GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Azospirillum brasilense Sp245

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 AZOBR_RS04130 AZOBR_RS04130 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__azobra:AZOBR_RS04130
          Length = 252

 Score =  186 bits (471), Expect = 5e-52
 Identities = 102/252 (40%), Positives = 148/252 (58%), Gaps = 11/252 (4%)

Query: 10  PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69
           PLL+ +GL K FGG+ A     + VA+G +  LIGPNGAGKTTL   LS  + PD G + 
Sbjct: 4   PLLSTNGLVKRFGGLAATDGLSLSVAEGELHALIGPNGAGKTTLIGQLSGELTPDSGTIR 63

Query: 70  FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGEN--FWQVQLQPQ 127
           FD   + +L  H+ AQ+G+ R+FQ+       + L+N+ LA Q   G +  FW+      
Sbjct: 64  FDRRDVTRLPVHKRAQRGLARSFQITSIFPSFTALDNVALAVQAHAGHSFRFWR------ 117

Query: 128 VVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPA 187
                +++L + A  +LE VGL  +A   A  L+ G+++ LE+  AL T P+L+LLDEP 
Sbjct: 118 -DAGRDRRLADPARAVLERVGLGARADTRADALAHGEKRQLELAMALATGPRLLLLDEPM 176

Query: 188 AGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247
           AG+ P   D      L    + G+T L++EH+MD + +L DR+ VL  G+NLA GTP +I
Sbjct: 177 AGMGPE--DSARMVELLQELKGGVTILLVEHDMDAVFALADRITVLVRGKNLASGTPEQI 234

Query: 248 QTNSQVLEAYLG 259
           + +  V EAYLG
Sbjct: 235 RNDPAVREAYLG 246


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: 142
Number of extensions: 4
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: 260
Length of database: 252
Length adjustment: 24
Effective length of query: 236
Effective length of database: 228
Effective search space:    53808
Effective search space used:    53808
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