GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Erythrobacter gangjinensis K7-2

Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate WP_047006779.1 AAW01_RS07470 glucose-1-phosphate thymidylyltransferase RfbA

Query= SwissProt::D4GYH1
         (243 letters)



>NCBI__GCF_001010925.1:WP_047006779.1
          Length = 293

 Score = 90.9 bits (224), Expect = 3e-23
 Identities = 66/215 (30%), Positives = 104/215 (48%), Gaps = 16/215 (7%)

Query: 2   QAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEIII 61
           + ++LA G GTRL PLT    K ++ V  KP++ +    L+  G   ++++   + +   
Sbjct: 4   KGIILAGGSGTRLYPLTRGVSKQLMPVYDKPMIYYPLSTLMLAGIRDILIITTPEDQPQF 63

Query: 62  QHY--DDEYRGVPITYAHQREQKGLAHALLTVEDHIDEDFM------LMLGDNIFNAN-L 112
           Q    D    GV ++YA Q    GLA A      HI  DF+      L+LGDNIF  + L
Sbjct: 64  QRVLGDGSDFGVALSYAVQPNPDGLAQAF-----HIGADFIGGDASALVLGDNIFYGHGL 118

Query: 113 GDVVKRQREDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFY 172
            +V+       A A+     V   + + YGV   +  G  + + EKPE+P SN  +TG Y
Sbjct: 119 PEVLHSAHARDAGASVFAYRVK--DPTAYGVVAFDANGRASSIEEKPEKPKSNYAVTGLY 176

Query: 173 TFTPAIFHACHLVQPSNRGEYEISEAIDLLIRSGR 207
            +   +      ++PS RGE EI++   L +  G+
Sbjct: 177 FYDDTVVERARALKPSARGELEITDLNRLYMDHGQ 211


Lambda     K      H
   0.318    0.138    0.404 

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: 216
Number of extensions: 12
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: 243
Length of database: 293
Length adjustment: 25
Effective length of query: 218
Effective length of database: 268
Effective search space:    58424
Effective search space used:    58424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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