Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_011385182.1 AMB_RS14105 citrate (Si)-synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_000009985.1:WP_011385182.1 Length = 438 Score = 197 bits (501), Expect = 5e-55 Identities = 128/380 (33%), Positives = 199/380 (52%), Gaps = 27/380 (7%) Query: 19 QTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRD 78 ++A++ + L +RGY + DLA + F EVAY +L GELP Q + + + Sbjct: 62 KSAITYIDGDAGVLLHRGYAISDLAENCSFLEVAYAILKGELPNAEQKTKFESDITRHSM 121 Query: 79 LPQALKEVLERIPADAHPMDVMRTGCSFLGNL----EPEQDFSQQHDK---TDRLLAAFP 131 L + + D+HPM VM C +G + D + H + + RL+A P Sbjct: 122 LNEQISFFFRGFRRDSHPMAVM---CGVVGAMAAFYHDSVDINDPHQRMIASYRLVAKMP 178 Query: 132 AIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGK-----KPSELHVKVMNVSLILYAE 186 I+ + Y++S QGQ +++S +FLH++ K S + + M+ LIL+A+ Sbjct: 179 TIVAWAYKYS-QGQPFMYPQNKLSYAENFLHMMFATPCEEYKVSPVLARAMDRILILHAD 237 Query: 187 HEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIEGT 246 HE NAST T R+ S+ ++ F+CI A I SL GP HGGANEA +EM+ S E Sbjct: 238 HEQNASTSTVRLAGSSGANPFACIAAGIASLWGPAHGGANEAVLEMLHEIGSVDRIPEYI 297 Query: 247 LGMLARKD--KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPVSEAIDKTMW 302 + D ++MGFGH +YK+ DPR +++ ++ +E+G D L ++ +++ Sbjct: 298 KKAKDKDDPFRLMGFGHRVYKNYDPRAKIMAKTCHEVLNELGNHDEPLLKLAMELERIAL 357 Query: 303 E-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRA--NNRII 355 E ++KLFPN DFY + MGIPT++FT +F +R GW A E + +I Sbjct: 358 EDPYFVERKLFPNVDFYSGIIFRAMGIPTQVFTCLFALARTVGWIAQWNEMLTDPDQKIG 417 Query: 356 RPSAEYTGVEQRKFVPIEQR 375 RP Y G QR FVP+ +R Sbjct: 418 RPRQLYVGPAQRDFVPLAKR 437 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: 393 Number of extensions: 18 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: 438 Length adjustment: 31 Effective length of query: 344 Effective length of database: 407 Effective search space: 140008 Effective search space used: 140008 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