Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_019865043.1 METMI_RS0104475 citrate (Si)-synthase
Query= BRENDA::Q8NSL1 (383 letters) >NCBI__GCF_000384075.1:WP_019865043.1 Length = 433 Score = 194 bits (493), Expect = 4e-54 Identities = 122/361 (33%), Positives = 184/361 (50%), Gaps = 12/361 (3%) Query: 29 ETNSLTYRGYAVEDLVENCSFEEVFYLLWHGELPTAQQLAEFNERGRSYRSLDAGLISLI 88 E L YRGY +E L E C+F EV YL+ +GELP + +LAEF + + L + Sbjct: 65 EEGVLLYRGYPIEQLAEQCNFLEVCYLILNGELPASGELAEFQYNVTMHTMVHDQLTNFF 124 Query: 89 HSLPKEAHPMDVMRTAVSYMGTKDSEYFTTDSEHIRKVGHT-LLAQLPMVLAMDIRRRKG 147 ++AHPM +M V + + S+ R++ L+A++P ++AM + G Sbjct: 125 KGFRRDAHPMAIMVGVVGALSAFYHDALDIRSKKDREISAIRLIAKVPTIVAMCHKYSTG 184 Query: 148 LDIIAPDSSKSVAENLLSMVFGTGPESPASNPADVRDFEKSLILYAEHSFNASTFTARVI 207 + + P + S EN L M+ T + +NP VR E+ LIL+A+H NAST T R+ Sbjct: 185 MPFMYPQNKLSYVENFLRMMHATPCDDYQANPVLVRALERILILHADHEQNASTSTVRLA 244 Query: 208 TSTKSDVYSAITGAIGALKGPLHGGANEFVMHTMLAIDDPNKAAAWINNALDNKNV--VM 265 S+ ++ ++ IT I L G HGGANE V++ + I D ++ +I A D + +M Sbjct: 245 GSSGANPFACITAGIACLWGSAHGGANEAVLNMLEKIGDVSRIPEFIKKAKDKNDPFRLM 304 Query: 266 GFGHRVYKRGDSRVPSMEKSFRELAAR---HDGEKWVAMYENMRDAMDARTGIK----PN 318 GFGHRVYK D R M + E+ HD + + E R A++ I+ PN Sbjct: 305 GFGHRVYKNHDPRAKLMRATCHEVLTELGLHDNKLFALALELERIALEDEYFIEKKLYPN 364 Query: 319 LDFPAGPAYHLLGFPVDFFTPLFVIARVAGWTAHIVEQYEN--NSLIRPLSEYNGEEQRE 376 +DF +G H LG P + FT +F + R GW AH E + + RP Y G +R+ Sbjct: 365 VDFYSGIVLHALGIPTNMFTAMFAMGRTVGWIAHWDEMIADPEQKIGRPRQLYTGAVRRD 424 Query: 377 V 377 V Sbjct: 425 V 425 Lambda K H 0.318 0.133 0.388 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: 386 Number of extensions: 16 Number of successful extensions: 4 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: 383 Length of database: 433 Length adjustment: 31 Effective length of query: 352 Effective length of database: 402 Effective search space: 141504 Effective search space used: 141504 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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