GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Echinicola vietnamensis KMM 6221, DSM 17526

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Cola:Echvi_1333
          Length = 243

 Score =  132 bits (331), Expect = 8e-36
 Identities = 77/234 (32%), Positives = 130/234 (55%), Gaps = 3/234 (1%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +L  EN+   Y K   ++  ++  VE GE+V ++GPNGAGK+T    I GL+ P++GK+ 
Sbjct: 2   ILRGENLIKIY-KGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGKVF 60

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMF 130
              + I  L   +  +LG+ Y+ Q A+VF  LSVEEN+     + N      K+K+  + 
Sbjct: 61  LDKEEITPLPMYRRAKLGIGYLAQEASVFRKLSVEENIMAVLEMTNLPKAAQKEKMEELL 120

Query: 131 PR--LSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQ 188
               L+  R+     LSGGER+   + +AL ++P  ++LDEP A + PI V ++   V +
Sbjct: 121 EEFSLTHVRKNLGMVLSGGERRRTEIARALAVDPKFVLLDEPFAGVDPIAVEEIQTIVAK 180

Query: 189 INQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
           +  +   I++ + N  + L + DR Y++  G+   +G  +EL  D +V ++YLG
Sbjct: 181 LKNKNIGILITDHNVNETLSITDRAYLMFEGKLLKAGTAEELAADEQVRKVYLG 234


Lambda     K      H
   0.317    0.136    0.377 

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: 164
Number of extensions: 6
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: 247
Length of database: 243
Length adjustment: 24
Effective length of query: 223
Effective length of database: 219
Effective search space:    48837
Effective search space used:    48837
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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