Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate RR42_RS36245 RR42_RS36245 excisionase
Query= SwissProt::O34002 (379 letters) >FitnessBrowser__Cup4G11:RR42_RS36245 Length = 392 Score = 91.3 bits (225), Expect = 4e-23 Identities = 98/382 (25%), Positives = 155/382 (40%), Gaps = 65/382 (17%) Query: 1 MTEPTIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPN 60 + + T+ GL + + +T I + L YRG LAA + E VA LLW + P Sbjct: 64 VAKATLSWGLPVLESGITLI-----EDGRLYYRGMDAVALAASDTVEAVAALLW--QCPQ 116 Query: 61 DSELKAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQ-DSSPEA 119 D+ A L A+ + + ++ + AQ SPE Sbjct: 117 DAAFGA--------APLAPAHLAAMQAAFSGRRSEEALLPLFTIASEDDPTAQWQRSPER 168 Query: 120 NLEK--------AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAAP 171 E A LL T P+ ++ ++ E DL Sbjct: 169 LAEGCGALVRLLAACLLHTAPASAPVHRQCASAWQVDEEGADL----------------- 211 Query: 172 EVVEAFNVSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMH 231 ++++L A+H NAS+FT+R + ST A L ++V + AL G LHGG V Sbjct: 212 -----IRMALVLCADHELNASSFTSRCVASTGASLRASVVAGLAALTGGLHGGTTARVEA 266 Query: 232 TFEEIGIRKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMI 291 ++E+G EA SK + + LA+ + + GFGH +Y GD R + L ++ Sbjct: 267 LWDELG--------EAQPASK--LRERLARGENLPGFGHHLYPAGDIRAAGL---LARIL 313 Query: 292 KHYDRPEMLGLYNGLEAAMEEAKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWT 351 H+ P+ + A + + +P++D+ + +F R GW Sbjct: 314 PHH--PQWQAFIDDAFALVGQ----RPSIDFALVALRRHLRLPPGAAFGMFALGRSIGWI 367 Query: 352 AHIMEQVADNALIRPLSEYNGP 373 AH +EQ AD LIRP + Y GP Sbjct: 368 AHALEQRADAELIRPRAAYVGP 389 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: 285 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 379 Length of database: 392 Length adjustment: 30 Effective length of query: 349 Effective length of database: 362 Effective search space: 126338 Effective search space used: 126338 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