GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Cupriavidus basilensis 4G11

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 RR42_RS16965 RR42_RS16965 ABC transporter

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__Cup4G11:RR42_RS16965
          Length = 258

 Score =  193 bits (491), Expect = 3e-54
 Identities = 102/252 (40%), Positives = 155/252 (61%), Gaps = 7/252 (2%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           LL+  G+ K FGG++A+ +  +++  G I GLIGPNGAGKTT FN+++    PD G  + 
Sbjct: 7   LLSVQGVNKRFGGLQALSDVGLQIKPGEIYGLIGPNGAGKTTFFNVITGLYTPDSGEFVL 66

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
            G+  Q    H++A+ G+ RTFQ  R    ++ LEN+++    +T    +    +P  V 
Sbjct: 67  GGKAYQPTAVHEVAKAGIARTFQNIRLFGEMTALENVMVGRHVRTKAGLFGAVFRPPSVR 126

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
           +EE  +++ A  LLE VG+ K A+  +  LS G ++ LE+ RAL T PKL+ LDEPAAG+
Sbjct: 127 REEHSVEDWAHDLLEYVGIGKYAHFTSRNLSYGHQRRLEIARALATEPKLLALDEPAAGM 186

Query: 191 NPR---LIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247
           N      +  + D+I    R DG T L+IEH++ ++M LC+R+ VL  G+ +A G P E+
Sbjct: 187 NATEKVELRGLLDKI----RSDGKTILLIEHDVKLVMGLCNRLTVLDYGKVIAQGLPHEV 242

Query: 248 QTNSQVLEAYLG 259
           Q+N  V+EAYLG
Sbjct: 243 QSNPAVIEAYLG 254


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: 180
Number of extensions: 7
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: 260
Length of database: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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