GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Pseudomonas fluorescens GW456-L13

Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate PfGW456L13_1205 Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24)

Query= BRENDA::P74285
         (388 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1205
          Length = 223

 Score = 97.1 bits (240), Expect = 4e-25
 Identities = 75/235 (31%), Positives = 112/235 (47%), Gaps = 30/235 (12%)

Query: 1   MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60
           MKAMILAAGKG R+RP+T T PKP++     P++E+ L  L   GF  I++N + L ++I
Sbjct: 1   MKAMILAAGKGERMRPLTLTTPKPLVRAGGVPLIEYHLRALAAAGFTDIVINHAWLGQQI 60

Query: 61  ESYFRDGQRFGVQIAYSFEGNIVD-GDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDA 119
           E Y  DG R+GV I YS EG  ++ G  + +AL   G            D+ FVV+ GD 
Sbjct: 61  EDYLGDGSRYGVSIQYSAEGEPLETGGGIFRALPLLG------------DEAFVVVNGDI 108

Query: 120 LIDLDLTTAVKLHREKGAIA-TIITKTVPQELVSSYGVVVTDDNGKILTFQEKPAVEEAL 178
             D D +    LH+    +A  ++    P      +G+V T    ++L  Q         
Sbjct: 109 WTDYDFSV---LHQPINGLAHLVLVSNPPHHPAGDFGLVET----RVLDGQ------PGA 155

Query: 179 STEINTGIYIFEPEVIDYIPSGQEYDLGGDLFPKLVDSGLPFYAVNMDFEWVDIG 233
            T   +GI +  P++ D    G  + L   L   + D  +      +   WVD+G
Sbjct: 156 GTLTYSGIAVLHPQLFDGCTEG-AFKLAPLLRKAMADGQVT--GEQLRGHWVDVG 207


Lambda     K      H
   0.321    0.141    0.418 

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: 218
Number of extensions: 16
Number of successful extensions: 1
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: 388
Length of database: 223
Length adjustment: 26
Effective length of query: 362
Effective length of database: 197
Effective search space:    71314
Effective search space used:    71314
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 (21.8 bits)
S2: 48 (23.1 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