKIREFVNMTGIKVHDNKPIIGTNAFTNKSRIHIDGLSKSKDTYLP 298 Query: 301 IKPEMVGNRRRIILGKHS 318 P+++G +I G +S Sbjct: 299 FDPQLIGEMSKICKGYYS 316 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: 407 Number of extensions: 24 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: 316 Length adjustment: 31 Effective length of query: 460 Effective length of database: 285 Effective search space: 131100 Effective search space used: 131100 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: 50 (23.9 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