GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK in Pseudomonas putida KT2440

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>lcl|FitnessBrowser__Putida:PP_0411 PP_0411 Polyamine ABC
           transporter, ATP-binding protein
          Length = 374

 Score =  229 bits (585), Expect = 7e-65
 Identities = 130/303 (42%), Positives = 180/303 (59%), Gaps = 22/303 (7%)

Query: 2   TTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61
           T +    + K Y + +   V++ NLDI   EF+  +GPSG GK+T+L M+AG E  T G 
Sbjct: 13  TLVSFRGVQKSY-DGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGE 71

Query: 62  LYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAE 121
           + +  + +N+  P  RDI MVFQNYAL+PHM+V EN+AF L +R   K DI++RV     
Sbjct: 72  IQLGGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLN 131

Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKI 181
           ++ L  F +R P  LSGGQ+QRVA+ RA+V + ++ LMDEPL  LD +LR  M+ EI  I
Sbjct: 132 MVQLDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHI 191

Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKF 241
           H+R+G T +YVTHDQ EA+T++DR+ +             G I+QI  P+ LY EP N F
Sbjct: 192 HQRLGVTVVYVTHDQGEALTMSDRVAVFHQ----------GEIQQIADPRTLYEEPCNTF 241

Query: 242 VAGFIGSPAMNFFEVTVEKERLVNQDG--LSLALPQGQ--EKILEEKGYLGKKVTLGIRP 297
           VA FIG       E       L+  DG    + LP+G+  E +    G  G+ VTL IRP
Sbjct: 242 VANFIG-------ENNRISGTLLASDGKRCQVQLPRGERVEALAVNVGQAGEPVTLSIRP 294

Query: 298 EDI 300
           E +
Sbjct: 295 ERV 297


Lambda     K      H
   0.318    0.135    0.379 

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: 305
Number of extensions: 11
Number of successful extensions: 3
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: 377
Length of database: 374
Length adjustment: 30
Effective length of query: 347
Effective length of database: 344
Effective search space:   119368
Effective search space used:   119368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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