GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Escherichia coli BW25113

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Keio:17511
          Length = 356

 Score =  337 bits (865), Expect = 2e-97
 Identities = 184/366 (50%), Positives = 245/366 (66%), Gaps = 11/366 (3%)

Query: 1   MAKVRLEHVWKRF-GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59
           MA ++L+ V K + GK   +K   L+  DGEF+V VGPSGCGK+T LRM+AGLE ++EG+
Sbjct: 1   MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60

Query: 60  IYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAAR 119
           I+I D+ V ++ PKDR IAMVFQNYALYPHM+V ENMA+GL++R   K +I  RVKEAAR
Sbjct: 61  IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGMGKQQIAERVKEAAR 120

Query: 120 ILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKL 179
           IL+++ LL R+PRELSGGQRQRVAMGRAIVR+P VFL DEPLSNLDAKLRV+MR E+ +L
Sbjct: 121 ILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQL 180

Query: 180 QRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSM 239
            RRL  T++YVTHDQVEAMTL  R++VM  G  +Q+ TP+ +Y+ PA+ FVA FIGSP+M
Sbjct: 181 HRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPAM 240

Query: 240 NFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPE 299
           N +   V  +G    L   G  +  N       + YAG+++ LG+RPEH+ L       +
Sbjct: 241 NLLTGRVNNEGTHFELDG-GIELPLN----GGYRQYAGRKMTLGIRPEHIALSS-----Q 290

Query: 300 EENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQRLHAFDL 359
            E  +   ++ +E LGA+   H       LV ++        G  + L     +LH FD 
Sbjct: 291 AEGGVPMVMDTLEILGADNLAHGRWGEQKLVVRLAHQERPTAGSTLWLHLAENQLHLFDG 350

Query: 360 ETDRTI 365
           ET + +
Sbjct: 351 ETGQRV 356


Lambda     K      H
   0.320    0.139    0.400 

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: 399
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: 376
Length of database: 356
Length adjustment: 30
Effective length of query: 346
Effective length of database: 326
Effective search space:   112796
Effective search space used:   112796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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