GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Acidovorax sp. GW101-3H11

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 Ac3H11_104 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_104
          Length = 249

 Score =  179 bits (453), Expect = 6e-50
 Identities = 98/252 (38%), Positives = 147/252 (58%), Gaps = 8/252 (3%)

Query: 10  PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69
           P+L+  G+   FG +KAVQ+   E   G IT +IGPNGAGK++LFNL+S  IRP  G V 
Sbjct: 3   PILSVKGISVQFGALKAVQDVSFEAQPGKITAVIGPNGAGKSSLFNLISGAIRPSSGAVR 62

Query: 70  FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQ-KQTGENFWQVQLQPQV 128
           FDGE +    PHQ+ + G+ R+FQ+      L V EN+ LAAQ  + G   ++   + Q 
Sbjct: 63  FDGEDVTGRAPHQLLRYGLSRSFQITNLFFELPVRENLRLAAQFLEQGRGLFRPLARSQT 122

Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188
                 +       LLE   L  KA E AG LS G+++ LE+  +L + P+++LLDEP  
Sbjct: 123 AAARVDE-------LLEQFDLRNKADELAGYLSHGEQRRLEIAVSLASRPRMLLLDEPTQ 175

Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248
           G++     +    I   +   G++ L++EH++D++M L D V V+ +GQ LA+GTPA+++
Sbjct: 176 GMSHGDTRETESLIRGLSHNHGLSILLVEHDVDLVMQLSDFVVVMHQGQKLAEGTPAQVR 235

Query: 249 TNSQVLEAYLGK 260
            N  V  AY G+
Sbjct: 236 ANPAVQAAYFGE 247


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: 132
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: 249
Length adjustment: 24
Effective length of query: 236
Effective length of database: 225
Effective search space:    53100
Effective search space used:    53100
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