Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate GFF2451 Psest_2499 citrate synthase I (hexameric type)
Query= SwissProt::O34002 (379 letters) >FitnessBrowser__psRCH2:GFF2451 Length = 423 Score = 194 bits (492), Expect = 5e-54 Identities = 127/388 (32%), Positives = 191/388 (49%), Gaps = 20/388 (5%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G + + I+ ++ D LL+RGYP+++LA K + + YLL N ELP + Sbjct: 42 TFDPGFMSTASCESKITYIDGDKGILLHRGYPIEQLAEKSDYLETCYLLLNGELPTAEQK 101 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123 FV+ ++H + E +K ++ HPM + V L A + + D + P Sbjct: 102 AQFVSTVKNHTMVHEQLKSFLNGFRRDAHPMAIMCGVVGALSAFYHDSLDINDPHHREIS 161 Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFG-----EEAAPEVVEAFN 178 A+ L+A P++ A + G+ L+ PR DL YS NFL M F + +P + +A + Sbjct: 162 AVRLVAKMPTIAAMVYKYSIGQPLMYPRNDLSYSENFLHMMFNTPCEIKPISPVLAKAMD 221 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGI 238 IL+A+H NAST T R+ ST A+ + + I AL GP HGGANEAV+ +EIG Sbjct: 222 RIFILHADHEQNASTSTVRLAGSTGANPFACIAAGIAALWGPAHGGANEAVLTMLDEIGD 281 Query: 239 RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKH--YDR 296 + A + K K+MGFGHRVYKN D R MK D ++ + Sbjct: 282 VSNVEKFLAKAKDK-------NDPFKLMGFGHRVYKNFDPRAKVMKQTCDEVLGELGIND 334 Query: 297 PEMLGLYNGLEAAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWTA 352 P++ E A+ + + + PN+D+ +G +G T MFT +F AR GW + Sbjct: 335 PQLDLAMKLEEIALNDPYFAERNLYPNVDFYSGIILKAIGIPTSMFTVIFALARTVGWIS 394 Query: 353 HIMEQVADNALI-RPLSEYNGPEQRQVP 379 H E +A I RP Y G +R +P Sbjct: 395 HWKEMIASGQKIGRPRQLYTGHTKRDLP 422 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: 380 Number of extensions: 23 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: 423 Length adjustment: 31 Effective length of query: 348 Effective length of database: 392 Effective search space: 136416 Effective search space used: 136416 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