GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natA in Pseudomonas fluorescens FW300-N2E3

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 AO353_13530 AO353_13530 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_13530 AO353_13530 ABC
           transporter ATP-binding protein
          Length = 289

 Score =  137 bits (344), Expect = 3e-37
 Identities = 86/252 (34%), Positives = 143/252 (56%), Gaps = 12/252 (4%)

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

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

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

Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248
           G+     +   +   +   +  +  +++EH+M  + S+ D V VL +G  LA+G+ A++Q
Sbjct: 220 GMTDAETEFTAELFKSLAGKHSL--MVVEHDMGFVGSIADHVTVLHQGSVLAEGSLAQVQ 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: 172
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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