GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Magnetospirillum magneticum AMB-1

Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate WP_011382506.1 AMB_RS00300 glucose-1-phosphate thymidylyltransferase

Query= SwissProt::D4GYH1
         (243 letters)



>NCBI__GCF_000009985.1:WP_011382506.1
          Length = 296

 Score = 87.8 bits (216), Expect = 2e-22
 Identities = 72/230 (31%), Positives = 113/230 (49%), Gaps = 10/230 (4%)

Query: 2   QAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEIII 61
           + +VLA G GTRL PLT    K ++ V  KP++ +    L+ LG  + ++++    ++  
Sbjct: 7   KGIVLAGGTGTRLHPLTLVTNKHLLPVFDKPMIYYPLTTLM-LGGIRDILIISTPDDLPR 65

Query: 62  QHY---DDEYRGVPITYAHQREQKGLAHALLTVEDHIDEDFM-LMLGDNIFNANLGDVVK 117
                 D    G+ ++YA Q +  GL  A L  E+ I    + LMLGDNIF  +    + 
Sbjct: 66  FERLLGDGRRWGINLSYAEQPKPAGLPQAFLIGEEFIGGARVGLMLGDNIFYGHGLPPLV 125

Query: 118 RQREDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFYTFTPA 177
           +Q  +   A      V   +  R+GV   +  G+   + EKP+ P SN  +TG Y +   
Sbjct: 126 QQAAEGTGATVFAHTVR--DPERFGVVTFDASGKAISIEEKPKAPKSNWAVTGLYFYDAD 183

Query: 178 IFHACHLVQPSNRGEYEISEAIDL-LIRSGRTIDAI-RIDGWRLDIGYPE 225
           +      ++PS RGE EIS    L L R G +++ + R   W LD+G PE
Sbjct: 184 VCQVAATLKPSARGELEISHLNSLYLERGGLSVELLGRGISW-LDVGTPE 232


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: 203
Number of extensions: 17
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: 296
Length adjustment: 25
Effective length of query: 218
Effective length of database: 271
Effective search space:    59078
Effective search space used:    59078
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