GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapP in Pseudomonas stutzeri RCH2

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 GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= TCDB::Q52815
         (257 letters)



>lcl|FitnessBrowser__psRCH2:GFF4241 Psest_4314 ABC-type metal ion
           transport system, ATPase component
          Length = 335

 Score =  165 bits (418), Expect = 1e-45
 Identities = 93/226 (41%), Positives = 133/226 (58%), Gaps = 2/226 (0%)

Query: 29  DFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVDGTELTN-DLKK 87
           D   L+   L++  GE   + G SG+GKST++R INRLEE   G+I+V+G ++T  D   
Sbjct: 17  DVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGRILVNGEDVTALDADG 76

Query: 88  IDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQAN 147
           +   R+ VGM+FQHFNL    T+ +N  +         +++ +      L+RV + E A 
Sbjct: 77  LRRFRQRVGMIFQHFNLLMSKTVADNVAMPLRLAGIRSRREIDARVAALLERVGLKEHAR 136

Query: 148 KYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVGLAEE-GMTML 206
           KYP QLSGGQ+QRV IAR+L   P I+L DE TSALDP+    VL  +  +  E  +T++
Sbjct: 137 KYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIV 196

Query: 207 CVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFL 252
            +THEM   R+V +RV  MD G IVEQ      F +P+H  T+ F+
Sbjct: 197 LITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVFLHPKHPTTQRFV 242


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: 225
Number of extensions: 8
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: 257
Length of database: 335
Length adjustment: 26
Effective length of query: 231
Effective length of database: 309
Effective search space:    71379
Effective search space used:    71379
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: 48 (23.1 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