GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Acidovorax sp. GW101-3H11

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate Ac3H11_2074 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= SwissProt::Q92RN6
         (256 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2074
          Length = 249

 Score =  135 bits (340), Expect = 8e-37
 Identities = 88/249 (35%), Positives = 136/249 (54%), Gaps = 9/249 (3%)

Query: 11  LRDRGVLVTGGG--SGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFI 68
           L+++  ++TGG   +G+G A     A QGA+VA +D+            AA+ G+    +
Sbjct: 3   LKNQVAIITGGAGINGLGFATARLMAEQGAKVAILDLEGADPAG----AAARLGEGHLGL 58

Query: 69  QADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFF 128
            AD+ +  +  AAA +  A  G +  LVNNA          +T   +D  L+V+LR   +
Sbjct: 59  VADVTDKASCEAAAAQVHAHFGRIDTLVNNAGITQPVKTLEITGADYDRILNVSLRGTLY 118

Query: 129 MCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEI--PAYSTAKAGIIGLTKSLAGKLGPDNI 186
           M QAV P ++ Q  GSI+  SS++       +  P YS AKAG++GL +++A + GP+NI
Sbjct: 119 MSQAVLPTLRAQQSGSIICISSVSAQRGGGILGGPHYSAAKAGVLGLARAMAREFGPENI 178

Query: 187 RVNAILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTA 246
           R+N I PG+I T+  +   LTEE  A + E   L R+  ADD+ G C+FLAS  S   T 
Sbjct: 179 RINCITPGLIGTDIIKGK-LTEEKKAEIAETIPLARLGRADDIAGACVFLASPLSTYCTG 237

Query: 247 QAMIIDGGV 255
             + ++GG+
Sbjct: 238 ITLDVNGGM 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: 144
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: 249
Length adjustment: 24
Effective length of query: 232
Effective length of database: 225
Effective search space:    52200
Effective search space used:    52200
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 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