Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate BWI76_RS08385 BWI76_RS08385 citrate (Si)-synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >FitnessBrowser__Koxy:BWI76_RS08385 Length = 427 Score = 196 bits (499), Expect = 8e-55 Identities = 132/366 (36%), Positives = 191/366 (52%), Gaps = 39/366 (10%) Query: 32 LTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRDLPQALKEVLERIP 91 L +RG+ + LA D+ + EV Y+LL GE PTQAQ D + + + + + + + Sbjct: 67 LLHRGFPIDQLATDSNYLEVCYILLNGEKPTQAQYDEFKTIVTRHTMIHEQITRLFHAFR 126 Query: 92 ADAHPMDVMRTGCSFLGNLEPEQDFSQQHDKTD------------RLLAAFP--AIMCYW 137 D+HPM VM C G L + HD D RLL+ P A MCY Sbjct: 127 RDSHPMAVM---CGITGALA-----AFYHDSLDVNNPRHRDIAAFRLLSKMPTMAAMCYK 178 Query: 138 YRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVSLILYAEHEFNAS 192 Y GQ +++S G+FL+++ + V + M+ LIL+A+HE NAS Sbjct: 179 YSI---GQPFVYPRNDLSYAGNFLNMMFSTPCEKYEVNPILERAMDRILILHADHEQNAS 235 Query: 193 TFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGTLGMLAR 252 T T R S+ ++ F+CI A I SL GP HGGANEAA++M+E SS + E + Sbjct: 236 TSTVRTAGSSGANPFACIAAGIASLWGPAHGGANEAALKMLEEISSVEHIPEFVRRAKDK 295 Query: 253 KD--KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPVSE----AIDKTMWEQ 304 D ++MGFGH +YK+ DPR V++ ++ E+G D +L E A++ + + Sbjct: 296 NDSFRLMGFGHRVYKNYDPRATVMRETCHEVLKELGTKDDLLEVAMELEHIALNDPYFIE 355 Query: 305 KKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANN-RIIRPSAEYTG 363 KKL+PN DFY MGIP+ +FT IF +R GW AH E ++ +I RP YTG Sbjct: 356 KKLYPNVDFYSGIILKAMGIPSSMFTVIFAMARTVGWIAHWNEMHSDGMKIARPRQLYTG 415 Query: 364 VEQRKF 369 E+R F Sbjct: 416 YEKRDF 421 Lambda K H 0.321 0.135 0.406 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: 392 Number of extensions: 24 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: 375 Length of database: 427 Length adjustment: 31 Effective length of query: 344 Effective length of database: 396 Effective search space: 136224 Effective search space used: 136224 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 (21.9 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