GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Acidovorax sp. GW101-3H11

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Ac3H11_631 Methionine ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_631
          Length = 351

 Score =  155 bits (393), Expect = 9e-43
 Identities = 89/218 (40%), Positives = 125/218 (57%), Gaps = 1/218 (0%)

Query: 38  GCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAK 97
           G    L  + L I  G++F I+G SG+GKS+LVR IN L  PT+G+V+  G ++  L   
Sbjct: 16  GPVEALRGIDLTIQPGEVFGIIGKSGAGKSSLVRVINLLNRPTTGQVIVGGRDLTQLNDA 75

Query: 98  ALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYD 157
            LR  R R + MVFQ F L+  RTV  N      + G+SK D RE     ++ VGL    
Sbjct: 76  QLREAR-REIGMVFQHFNLLSSRTVFDNAALPLELAGMSKTDIRERVNPLLELVGLDHLA 134

Query: 158 AKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTI 217
            ++P Q+SGG KQRVG+ARALA+   V+L DEA SALDP     + D L Q+ R L  T+
Sbjct: 135 DRYPAQISGGQKQRVGIARALASRPKVLLSDEATSALDPETTRSILDLLRQVNRELGLTV 194

Query: 218 VFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNP 255
           V ITH +    ++   +A++  G++V+ G   D+   P
Sbjct: 195 VLITHQMQVIKQVADHVAVIEAGRIVEQGRVLDVFTRP 232


Lambda     K      H
   0.323    0.139    0.397 

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: 261
Number of extensions: 10
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: 275
Length of database: 351
Length adjustment: 27
Effective length of query: 248
Effective length of database: 324
Effective search space:    80352
Effective search space used:    80352
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 (21.9 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