GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK in Burkholderia phytofirmans PsJN

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 BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS17470 BPHYT_RS17470
           glycerol-3-phosphate ABC transporter ATP-binding protein
          Length = 362

 Score =  318 bits (816), Expect = 1e-91
 Identities = 180/378 (47%), Positives = 236/378 (62%), Gaps = 17/378 (4%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  L L  + K Y + K + +   ++D+ D EF+V VGPSGCGKST LRM+AGLE I+EG
Sbjct: 1   MAALTLQGVKKTY-DGKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEG 59

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
           ++ I  K++N   PKDR+IAMVFQNYALYPHMSV ENM + LK+    +  I KRV  AA
Sbjct: 60  SISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAA 119

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           +IL L   L+RKP +LSGGQRQRVAMGRAIVR+  VFL DEPLSNLDA+LRV MR EI +
Sbjct: 120 QILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQR 179

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H R+  T++YVTHDQ EAMTLA R+++M+           G  EQIG P E+Y  PA  
Sbjct: 180 LHARLATTSLYVTHDQIEAMTLAQRVIVMNK----------GHAEQIGAPTEVYERPATV 229

Query: 241 FVAGFIGSPAMNFFEVTVEKE-RLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPED 299
           FVA FIGSP MN  E  V  +       G    LP      +  +   G++ TLGIRPE 
Sbjct: 230 FVASFIGSPGMNLLEGRVSDDGAFFEVAGNGPKLPLTDVASIGREVARGREWTLGIRPEH 289

Query: 300 ISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLT 359
           +S  Q      P+A++T D    ELLG++++ + ++G  + T R+      + GE +Q+ 
Sbjct: 290 MSPGQ---ADAPHATLTVD--SCELLGADNLAHGRWGKHDVTVRLPHAHRPAAGEALQVA 344

Query: 360 FNIAKGHFFDLETEKRIN 377
                 HFFD  + +R N
Sbjct: 345 LPARHLHFFDPASGRRAN 362


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: 358
Number of extensions: 15
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: 362
Length adjustment: 30
Effective length of query: 347
Effective length of database: 332
Effective search space:   115204
Effective search space used:   115204
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