GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_0411
          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:

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