GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK 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_1960 Various polyols ABC transporter, ATP-binding component

Query= TCDB::Q8DT25
         (377 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1960 Various polyols ABC
           transporter, ATP-binding component
          Length = 365

 Score =  314 bits (804), Expect = 3e-90
 Identities = 175/373 (46%), Positives = 238/373 (63%), Gaps = 26/373 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M TLK++N+ K +       ++  +L++ DKEF+VFVGPSGCGKST LR+IAGLED+T G
Sbjct: 1   MATLKIENLKKGFEGLS--IIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + +D + + + +P  RD+AMVFQ YALYPHM+V +N++F L L   KK D+ ++V EAA
Sbjct: 59  TIELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            IL L   L+RKP  LSGGQRQRVA+GRAIVR+ K+FL DEPLSNLDA LRV  R E+++
Sbjct: 119 RILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSR 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+ + AT IYVTHDQ EAMTLA ++V+++A          GRIEQIG+P ELY+ PAN 
Sbjct: 179 LHKELQATMIYVTHDQVEAMTLATKVVVLNA----------GRIEQIGSPLELYHHPANL 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKG---YLGKKVTLGIRP 297
           FVAGF+G+P M F + TV     V+  G+ +    G   ++        +G+ VT+GIRP
Sbjct: 229 FVAGFLGTPKMGFLQATV---HAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRP 285

Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTE-FTARVNARDSHSPGEKV 356
           E ++             VT D  V+E LGS++  +V   S E  T RV          + 
Sbjct: 286 EHLTL-----SAEGQVPVTTD--VTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARR 338

Query: 357 QLTFNIAKGHFFD 369
            LT ++A  H FD
Sbjct: 339 YLTLDVAHCHLFD 351


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: 340
Number of extensions: 16
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: 365
Length adjustment: 30
Effective length of query: 347
Effective length of database: 335
Effective search space:   116245
Effective search space used:   116245
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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