GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Marinobacter adhaerens HP15

Align NatA, 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 GFF3115 HP15_3058 leucine/isoleucine/valine transporter ATP-binding subunit

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Marino:GFF3115
          Length = 251

 Score =  199 bits (507), Expect = 4e-56
 Identities = 98/250 (39%), Positives = 161/250 (64%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L    L   FGG+ AV E  ++V +  I  +IGPNGAGKTT+FN +S F +P  G+++F
Sbjct: 1   MLEVQNLSMRFGGLLAVDEVSLDVQEHEIVSIIGPNGAGKTTVFNCMSGFYKPTGGKILF 60

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
           +G+ +Q    ++I++ GMVRTFQ  R  S+++V+EN+L+A  +    N     +Q     
Sbjct: 61  EGKEVQGKPDYKISRLGMVRTFQHVRLFSQMTVVENLLVAQHRHLNTNLISGLIQTPSYR 120

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
           K+E++  ++A + L+ VGL   A   AG L+ GQ++ LE+ R ++T PKL++LDEPAAG+
Sbjct: 121 KKEQKSLDRAAYWLDRVGLLDMANREAGNLAYGQQRRLEIARCMVTEPKLLMLDEPAAGL 180

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
           NP    ++   I++      ++ ++IEH+M ++M + DR+ V+ +G+ LA GTP EI+ N
Sbjct: 181 NPAETKELNQLIISLKEDYNVSVVLIEHDMSLVMDISDRINVINQGRPLASGTPEEIRQN 240

Query: 251 SQVLEAYLGK 260
             V++AYLG+
Sbjct: 241 DDVIKAYLGE 250


Lambda     K      H
   0.319    0.136    0.391 

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: 171
Number of extensions: 7
Number of successful extensions: 1
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: 260
Length of database: 251
Length adjustment: 24
Effective length of query: 236
Effective length of database: 227
Effective search space:    53572
Effective search space used:    53572
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 (21.7 bits)
S2: 47 (22.7 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