GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1346 Urea ABC transporter, ATPase protein UrtD

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1346
          Length = 289

 Score =  140 bits (352), Expect = 4e-38
 Identities = 87/252 (34%), Positives = 144/252 (57%), Gaps = 12/252 (4%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           +L    +  SF G KA+ +  + +  G +  +IGPNGAGKTTL ++++   RP  G+  F
Sbjct: 48  ILTLEDISVSFDGFKALNDLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 107

Query: 71  DGEPIQ--QLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128
            GE +   Q+   QIAQ G+ R FQ       LSV EN+ LA  ++T ++ W   L+ ++
Sbjct: 108 -GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA--QKTDKSVW-ASLRARL 163

Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188
             +++ ++ E    +LE++ L       AG LS GQ++ LE+G  LM +P+L+LLDEP A
Sbjct: 164 SGEQKDRISE----VLETIRLTASVNRPAGMLSHGQKQFLEIGMLLMQDPQLLLLDEPVA 219

Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248
           G+     +   +  L  +     + +++EH+M  + S+ D V VL +G  LA+G+  ++Q
Sbjct: 220 GMTDAETEFTAE--LFKSLAGKHSLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQ 277

Query: 249 TNSQVLEAYLGK 260
            N +V+E YLG+
Sbjct: 278 DNERVIEVYLGR 289


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: 170
Number of extensions: 7
Number of successful extensions: 4
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: 289
Length adjustment: 25
Effective length of query: 235
Effective length of database: 264
Effective search space:    62040
Effective search space used:    62040
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