Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate Dsui_2216 Dsui_2216 citrate synthase I, hexameric type
Query= SwissProt::O34002 (379 letters) >FitnessBrowser__PS:Dsui_2216 Length = 431 Score = 200 bits (509), Expect = 5e-56 Identities = 132/391 (33%), Positives = 198/391 (50%), Gaps = 26/391 (6%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G + + I+ ++ D LLYRGYP+++LA C+F +VAYLL N ELPN S+ Sbjct: 43 TYDSGFLSTASCKSKITFIDGDKGELLYRGYPIEQLAENCNFLEVAYLLKNGELPNASQK 102 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKA 124 AF + ++H + E + HPM V V L A + A D S + + Sbjct: 103 TAFEDTIKNHTMVHEQLAKFFSGFRRDAHPMAVMVGVVGALSAFYHEAMDFSDAEHRSIS 162 Query: 125 MS-LLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGE-----EAAPEVVEAFN 178 + ++A P++VA + G+ + PR DLDY+ANF+ M FG + P +V A + Sbjct: 163 FNRIIAKMPTIVAMAYKYTTGQPFMYPRNDLDYTANFMHMMFGTPCETYKPNPVLVRALD 222 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIG- 237 + L+A+H NAST T R+ S+ A+ + ++ I L GP HGGANEA + EEIG Sbjct: 223 IIFTLHADHEQNASTSTVRLAGSSGANPFACISAGIACLWGPAHGGANEACLQMLEEIGD 282 Query: 238 -IRKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKH--Y 294 R E + A ++ ++ K+MGFGHRVYKN D R M+ + ++K Sbjct: 283 VSRVGEYIARAKDKNDSF---------KLMGFGHRVYKNFDPRAKLMRQVCNDVLKELGL 333 Query: 295 DRPEMLGLYNGLE-AAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349 + + L LE A+E+ K++ PN+D+ +G +G T MFT +F AR G Sbjct: 334 ENDRLFKLAMELEKIALEDPYFVEKKLYPNVDFYSGIVQKALGIPTSMFTCIFALARTVG 393 Query: 350 WTAHIMEQVAD--NALIRPLSEYNGPEQRQV 378 W E + D + RP Y G +R V Sbjct: 394 WMTQWEEMITDPEYKIGRPRQLYIGAAKRDV 424 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: 381 Number of extensions: 14 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: 431 Length adjustment: 31 Effective length of query: 348 Effective length of database: 400 Effective search space: 139200 Effective search space used: 139200 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 17 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