Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate BPHYT_RS27440 BPHYT_RS27440 type II citrate synthase
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__BFirm:BPHYT_RS27440 Length = 432 Score = 193 bits (491), Expect = 7e-54 Identities = 122/385 (31%), Positives = 200/385 (51%), Gaps = 21/385 (5%) Query: 11 GLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYL 70 G A + ++ + + L YRGY + +LA A F E YLLL GELPN QQ + ++ Sbjct: 49 GFMSTAACNSEITYIDGDKGELLYRGYPIDNLAQNADFLETCYLLLKGELPNAQQKEEFV 108 Query: 71 KKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTL---EPELSFDQQRDV-ADRL 126 K + + + +DAHPM ++ L ++ RD+ A R+ Sbjct: 109 KTVTQHTMVHDQMHFFFRGFRRDAHPMAILVAAVGALSAFYHDSLDIGNPLHRDISAIRM 168 Query: 127 LAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSL 181 +A P ++ Y++T GQ ++ + +F+ ++ K +++ V+ ++ L Sbjct: 169 IAKLPTLVAMAYKYT-VGQPFVYPKNDLSYSANFMRMMFSSPAQEYKVNDVLVRALDRIL 227 Query: 182 ILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQE 241 IL+A+HE NAST T R+ S+ ++ ++C+ I L GP HGGANEAA+ ++E S Sbjct: 228 ILHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGPAHGGANEAALNMLEEIGSVDN 287 Query: 242 ATAELLKMLERKD--KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVG--DKVLFAVSEAI 297 + K+ ++ K+MGFGH +YK+ DPR ++++ ++ +E+G D LF ++ A+ Sbjct: 288 IPEFIAKVKDKDSGVKLMGFGHRVYKNYDPRAKLMRETCHEVLEELGLHDDPLFKLAMAL 347 Query: 298 DKTMWE-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRAN- 351 +K E +KL+PN DFY +GIPT +FT IF +RT GW A E A+ Sbjct: 348 EKIALEDEYFVSRKLYPNVDFYSGIVQRALGIPTAMFTCIFAMARTVGWIAQWNEMIADP 407 Query: 352 -NRIIRPSAEYTGVEQRAFVPLEQR 375 +I RP + G QR PL +R Sbjct: 408 EQKIGRPRQLFVGESQREATPLAKR 432 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: 403 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: 432 Length adjustment: 31 Effective length of query: 344 Effective length of database: 401 Effective search space: 137944 Effective search space used: 137944 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