GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_807 Various polyols ABC transporter, ATP-binding component

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_807
          Length = 367

 Score =  317 bits (812), Expect = 3e-91
 Identities = 182/375 (48%), Positives = 243/375 (64%), Gaps = 24/375 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  LK+ N+ K +       ++  +L+++D+EF+VFVGPSGCGKST LR+IAGLE++++G
Sbjct: 1   MANLKIKNLQKGFEGFS--IIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVSDG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + +D + + + SP  RD+AMVFQ YALYPHMSV +NM+F L L    K ++ K+V+EAA
Sbjct: 59  TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVPKAEVEKKVNEAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            IL L   LERKP  LSGGQRQRVA+GRAIVR+ K+FL DEPLSNLDA LRV MR E+A+
Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+ + AT IYVTHDQ EAMTLAD++V+++           GRIEQ+G+P ELY++PAN 
Sbjct: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNG----------GRIEQVGSPLELYHQPANL 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKG---YLGKKVTLGIRP 297
           FVAGF+G+P M F +  V     ++  G  + L  G    L   G    +G  VTLGIRP
Sbjct: 229 FVAGFLGTPKMGFLKGKVTG---LDSQGCEVLLDAGTRINLPRSGANLSVGGAVTLGIRP 285

Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTE-FTARVNARDSHSPGEKV 356
           E ++  Q    T     VTAD  VSE LGS++  +V   S E  T RV    +   GE++
Sbjct: 286 EHLNLAQPGDCTL---QVTAD--VSERLGSDTFCHVVTASGEALTMRVRGDLASRFGEQL 340

Query: 357 QLTFNIAKGHFFDLE 371
            L  +    H FD E
Sbjct: 341 SLHLDAEHCHLFDAE 355


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: 339
Number of extensions: 17
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: 367
Length adjustment: 30
Effective length of query: 347
Effective length of database: 337
Effective search space:   116939
Effective search space used:   116939
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: 49 (23.5 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