GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galU in Methanospirillum lacunae Ki8-1

Align UTP--glucose-1-phosphate uridylyltransferase AglF; Archaeal glycosylation protein F; EC 2.7.7.9 (characterized)
to candidate WP_109968440.1 DK846_RS08095 sugar phosphate nucleotidyltransferase

Query= SwissProt::D4GYH1
         (243 letters)



>NCBI__GCF_003173355.1:WP_109968440.1
          Length = 388

 Score =  107 bits (266), Expect = 5e-28
 Identities = 76/235 (32%), Positives = 121/235 (51%), Gaps = 21/235 (8%)

Query: 1   MQAVVLAAGKGTRLRPLTEDKPKGMVEVDGKPILTHCFDQLVDLGAEKLVVVVGYKKEII 60
           +QAV+LAAG+GTR+RPLT+++PK ++ V  +PIL H  + L+  G   ++VVVGY+KE +
Sbjct: 3   VQAVILAAGEGTRIRPLTQNRPKALIPVANRPILEHLIESLLSCGVRDIIVVVGYRKEQV 62

Query: 61  IQHYDDEYRGVPITYAHQREQKGLAHALLTVEDHIDEDFMLMLGDNIFN-ANLGDVVKRQ 119
           ++H    +  V +    Q+ Q G  HAL    D I  D +++ GDN  + A+L +V+K +
Sbjct: 63  MRHL--IHLPVEVRIVEQQHQIGTGHALNCALDLITGDLLVLPGDNYIDPASLKEVLKIK 120

Query: 120 REDRADAAFLVEEVDWDEASRYGVCVTNDYGEITEVIEKPEEPPSNLVMTGFYTFTPAIF 179
                  + L+        S +GV    D G +  ++EKP       V  G Y     + 
Sbjct: 121 N------SMLI--TTHQHPSNFGVVDVED-GVVLGIVEKPVHAKRMTVSCGVYYLEQDLL 171

Query: 180 HACHLVQPSNRGEYEISEAIDLLIRSGRTIDAIRIDGWRLDIGYPEDRDEAEQRL 234
                   S   + ++S+AI+ LI  G +I A+    W+ D  YP D     +RL
Sbjct: 172 --------SGMIDNQLSDAINELIVRGTSISAVYAHEWQ-DAIYPWDLICMNERL 217


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: 211
Number of extensions: 11
Number of successful extensions: 2
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: 388
Length adjustment: 27
Effective length of query: 216
Effective length of database: 361
Effective search space:    77976
Effective search space used:    77976
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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