GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Escherichia coli BW25113

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 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Keio:17511
          Length = 356

 Score =  325 bits (832), Expect = 2e-93
 Identities = 186/378 (49%), Positives = 242/378 (64%), Gaps = 24/378 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  LKL  + K + + K   ++   LD+ D EFIV VGPSGCGKST LRM+AGLE +TEG
Sbjct: 1   MAGLKLQAVTKSW-DGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEG 59

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
           +++I+D+ + +  PKDR IAMVFQNYALYPHMSV ENMA+GLK+R   K  I +RV EAA
Sbjct: 60  DIWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAA 119

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            IL L   L+R+P +LSGGQRQRVAMGRAIVRD  VFL DEPLSNLDAKLRV MR E+ +
Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQ 179

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +HRR+  T++YVTHDQ EAMTLA R+++M+           G  EQIGTP E+Y +PA+ 
Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNG----------GVAEQIGTPVEVYEKPASL 229

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILE--EKGYLGKKVTLGIRPE 298
           FVA FIGSPAMN           VN +G    L  G E  L    + Y G+K+TLGIRPE
Sbjct: 230 FVASFIGSPAMNLL------TGRVNNEGTHFELDGGIELPLNGGYRQYAGRKMTLGIRPE 283

Query: 299 DISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQL 358
            I+         P    T      E+LG++++ + ++G  +   R+  ++  + G  + L
Sbjct: 284 HIALSSQAEGGVPMVMDTL-----EILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWL 338

Query: 359 TFNIAKGHFFDLETEKRI 376
                + H FD ET +R+
Sbjct: 339 HLAENQLHLFDGETGQRV 356


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: 336
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: 356
Length adjustment: 30
Effective length of query: 347
Effective length of database: 326
Effective search space:   113122
Effective search space used:   113122
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