Align Mannokinase (EC 2.7.1.7) (characterized)
to candidate 6937023 Sama_1197 putative ROK-family protein (RefSeq)
Query= reanno::Smeli:SMc03109 (298 letters) >FitnessBrowser__SB2B:6937023 Length = 335 Score = 169 bits (427), Expect = 1e-46 Identities = 113/311 (36%), Positives = 155/311 (49%), Gaps = 16/311 (5%) Query: 1 MFIGIDWGGTKMEVIALDRDGETRARHRVPTPTSGYEDCIRAVVELVASAESTAGE---- 56 M G+D GGTK+ + D R ++PTP + Y + V + A+ A + Sbjct: 1 MHYGLDIGGTKIALALFDDSMACVERWQIPTPVADYGQFLDEVCAQIERADELAQQHSGV 60 Query: 57 --------RGSIGIGIPGSPNPRTGIVRNSNAVLINGKPLGRDLAAALGREVRLANDANC 108 +GS+GI +PG G V +SN +NG+ + ++L LGR V L ND C Sbjct: 61 TVQPAEVSKGSVGIALPGVILS-DGTVLSSNVPCLNGRTVAQELTVRLGRPVALGNDCRC 119 Query: 109 LAVSEAVDGAGKDAGVVFGVIVGTGHGGGLAIGKKVHAGYQGVAAEIGHYPLP--WMTKD 166 A+SE + GAG V GVI+GTG GGG+ I +K+ G +A E GH LP + K Sbjct: 120 FALSEVLLGAGVGFERVLGVILGTGLGGGVCISQKLILGAHCLAGEFGHIGLPASVIIKH 179 Query: 167 EYPGHRCWCGKLGCLDMYACGTGLELDYRMTTGTDRRGRDIIEAKRAGDPVAIGVYGRFV 226 + P C CG GC + Y GTGL Y+ GT + + R+G AI + ++ Sbjct: 180 QLPLFECGCGLTGCAETYVSGTGLGRLYQHFGGTADTYVWLAD-YRSGKAEAISTFDAYM 238 Query: 227 DRLARSLALLTNIVDPDVFVLGGGMSNVDEIYGELPASITRYLFGDSFETPIRKAVHGDS 286 D L LA +DPD V GGG+S V EI LP + R+LF + R A G + Sbjct: 239 DALGSVLAGQILSLDPDCLVFGGGISEVKEIIAALPDATARHLFASAKLPEFRVAEFGAA 298 Query: 287 SGVRGAAWLWK 297 SGVRGAA L K Sbjct: 299 SGVRGAALLGK 309 Lambda K H 0.319 0.140 0.436 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: 258 Number of extensions: 20 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: 298 Length of database: 335 Length adjustment: 27 Effective length of query: 271 Effective length of database: 308 Effective search space: 83468 Effective search space used: 83468 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 (21.7 bits) S2: 48 (23.1 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