GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Escherichia coli BW25113

Align Maltose transport system permease protein malF aka TT_C1628, 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 15431 b1311 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= TCDB::Q72H67
         (291 letters)



>FitnessBrowser__Keio:15431
          Length = 293

 Score =  162 bits (409), Expect = 1e-44
 Identities = 92/277 (33%), Positives = 150/277 (54%), Gaps = 4/277 (1%)

Query: 10  AWILVLPTLLVVVLVAGYPLAQVFYWSFFKADIAFVEPPEFVGLENYAYLFQDPDFRQAL 69
           A +L+ P+LL++  +  +P+      SF +  +       FVG+ NY  +  DP F  +L
Sbjct: 14  ALLLLAPSLLLLGGLVAWPMVSNIEISFLRLPLNPNIESTFVGVSNYVRILSDPGFWHSL 73

Query: 70  WNTLKFTVVSVSLETVLGLAIALIIHSNFRGRGLVRTAILIPWAIPTVVSAKMWQWMLND 129
           W T+ +T + V+  TVLGLA+A+  +  FR R   R+ +++ +  P++     W++M N+
Sbjct: 74  WMTVWYTALVVAGSTVLGLAVAMFFNREFRLRKTARSLVILSYVTPSISLVFAWKYMFNN 133

Query: 130 VYGVINVLGVK-LGLLSQKVAFLARPELLLPSIIAVDVWKTTPFMALLLLAGLQMIPEEL 188
            YG++N LGV  L L  Q   +   P      ++   +W+  P+  +  LA LQ I + L
Sbjct: 134 GYGIVNYLGVDLLHLYEQAPLWFDNPGSSFVLVVLFAIWRYFPYAFISFLAILQTIDKSL 193

Query: 189 YEAASIDGASRWQQFWSITLPLLTPALVVALIFRTLDALRVFDVVFVMSGVNPATRTLAV 248
           YEAA +DGA+ WQ+F  +TLP + P L   +  RT+    +F  V++++        L V
Sbjct: 194 YEAAEMDGANAWQRFRIVTLPAIMPVLATVVTLRTIWMFYMFADVYLLT---TKVDILGV 250

Query: 249 YNRQTLVDFQDLGYGSAISVAILVIIFAFVLLYMRTV 285
           Y  +T   F DLG  +AISV + +IIFA +LL  + V
Sbjct: 251 YLYKTAFAFNDLGKAAAISVVLFIIIFAVILLTRKRV 287


Lambda     K      H
   0.329    0.142    0.433 

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: 289
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: 291
Length of database: 293
Length adjustment: 26
Effective length of query: 265
Effective length of database: 267
Effective search space:    70755
Effective search space used:    70755
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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