GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pseudomonas fluorescens FW300-N1B4

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate Pf1N1B4_4943 Oxidoreductase, short chain dehydrogenase/reductase family

Query= SwissProt::Q92RN6
         (256 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4943
          Length = 263

 Score =  117 bits (293), Expect = 2e-31
 Identities = 79/245 (32%), Positives = 121/245 (49%), Gaps = 4/245 (1%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70
           L  +  L+TG  SGIG A+  AFAR+GA VA   +          +   Q G+    +  
Sbjct: 18  LEGKIALITGADSGIGRAVAIAFAREGADVAIAYLNETEDAQETARWVEQAGRQSLLLPG 77

Query: 71  DLRNVEAVRAAADEAVAKLGSVRVLVNNAA-RDDRQALEAVTEESWDESLSVNLRHLFFM 129
           D+      +A  D+ + + G + +LVNNAA +   + LE + +E W  +  VN+  +F +
Sbjct: 78  DVAQKAHCQALVDKTIERFGRIDILVNNAAFQMTHENLEDIPDEEWVMTFDVNITAMFRL 137

Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVN 189
           CQA   HM  + G SI+N SS+   +  P + AY+T K  I   +  LA  LGP NIRVN
Sbjct: 138 CQAALKHM--KPGSSIINTSSVNSDMPKPTLLAYATTKGAIANFSAGLAQMLGPKNIRVN 195

Query: 190 AILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAM 249
           ++ PG I T       + EE +     +  L R     ++    + LASD ++ +T Q  
Sbjct: 196 SVAPGPIWTPLIVST-MPEEDVQNFGAQTPLGRPGQPVEVAPIYVLLASDEASYITGQRY 254

Query: 250 IIDGG 254
            + GG
Sbjct: 255 GVTGG 259


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: 140
Number of extensions: 8
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: 263
Length adjustment: 24
Effective length of query: 232
Effective length of database: 239
Effective search space:    55448
Effective search space used:    55448
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.

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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