GapMind for catabolism of small carbon sources

 

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

Align UDP-glucose 4-epimerase; UDP-galactose 4-epimerase; Uridine diphosphate galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate 7026960 Shewana3_4089 NAD-dependent epimerase/dehydratase (RefSeq)

Query= SwissProt::A0R5C5
         (313 letters)



>FitnessBrowser__ANA3:7026960
          Length = 335

 Score =  159 bits (403), Expect = 7e-44
 Identities = 110/334 (32%), Positives = 170/334 (50%), Gaps = 29/334 (8%)

Query: 1   MRTLVTGAAGFIGSTLVDRLLADGHGVVGLDDLSSG-----RAENLHSAENSDKFEFVKA 55
           M+ LVTGAAGFIG+ + +RL A GH VVG+D+L+       +   L   E    F F+K 
Sbjct: 1   MKYLVTGAAGFIGAKVSERLCAQGHEVVGIDNLNDYYDVGLKLARLAPLEALSNFRFIKL 60

Query: 56  DIVDAD-LTGLLAEFKPEVIFHLAAQISVKRSVDDPPFDATVNVVGTVRLAEAARLAGVR 114
           D+ D D +  L AE     + HLAAQ  V+ S+D+P   A  N+VG + + E  R   + 
Sbjct: 61  DLADRDGIATLFAEQGFRRVIHLAAQAGVRYSLDNPLAYADSNLVGHLTILEGCRHHKIE 120

Query: 115 KVVHTSSGGSVYGTPPAYP-TSEDMPVNPASPYAAGKVAGEVYLNMYRNLYDLDCSHIAP 173
            +V+ SS  SVYG     P ++ED   +P S YAA K A E+  + Y +LY L  + +  
Sbjct: 121 HLVYASS-SSVYGLNQKMPFSTEDSVDHPISLYAATKKANELMSHTYSHLYQLPTTGLRF 179

Query: 174 ANVYGPRQDPHGEAGVVAIFSEALLAGRTTKIFGDGSDTRDYVFVDDVVDAFVR------ 227
             VYGP   P      +  F++A+LAG    ++  G  +RD+ ++DD+V+  +R      
Sbjct: 180 FTVYGPWGRPD---MALFKFTKAILAGDIIDVYNHGDLSRDFTYIDDIVEGIIRVQDKPP 236

Query: 228 ---------AGGPAGGG---QRFNVGTGVETSTRELHTAIAGAVGAPDEPEFHPPRLGDL 275
                     G PA      + FN+G G      +  TA+  A+G     +F P + GD+
Sbjct: 237 RPTPDWRVETGTPANSSAPYRVFNIGNGSPVQLLDFITALESALGIEANKQFLPMQPGDV 296

Query: 276 RRSRLDNTRAREVLGWQPQVALAEGIAKTVEFFR 309
             +  D     + +G++PQV +  G+ + VE++R
Sbjct: 297 HSTWADTEDLFKAVGYKPQVDINTGVGRFVEWYR 330


Lambda     K      H
   0.317    0.136    0.396 

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: 265
Number of extensions: 13
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: 313
Length of database: 335
Length adjustment: 28
Effective length of query: 285
Effective length of database: 307
Effective search space:    87495
Effective search space used:    87495
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 (21.6 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