GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natA in Pseudomonas stutzeri RCH2

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 GFF1276 Psest_1309 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::Q7A2H0
         (260 letters)



>lcl|FitnessBrowser__psRCH2:GFF1276 Psest_1309 ABC-type
           branched-chain amino acid transport systems, ATPase
           component
          Length = 255

 Score =  205 bits (522), Expect = 7e-58
 Identities = 103/251 (41%), Positives = 156/251 (62%)

Query: 10  PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69
           P+L   GL   FGG+ AV E  + V    +  +IGPNGAGKTT+FN L+ F +P  G ++
Sbjct: 4   PILEVRGLMMRFGGLLAVNEVGLTVHDKQVVSMIGPNGAGKTTVFNCLTGFYQPTAGEIL 63

Query: 70  FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129
            DG PI  L  H+IA+QG+VRTFQ  R    ++ +EN+L+A  +    NF    L+    
Sbjct: 64  LDGTPIHGLPGHKIARQGVVRTFQNVRLFKDMTAVENLLVAQHRHLNTNFLAGLLKTPGF 123

Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189
            K E+   + A   LE V L   A   AG L+ GQ++ LE+ R +MT P++++LDEPAAG
Sbjct: 124 RKSERAAMDFAAHWLEQVNLTDVANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183

Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249
           +NP+  +D+   I     + G+T L+IEH+M ++MS+ D ++V+ +G  LADG+P +++ 
Sbjct: 184 LNPKETEDLKALIAMLRDEHGVTVLLIEHDMKLVMSISDHIYVINQGTPLADGSPEQVRN 243

Query: 250 NSQVLEAYLGK 260
           N  V++AYLG+
Sbjct: 244 NPDVIKAYLGE 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: 160
Number of extensions: 5
Number of successful extensions: 1
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: 255
Length adjustment: 24
Effective length of query: 236
Effective length of database: 231
Effective search space:    54516
Effective search space used:    54516
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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