GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Pseudomonas putida KT2440

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 PP_1300 PP_1300 putative amino acid ABC transporter - ATP-binding subunit

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__Putida:PP_1300
          Length = 254

 Score =  410 bits (1055), Expect = e-119
 Identities = 194/243 (79%), Positives = 224/243 (92%)

Query: 15  EVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKI 74
           E  +++  +NKWYG FHVL+DINL V +GERIV+ GPSGSGKST IRC+NRLEEHQ+G+I
Sbjct: 12  EGIIQMQGVNKWYGQFHVLKDINLNVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRI 71

Query: 75  VVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAM 134
           VVDG ELTNDLK+I+ +RREVGMVFQHFNLFPHL+ILENCTLAP+WVRKMP+++AEE+AM
Sbjct: 72  VVDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLSILENCTLAPMWVRKMPRRKAEEIAM 131

Query: 135 HFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDT 194
           H+L+RV+IPEQA+KYPGQLSGGQQQRVAIAR+LCM PKIMLFDEPTSALDPEM+KEVLDT
Sbjct: 132 HYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDT 191

Query: 195 MVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQ 254
           MVGLAE+GMTMLCVTHEMGFAR VANRVIFMD+G+IVEQ  P  FFD P+ +RTKLFLSQ
Sbjct: 192 MVGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPDDFFDRPRSDRTKLFLSQ 251

Query: 255 ILH 257
           ILH
Sbjct: 252 ILH 254


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: 295
Number of extensions: 9
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: 254
Length adjustment: 24
Effective length of query: 233
Effective length of database: 230
Effective search space:    53590
Effective search space used:    53590
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: 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