GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Marinobacter adhaerens HP15

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF3963 HP15_3903 methionine import ATP-binding protein MetN 2

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Marino:GFF3963
          Length = 310

 Score =  164 bits (416), Expect = 2e-45
 Identities = 92/218 (42%), Positives = 134/218 (61%), Gaps = 2/218 (0%)

Query: 48  LKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRV 107
           + I  G++F I+G SG+GKSTLVR IN L  PT G +L D +NI D  A  LRAFR R+V
Sbjct: 1   MTIETGEVFGIVGHSGAGKSTLVRLINLLEPPTGGRILIDDENITDYDAAELRAFR-RKV 59

Query: 108 SMVFQSFALMPHRTVLQNVVYGQRVRGV-SKDDAREIGMKWIDTVGLSGYDAKFPHQLSG 166
            M+FQ F L+  +TV  N+ +  ++ G+ SK + R+   + +  V L+ +  K+P QLSG
Sbjct: 60  GMIFQHFNLLSSKTVADNIAFPMKLAGIYSKTEIRDRVEELLARVSLTDHANKYPSQLSG 119

Query: 167 GMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDE 226
           G KQRVG+ARALA    ++L DEA SALDP     +   L  + R L  TIV ITH++D 
Sbjct: 120 GQKQRVGIARALACRPTILLCDEATSALDPQTTQSVLKLLADINRELGLTIVLITHEMDV 179

Query: 227 ALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
             R+   +A++  G+VV++G  +++  +P +     FV
Sbjct: 180 VRRVCDRVAVMDAGEVVEMGPVSEVFLHPKHPTTRDFV 217


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: 225
Number of extensions: 13
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: 275
Length of database: 310
Length adjustment: 26
Effective length of query: 249
Effective length of database: 284
Effective search space:    70716
Effective search space used:    70716
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