Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_057687496.1 ABB28_RS16700 citrate synthase
Query= SwissProt::O34002 (379 letters) >NCBI__GCF_001431535.1:WP_057687496.1 Length = 425 Score = 200 bits (508), Expect = 7e-56 Identities = 133/392 (33%), Positives = 204/392 (52%), Gaps = 33/392 (8%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G + +AI+ ++ D LLYRGYP+++L+ K S+ +V YLL N E P+ ++L Sbjct: 43 TYDSGFTATASCKSAITYIDGDKGVLLYRGYPIEQLSEKSSYVEVVYLLINGERPDAAQL 102 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVL-GANHARAQDSSPEANLEK 123 KAF + +D +V I + HPM + A++ L G HA S E + Sbjct: 103 KAFNEELAAEATVDASVNTLIGSFAKDAHPMAILTAAIAQLSGIYHASLDLSDAEQRRKA 162 Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGE-----EAAPEVVEAFN 178 A+ L+A P++ A R +G P LDY + FL TF E +VV+A + Sbjct: 163 AVRLIAKVPTLSALIYRHGKGLPANTPDTSLDYVSRFLKQTFESADGQYELNQDVVKALD 222 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGI 238 + IL+A+H NAST T R++ ST A+ +++V + AL GP HGGANEAV+ EEIG Sbjct: 223 LLFILHADHEQNASTSTVRMVGSTGANPYASVAAGVTALWGPAHGGANEAVLKMLEEIG- 281 Query: 239 RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYDRPE 298 ++++ A ++K ++MGFGHRVYKN D R + ++ E Sbjct: 282 -SADNVESAVVKAK-----DKTSGFRLMGFGHRVYKNFDPRAKVIGVMTGKVL------E 329 Query: 299 MLGLYNGL--------EAAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAAR 346 LG+ + L +AA+++ A+++ PN+D+ +G Y + TEMFT +F R Sbjct: 330 QLGVQDPLLDVAVKLEQAALQDDYFVARKLYPNVDFYSGIIYKALQIPTEMFTVMFALGR 389 Query: 347 ITGWTAHIMEQVADNALI--RPLSEYNGPEQR 376 +GW AH +EQ D + RP Y G + R Sbjct: 390 TSGWVAHWLEQQVDPEMKIGRPRQVYTGSDVR 421 Lambda K H 0.316 0.130 0.376 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: 378 Number of extensions: 17 Number of successful extensions: 5 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: 379 Length of database: 425 Length adjustment: 31 Effective length of query: 348 Effective length of database: 394 Effective search space: 137112 Effective search space used: 137112 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 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