GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Shewanella amazonensis SB2B

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate 6936094 Sama_0291 carbohydrate kinase (RefSeq)

Query= reanno::SB2B:6936373
         (343 letters)



>FitnessBrowser__SB2B:6936094
          Length = 337

 Score =  315 bits (806), Expect = 1e-90
 Identities = 172/326 (52%), Positives = 211/326 (64%), Gaps = 11/326 (3%)

Query: 3   KRVLCFGEALIDFLCTGSDEDDGLMLPCYRQYPGGAPANAAVAVAKLGGQARFAGLVGKD 62
           K++LCFGEALIDFL  G+     L LP +RQYPGGAPANAAVAVA+LGG A FAG VG+D
Sbjct: 2   KKILCFGEALIDFLNIGAGHQGPLTLPEFRQYPGGAPANAAVAVARLGGHACFAGQVGQD 61

Query: 63  TFGDFLANSLVRYGVDISLLGRHSSAPTSLAFVHLNDDGDRSFSFYRDGGADTLFDASVA 122
            FG+FLA +L  YGVD   L +H  A T+LAFV L+ DGDRSFSF+R   AD +      
Sbjct: 62  PFGEFLAAALQEYGVDTRFLLKHPQAKTALAFVMLDADGDRSFSFHRHETADVILTEEQV 121

Query: 123 EASWFENTAVLHLCSNTLTTAQSAEATLTMADRAVAAGLAVSVDVNLRHNLWQGGAACKA 182
              WF    ++H CSNTLTT Q A+ T  + +RA  AG  +S DVNLRHNLWQ GAA  A
Sbjct: 122 SDDWFSGDTIVHFCSNTLTTPQIAQCTRHVLNRAKHAGNLISFDVNLRHNLWQQGAADSA 181

Query: 183 TVMSLVHKAHVLKFAQEELEYLAGSEPQGFIQQLLDSGCKLLLITDGGNPIRAFTGKQCL 242
            V  LV +A V+KF+++ELEYLA  +   +I Q L S C+LLL+TDG N I  FT +   
Sbjct: 182 LVNELVKQADVVKFSRDELEYLAAGDTATYISQCLASQCQLLLVTDGANRIDYFTAEHQG 241

Query: 243 TLPVPKMDVVDTTAGGDGFIGGLLHRIARDGLDTLLESETTFKDA------LGFAIGCGA 296
            +  PK+ VVDTTAGGD FIGG L+     GL  +  ++  F D       L FA  CGA
Sbjct: 242 HIQPPKVKVVDTTAGGDAFIGGFLY-----GLGCMENAKAVFADTRELESLLLFATHCGA 296

Query: 297 LAVSRPGAFPALPGLAEAEAFQASMG 322
            AV++PGAFPALPGLA+ +      G
Sbjct: 297 YAVTQPGAFPALPGLADIQTQVTQQG 322


Lambda     K      H
   0.321    0.136    0.411 

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: 334
Number of extensions: 14
Number of successful extensions: 2
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: 343
Length of database: 337
Length adjustment: 28
Effective length of query: 315
Effective length of database: 309
Effective search space:    97335
Effective search space used:    97335
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 (21.8 bits)
S2: 49 (23.5 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