GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Jannaschia aquimarina GSW-M26

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_043918249.1 jaqu_RS07060 3-hydroxybutyrate dehydrogenase

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_000877395.1:WP_043918249.1
          Length = 261

 Score =  125 bits (314), Expect = 9e-34
 Identities = 82/262 (31%), Positives = 129/262 (49%), Gaps = 19/262 (7%)

Query: 6   SQFPDLRDRGVLVTGGGSGIGAALVEAFARQGARV---AFVDIAAESSLALCEKVAAQTG 62
           S +  L+ +  +VTG  SGIG  +  +FA  G  V   +F D   +   AL +++AA+T 
Sbjct: 2   SDYAALKGKTAIVTGSNSGIGLGIARSFAAAGLDVVLNSFTD--RDEDHALAKEIAAETR 59

Query: 63  QAPHFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVN 122
               +I+ADL N +  RA  ++A    G+  VLVNNA       ++      WD  +++N
Sbjct: 60  TKTRYIKADLSNGDEARALVEQA----GACDVLVNNAGIQHVAGIDEFPAAKWDAIIAIN 115

Query: 123 LRHLFFMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLG 182
           L   F    A  P M++ G G ++N +S   L   P   AY  AK G++G+TK +A +  
Sbjct: 116 LSSAFHTTAAALPMMRKAGWGRVINIASAHGLTASPFKSAYVAAKHGVVGMTKVVALETA 175

Query: 183 PDNIRVNAILPGMIVT--------ERQRRLWLTEESIAR--MQERQCLKRMLVADDLVGP 232
            + I  NAI PG ++T        +   +  +  E+  R  + +RQ  K     D L G 
Sbjct: 176 EEPITANAICPGYVMTPLVESQIPDTMEKYGMDRETAIREVLLQRQPSKEFATTDQLGGT 235

Query: 233 CLFLASDSSAAMTAQAMIIDGG 254
            LFL +D +A +T   + +DGG
Sbjct: 236 ALFLCTDHAAQITGTTISVDGG 257


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: 97
Number of extensions: 6
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: 261
Length adjustment: 24
Effective length of query: 232
Effective length of database: 237
Effective search space:    54984
Effective search space used:    54984
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