GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Shewanella sp. ANA-3

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 7025639 Shewana3_2790 fructokinase (RefSeq)

Query= SwissProt::P23917
         (302 letters)



>FitnessBrowser__ANA3:7025639
          Length = 306

 Score =  362 bits (929), Expect = e-105
 Identities = 180/307 (58%), Positives = 219/307 (71%), Gaps = 12/307 (3%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60
           +R+GIDLGGTK E++AL + G +L+R R+ TPRD Y+ T+  I  LV+ AE   G++GTV
Sbjct: 2   IRMGIDLGGTKIELVALSEEGNELFRKRINTPRD-YQGTLNAIVDLVNEAEATLGEKGTV 60

Query: 61  GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120
           G+GIPG ISPY+G+VKNANSTW+NG P D +L   L REVR+ANDANC AVSEAVDGAAA
Sbjct: 61  GVGIPGVISPYSGLVKNANSTWINGHPLDVNLGELLGREVRVANDANCFAVSEAVDGAAA 120

Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180
           G   VF VIIGTGCGAGVA NG+ H GGNG  GEWGHNPLPWM ++E        C+CG 
Sbjct: 121 GKSVVFGVIIGTGCGAGVAINGKVHAGGNGIGGEWGHNPLPWMTKEEF---NTTRCFCGN 177

Query: 181 QGCIETFISGTGFAMDYRRLSGHAL--------KGSEIIRLVEESDPVAELALRRYELRL 232
             CIETFISGTGF  DY      A+         G+EI+ LV+  D +A  A  RY  RL
Sbjct: 178 PDCIETFISGTGFVRDYNEALSRAVNVQAAPAKSGTEIMALVDAGDEMAIAAFDRYMDRL 237

Query: 233 AKSLAHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGV 292
           A+SLAHV+N+LDPD IVLGGGMSN++  Y  +  L+ ++V G EC TPV +  +G SSGV
Sbjct: 238 ARSLAHVINMLDPDAIVLGGGMSNIEATYPRLPALLTRYVVGRECRTPVVQNLYGCSSGV 297

Query: 293 RGAAWLW 299
           RGAAWLW
Sbjct: 298 RGAAWLW 304


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: 371
Number of extensions: 17
Number of successful extensions: 5
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: 306
Length adjustment: 27
Effective length of query: 275
Effective length of database: 279
Effective search space:    76725
Effective search space used:    76725
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