Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate CA265_RS08845 CA265_RS08845 citrate (Si)-synthase
Query= SwissProt::O34002 (379 letters) >FitnessBrowser__Pedo557:CA265_RS08845 Length = 429 Score = 194 bits (493), Expect = 4e-54 Identities = 128/389 (32%), Positives = 201/389 (51%), Gaps = 24/389 (6%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T+ G + + I+ ++ + L YRGY ++ELAAK SF +V YL+ +LP ++L Sbjct: 41 TLDTGFKNTGSTKSKITFLDGEKGILKYRGYSIEELAAKSSFLEVIYLIIYGDLPTQAQL 100 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKA 124 + H + E++K D + HPM + + L + + A + Sbjct: 101 EGLQAEISKHTLIHEDMKKFFDGYPSRSHPMGQLGSLIFSLSTFYPECLKPNQTAEEQDL 160 Query: 125 --MSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGE-----EAAPEVVEAF 177 + LLA FP++V++ ++ G LI P+ DY NFLWMTFG+ + P VV A Sbjct: 161 TIIKLLAKFPTIVSFVYKKSLGHPLIYPKNKYDYVTNFLWMTFGQRTEDYDVNPIVVNAM 220 Query: 178 NVSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIG 237 N +IL+A+H N S T R++ S+ +L++++ I AL GPLHGGAN+AV+ E I Sbjct: 221 NKLLILHADHEQNCSASTVRIVGSSDCNLYASIAAGIAALWGPLHGGANQAVIDMLELI- 279 Query: 238 IRKDESLDEAATRSKAWMVDALAQKK--KVMGFGHRVYKNGDSRVPTMKSALDAMIKH-- 293 K + D ++ W+ A + ++MGFGHRVYKN D R +K A D ++++ Sbjct: 280 --KADGGD-----TEKWIAKAKDKNDPFRMMGFGHRVYKNFDPRAKIIKKACDDILENLG 332 Query: 294 YDRPEMLGLYNGLEAAMEEA----KQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349 D P + EAA+ + +++ PN+D+ +G Y +GF +EMFT LF R+ G Sbjct: 333 IDDPILEIAKKLEEAALTDQYFIDRKLYPNVDFYSGIIYRALGFPSEMFTVLFALGRLPG 392 Query: 350 WTAHIMEQVADNALI-RPLSEYNGPEQRQ 377 W A E + I RP Y G R+ Sbjct: 393 WIAQWKEMHENKEPIGRPRQIYVGETDRE 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: 357 Number of extensions: 13 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: 429 Length adjustment: 31 Effective length of query: 348 Effective length of database: 398 Effective search space: 138504 Effective search space used: 138504 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