Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_003940025.1 C1M55_RS23230 citrate synthase 2
Query= BRENDA::Q9I5E3 (375 letters) >NCBI__GCF_002893965.1:WP_003940025.1 Length = 375 Score = 160 bits (404), Expect = 7e-44 Identities = 117/375 (31%), Positives = 186/375 (49%), Gaps = 43/375 (11%) Query: 10 AGLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAI-FEEVAYLLLYGELPNKQQLDA 68 +GL G VA + ++ ++G L YRG D+ DL + F V LL+ G Sbjct: 13 SGLEGVVAFTSDIAEPDKDGGALRYRGVDIEDLVGQRVTFGNVWALLVDGRFGP------ 66 Query: 69 YLKKLQGQRDLPQALKEVLERIPKDAHPMDV---MRTGASVLGTL---EPELSFDQQRDV 122 LP A E P H DV ++ G ++L + +P L D + Sbjct: 67 ---------GLPPA-----EPFPLPIHTGDVRVDVQAGLAMLAPIWGYQPLLDIDDET-A 111 Query: 123 ADRLLAAFPAIMTYW-------YRFTHEGQRIDCNSDEPTIGGHFLALLHGKKPSELHVK 175 D+L A ++Y Y+ RID + T+ F+ G+ P HV+ Sbjct: 112 RDQLARASVMALSYVAQSARGIYQPAVPQSRID---EAKTVTERFMVRWKGE-PDPAHVE 167 Query: 176 VMNVSLILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIER 235 ++ + AEH NASTFTARV AST +D+ + ++GAIG++ GPLHGGA + +IE Sbjct: 168 AIDAYWVSAAEHGMNASTFTARVIASTGADVAASLSGAIGAMSGPLHGGAPARVLPMIEE 227 Query: 236 FSSPQEATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSE 295 +A A + +L+RK+K+MGFGH +Y+ DPR V++ +K+L + + A+ + Sbjct: 228 TEKTGDARALVKGILDRKEKLMGFGHRVYRAEDPRARVLRATAKRL-NAPRYEAAAALEQ 286 Query: 296 AIDKTMWEQ---KKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANN 352 A + E+ + + N +F+ A F +P + +F C RT+GW AH+ EQ+ Sbjct: 287 AALAELRERRPDRAIETNVEFWAAVILDFAEVPAHMMPAMFTCGRTAGWCAHILEQKRLG 346 Query: 353 RIIRPSAEYTGVEQR 367 +++RP+A YTG R Sbjct: 347 KLVRPAAIYTGPAPR 361 Lambda K H 0.319 0.134 0.396 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: 316 Number of extensions: 13 Number of successful extensions: 3 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: 375 Length of database: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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