GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Paucidesulfovibrio gracilis DSM 16080

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_900167125.1:WP_078715956.1
          Length = 247

 Score =  119 bits (299), Expect = 5e-32
 Identities = 78/240 (32%), Positives = 114/240 (47%), Gaps = 2/240 (0%)

Query: 17  LVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQADLRNVE 76
           LVTGG  GIG A  E  A  G  V    ++   +     +  A  G     +Q D  + E
Sbjct: 9   LVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSDRE 68

Query: 77  AVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMCQAVAPH 136
           AV +   + +     +  LVNNA       L  +  E WD  L +NL   F   Q  A  
Sbjct: 69  AVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFSCLQEAAKI 128

Query: 137 MQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNAILPGMI 196
           M RQ GGSI+N SS+   +       Y  AKAG+IGLTK+ A +L    +RVNA+ PG I
Sbjct: 129 MARQRGGSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAPGFI 188

Query: 197 VTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMIIDGGVF 256
            T+  +   L E+++  M+    L R+    D+     FLA + +  +T Q + ++GG++
Sbjct: 189 ETDMTKD--LPEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLAVNGGMY 246


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: 142
Number of extensions: 6
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: 247
Length adjustment: 24
Effective length of query: 232
Effective length of database: 223
Effective search space:    51736
Effective search space used:    51736
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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