GapMind for catabolism of small carbon sources

 

Aligments for a candidate for scrK in Shewanella amazonensis SB2B

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 6937023 Sama_1197 putative ROK-family protein (RefSeq)

Query= SwissProt::P23917
         (302 letters)



>lcl|FitnessBrowser__SB2B:6937023 Sama_1197 putative ROK-family
           protein (RefSeq)
          Length = 335

 Score =  158 bits (399), Expect = 2e-43
 Identities = 105/315 (33%), Positives = 156/315 (49%), Gaps = 25/315 (7%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQ---- 56
           M  G+D+GGTK  +    D+   + R ++PTP  DY Q ++ +   ++ A++   Q    
Sbjct: 1   MHYGLDIGGTKIALALFDDSMACVERWQIPTPVADYGQFLDEVCAQIERADELAQQHSGV 60

Query: 57  --------RGTVGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANC 108
                   +G+VG+ +PG I    G V ++N   LNG+   ++L+ RL R V L ND  C
Sbjct: 61  TVQPAEVSKGSVGIALPGVILS-DGTVLSSNVPCLNGRTVAQELTVRLGRPVALGNDCRC 119

Query: 109 LAVSEAVDGAAAGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDEL 168
            A+SE + GA  G + V  VI+GTG G GV  + +  +G +  AGE+GH  LP      +
Sbjct: 120 FALSEVLLGAGVGFERVLGVILGTGLGGGVCISQKLILGAHCLAGEFGHIGLP----ASV 175

Query: 169 RYREEVP---CYCGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAEL-- 223
             + ++P   C CG  GC ET++SGTG    Y+   G A      + L +     AE   
Sbjct: 176 IIKHQLPLFECGCGLTGCAETYVSGTGLGRLYQHFGGTA---DTYVWLADYRSGKAEAIS 232

Query: 224 ALRRYELRLAKSLAHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRK 283
               Y   L   LA  +  LDPD +V GGG+S V  +   +     + +F        R 
Sbjct: 233 TFDAYMDALGSVLAGQILSLDPDCLVFGGGISEVKEIIAALPDATARHLFASAKLPEFRV 292

Query: 284 AKHGDSSGVRGAAWL 298
           A+ G +SGVRGAA L
Sbjct: 293 AEFGAASGVRGAALL 307


Lambda     K      H
   0.318    0.137    0.418 

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: 356
Number of extensions: 16
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: 302
Length of database: 335
Length adjustment: 27
Effective length of query: 275
Effective length of database: 308
Effective search space:    84700
Effective search space used:    84700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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