GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Desulfovibrio vulgaris Miyazaki F

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)

Query= TCDB::Q52663
         (338 letters)



>FitnessBrowser__Miya:8502446
          Length = 271

 Score =  105 bits (263), Expect = 1e-27
 Identities = 79/253 (31%), Positives = 115/253 (45%), Gaps = 10/253 (3%)

Query: 1   MKKSVFFGSVALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVY-QGFDV 59
           MK+ V         L    A A  ++D+KARG L+CG       F   D       GFD+
Sbjct: 1   MKRLVLLAVALCVVLTGTMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDI 60

Query: 60  AVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAV 119
            +CKAVA   LG  +++K V  T  TR   L  G VD++    T  F RD    +DF   
Sbjct: 61  DICKAVADK-LGVKLELKTV--TSATRIPMLTQGSVDMVAATMTHKFERDD--VIDFSIT 115

Query: 120 NYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAE 179
            + DGQ  +V K  GV SA +L G  +    G+T+E N+    KA     T V+  +  +
Sbjct: 116 YFMDGQKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNI----KAAQPEATVVSFDEYPQ 171

Query: 180 GQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIV 239
                  G  ++ TTD++ L   R + P      I+ + IS EP G  +   D+ + D+V
Sbjct: 172 AFLALKQGKAEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDLV 231

Query: 240 RWSFYALVAAEEY 252
             +   L  + EY
Sbjct: 232 NRTLVDLWNSGEY 244


Lambda     K      H
   0.316    0.132    0.384 

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: 188
Number of extensions: 9
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: 338
Length of database: 271
Length adjustment: 27
Effective length of query: 311
Effective length of database: 244
Effective search space:    75884
Effective search space used:    75884
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 (21.6 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