GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Dinoroseobacter shibae DFL-12

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate 3607835 Dshi_1243 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= SwissProt::Q92RN6
         (256 letters)



>FitnessBrowser__Dino:3607835
          Length = 258

 Score =  236 bits (601), Expect = 5e-67
 Identities = 123/251 (49%), Positives = 162/251 (64%), Gaps = 2/251 (0%)

Query: 5   SSQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQA 64
           ++ F DL    V VTGGGSGIGAAL + F  QGA+VAF  I    + A   K+ A  G+A
Sbjct: 6   NATFHDLDGASVFVTGGGSGIGAALTDGFLAQGAQVAF--IGRSDASAFVAKMRAAHGRA 63

Query: 65  PHFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLR 124
           P F+Q D+ + +A+RAA  +A A  G +  LVNNAA D R +   VT E WD+  ++NL+
Sbjct: 64  PLFVQGDITDTDALRAAIAQATAAHGPITALVNNAANDKRHSTAEVTPEFWDQMQAINLK 123

Query: 125 HLFFMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPD 184
             FF  QAV P M   GGG+IVNFSSI++++     PAY+ A AGI GLT+SLA + GPD
Sbjct: 124 AYFFAAQAVTPGMAEAGGGAIVNFSSISYMMGNAGYPAYTAANAGITGLTRSLAREFGPD 183

Query: 185 NIRVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAM 244
            IRVNA+ PG ++T +Q  +W T E +A   +RQCLK  L  +D+V   LFLAS +S  M
Sbjct: 184 GIRVNALAPGWVLTPKQLEMWATPEDLAAHLDRQCLKTHLAPEDIVEATLFLASGASKMM 243

Query: 245 TAQAMIIDGGV 255
           T Q M++DGGV
Sbjct: 244 TGQCMVVDGGV 254


Lambda     K      H
   0.321    0.133    0.377 

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: 167
Number of extensions: 4
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: 256
Length of database: 258
Length adjustment: 24
Effective length of query: 232
Effective length of database: 234
Effective search space:    54288
Effective search space used:    54288
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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