Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate BPHYT_RS33920 BPHYT_RS33920 type II citrate synthase
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__BFirm:BPHYT_RS33920 Length = 433 Score = 192 bits (487), Expect = 2e-53 Identities = 123/386 (31%), Positives = 206/386 (53%), Gaps = 23/386 (5%) Query: 11 GLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYL 70 G A +A++ + + L YRGY + +LA A F E YLLL GELPN +Q ++ Sbjct: 50 GFMSTAACNSAITYIDGDKGELLYRGYPIDNLAQNADFLETCYLLLKGELPNAEQNAEFV 109 Query: 71 KKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTL---EPELSFDQQRDV-ADRL 126 K + + + + +DAHPM ++ L +++ + R+V A R+ Sbjct: 110 KTVTNHTMVHEQMHFFFRGFRRDAHPMAILVAAVGALSAFYHDSLDINNPRHREVSAIRM 169 Query: 127 LAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSL 181 +A P ++ Y+++ GQ ++ + +F+ ++ K +++ V+ ++ L Sbjct: 170 IAKLPTLVAMAYKYSI-GQPFAYPKNDLSYSANFMHMMFSNPCEEYKVNDVLVRALDRIL 228 Query: 182 ILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQE 241 IL+A+HE NAST T R+ S+ ++ ++C+ I L GP HGGANEAA+ ++E S + Sbjct: 229 ILHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGPAHGGANEAALNMLEEIGS-VD 287 Query: 242 ATAELLKMLERKD---KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVG--DKVLFAVSEA 296 E +K ++ K+ K+MGFGH +YK+ DPR ++++ ++ +E+G D LF ++ A Sbjct: 288 NIPEFIKQVKDKNSGVKLMGFGHRVYKNYDPRAKLMRETCHEVLEELGLHDDPLFKLAMA 347 Query: 297 IDKTMWE-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRAN 351 ++K E +KL+PN DFY +GIPT +FT IF +RT GW A E A+ Sbjct: 348 LEKIALEDEYFVSRKLYPNVDFYSGIVQRALGIPTSMFTCIFAMARTVGWIAQWNEMIAD 407 Query: 352 --NRIIRPSAEYTGVEQRAFVPLEQR 375 +I RP + G QR P+ QR Sbjct: 408 PEQKIGRPRQLFIGDTQREAKPIAQR 433 Lambda K H 0.319 0.134 0.396 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: 402 Number of extensions: 25 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: 375 Length of database: 433 Length adjustment: 31 Effective length of query: 344 Effective length of database: 402 Effective search space: 138288 Effective search space used: 138288 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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