GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mak in Shewanella amazonensis SB2B

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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