GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapP in Herbaspirillum seropedicae SmR1

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate HSERO_RS19240 HSERO_RS19240 arginine ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19240 HSERO_RS19240 arginine
           ABC transporter ATP-binding protein
          Length = 242

 Score =  270 bits (690), Expect = 2e-77
 Identities = 134/239 (56%), Positives = 175/239 (73%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +E+ N++KWYG F VL D +  V +G+ +V+ GPSGSGKST+I+ +N LE  QKG I VD
Sbjct: 2   IELNNVSKWYGSFQVLTDCSTSVKKGDVVVVCGPSGSGKSTLIKTVNGLEPFQKGTITVD 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G  + +    + ++R  +GMVFQ+F LFPHL+I EN T+  I V    K++A E  + +L
Sbjct: 62  GVSVGDPKTNLSKLRARIGMVFQNFELFPHLSIRENLTIGQIKVLGRSKEEATEKGLKYL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            RV +    +K+PGQLSGGQQQRVAIAR+L M+P  MLFDEPTSALDPEMI EVLD MVG
Sbjct: 122 DRVGLLAHKDKFPGQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMVG 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQIL 256
           LA+EGMTM+ VTHEMGFAR+VANRV+FMD+G +VE      FF  P+ ER + FL++I+
Sbjct: 182 LAQEGMTMMVVTHEMGFARKVANRVVFMDKGVVVEDCAKDEFFAQPRSERARDFLAKII 240


Lambda     K      H
   0.321    0.135    0.394 

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: 178
Number of extensions: 6
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: 257
Length of database: 242
Length adjustment: 24
Effective length of query: 233
Effective length of database: 218
Effective search space:    50794
Effective search space used:    50794
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 (21.9 bits)
S2: 46 (22.3 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