GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Phyllobacterium leguminum ORS 1419

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_110751435.1 C7477_RS09440 L-iditol 2-dehydrogenase

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_003217235.1:WP_110751435.1
          Length = 258

 Score =  131 bits (329), Expect = 2e-35
 Identities = 90/258 (34%), Positives = 131/258 (50%), Gaps = 22/258 (8%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70
           L  +   +TG   GIG A  EAFAR+GA VA  DI     L   ++ AA+ G+  + +Q 
Sbjct: 5   LEGKSAFITGAARGIGFAFAEAFAREGATVALADI----DLDRAQESAAKIGERAYAVQI 60

Query: 71  DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130
           D+ ++ ++  A  EAVAK G + +LVNNAA  D   +  +T ES++   +VN+  + F  
Sbjct: 61  DVTDIASIERAVAEAVAKTGGIDILVNNAALFDMAPMVEITRESFERLYAVNVHGVLFTM 120

Query: 131 QAVAPHMQRQG-GGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189
           QAVA  M  +G GG I+N +S A       +  Y + KA +I LT+S    L    I VN
Sbjct: 121 QAVARAMIARGRGGKIINMASQAGRRGEALVAVYCSTKAAVISLTQSAGLDLIRHGINVN 180

Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCL--KRMLVA-----------DDLVGPCLFL 236
           AI PG++  E     W   +++    E + L  K+ LV            +DL G  +FL
Sbjct: 181 AIAPGVVDGEH----WAGVDALFAKHENRPLGEKKRLVGEAVPFGRMGRPEDLTGMAIFL 236

Query: 237 ASDSSAAMTAQAMIIDGG 254
           A   S  + AQ   +DGG
Sbjct: 237 AGPESDYVVAQTYNVDGG 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: 122
Number of extensions: 6
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: 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 24 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