GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Pseudomonas fluorescens FW300-N2E3

Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate AO353_11880 AO353_11880 glucose-1-phosphate thymidylyltransferase

Query= SwissProt::D4GYH1
         (243 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_11880
          Length = 291

 Score = 92.8 bits (229), Expect = 7e-24
 Identities = 75/241 (31%), Positives = 119/241 (49%), Gaps = 9/241 (3%)

Query: 1   MQAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEII 60
           M+ +VLA G GTRL P+T    K ++ V  KP++ +    L+  G ++++V+   +    
Sbjct: 2   MKGIVLAGGSGTRLHPITLGVSKQLLPVYDKPMIYYPISVLMLAGIKEILVISTPQDLPQ 61

Query: 61  IQHY--DDEYRGVPITYAHQREQKGLAHALLTVEDHIDEDFM-LMLGDNIFNA-NLGDVV 116
            ++   D    GV  +YA Q    GLA A L  E+ I +D + L+LGDNIF+  +  + +
Sbjct: 62  YRNLLGDGSQFGVHFSYAEQPSPDGLAQAFLIGEEFIGDDSVCLILGDNIFHGQHFTEKL 121

Query: 117 KRQREDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFYTFTP 176
           +R  E    A      V   +  R+GV   +D G    + EKP  P S+  +TG Y +  
Sbjct: 122 QRAAEHTGGATVFGYWVK--DPQRFGVIDFDDQGNALSIEEKPLHPKSSYAVTGLYFYDN 179

Query: 177 AIFHACHLVQPSNRGEYEISEAIDLLIRSG--RTIDAIRIDGWRLDIGYPEDRDEAEQRL 234
           ++      V+PS RGE EI++  +  ++ G  R     R   W LD G  +   EA Q +
Sbjct: 180 SVVEIAKAVKPSARGELEITDINNAYLQRGDLRVERFGRGFAW-LDTGTHDSLLEASQYV 238

Query: 235 Q 235
           Q
Sbjct: 239 Q 239


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: 179
Number of extensions: 10
Number of successful extensions: 4
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: 291
Length adjustment: 25
Effective length of query: 218
Effective length of database: 266
Effective search space:    57988
Effective search space used:    57988
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 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