GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937023
          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 (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