GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Desulfovibrio vulgaris Miyazaki F

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate 8501727 DvMF_2444 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= SwissProt::Q92RN6
         (256 letters)



>FitnessBrowser__Miya:8501727
          Length = 306

 Score =  105 bits (261), Expect = 1e-27
 Identities = 87/283 (30%), Positives = 127/283 (44%), Gaps = 33/283 (11%)

Query: 4   PSSQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQ--- 60
           P S    L  R  LVTGG  GIG  +VE     G RVA +D  AE+   L   ++A+   
Sbjct: 18  PLSAAHPLAGRVALVTGGAQGIGRGIVEHLLACGMRVAAMDADAEALAELAGALSAELAA 77

Query: 61  ---------------TGQAPH---FIQADLRNVEAVRAAADEAVA----KLGSVRVLVNN 98
                             APH   F    L    A +A AD  VA    + G + +LVNN
Sbjct: 78  EPVADNEASLPAHPDASAAPHSPTFPMLTLHGSVADQADADRCVAATVARFGGLHLLVNN 137

Query: 99  AARDDRQA----LEAVTEESWDESLSVNLRHLFFMCQAVAPHMQRQGGGSIVNFSSIAFL 154
           A   +  +    + A+  + W   L VNL     M +A  PH+ R   G++VN +S   +
Sbjct: 138 AGIANPHSGPADVAAMDMDRWQHMLDVNLTGPMRMVRAAVPHL-RAARGAVVNIASTRAV 196

Query: 155 LNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNAILPGMIVTERQRRLWLTEESIARM 214
            + P   AY+ +K G++ LT +LA  LGP+ + VN I PG I     R+    E  +   
Sbjct: 197 QSEPHTEAYAASKGGLVALTHALAVSLGPE-VPVNCISPGWIEVRHLRKAAHRETPVHTD 255

Query: 215 QER--QCLKRMLVADDLVGPCLFLASDSSAAMTAQAMIIDGGV 255
            +R    + R+    D+     FLA D +  +T Q  ++DGG+
Sbjct: 256 ADRAQHPVGRVGTVRDVAALVAFLAGDDAGFVTGQNWLVDGGM 298


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: 176
Number of extensions: 10
Number of successful extensions: 3
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: 306
Length adjustment: 26
Effective length of query: 230
Effective length of database: 280
Effective search space:    64400
Effective search space used:    64400
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