Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate Pf1N1B4_3676 Citrate synthase (si) (EC 2.3.3.1)
Query= SwissProt::O34002 (379 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3676 Length = 428 Score = 191 bits (486), Expect = 3e-53 Identities = 131/394 (33%), Positives = 196/394 (49%), Gaps = 33/394 (8%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G + + I+ ++ D LL+RGYP+++LA K + + YLL N ELP + Sbjct: 42 TFDPGFMSTASCESKITYIDGDNGILLHRGYPIEQLAEKSDYLETCYLLLNGELPTAEQK 101 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123 FV ++H + E +K + HPM V V L A + + D ++P+ Sbjct: 102 AQFVGTVKNHTMVHEQLKTFFNGFRRDAHPMAVMCGVVGALSAFYHDSLDINNPQHREIS 161 Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFG-----EEAAPEVVEAFN 178 A+ L+A P++ A + G+ ++ PR DL Y+ NFL M F + +P + +A + Sbjct: 162 AIRLVAKMPTLAAMVYKYSMGQPMMYPRNDLSYAENFLHMMFNTPCEIKPISPVLAKAMD 221 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGI 238 IL+A+H NAST T R+ S+ A+ + + I AL GP HGGANEAV+ +EIG Sbjct: 222 RIFILHADHEQNASTSTVRLAGSSGANPFACIAAGIAALWGPAHGGANEAVLTMLDEIG- 280 Query: 239 RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYDRPE 298 ++D+ ++K K+MGFGHRVYKN D R MK D ++K Sbjct: 281 -DVSNIDKYIAKAK-----DKNDPFKLMGFGHRVYKNRDPRATVMKQTCDEVLKE----- 329 Query: 299 MLGLYNG--LEAAM--EE---------AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAA 345 LG+ N LE AM EE + + PN+D+ +G +G T MFT +F A Sbjct: 330 -LGITNDPQLELAMRLEEIALTDPYFIERSLYPNVDFYSGIILKAIGIPTSMFTVIFALA 388 Query: 346 RITGWTAHIMEQVADNALI-RPLSEYNGPEQRQV 378 R GW +H E ++ I RP Y G E R + Sbjct: 389 RTVGWISHWKEMLSSPYKIGRPRQLYTGYESRDI 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: 352 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: 428 Length adjustment: 31 Effective length of query: 348 Effective length of database: 397 Effective search space: 138156 Effective search space used: 138156 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