GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Escherichia coli BW25113

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate 15562 b1441 predicted spermidine/putrescine transporter subunit (NCBI)

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__Keio:15562
          Length = 337

 Score =  226 bits (576), Expect = 6e-64
 Identities = 123/323 (38%), Positives = 195/323 (60%), Gaps = 12/323 (3%)

Query: 4   LQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFD 63
           ++  ++ + +G    + GVS+ IK GEF   +GPSG GK+T LRLIAG E+++ G ++  
Sbjct: 5   VEFDNVSRLYGDVRAVDGVSIAIKDGEFFSMLGPSGSGKTTCLRLIAGFEQLSGGAISIF 64

Query: 64  GQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQL 123
           G+  + L P  R +  VFQ YAL+PHM++ +N+A+G+ + G +K+Q     + A E + L
Sbjct: 65  GKPASNLPPWERDVNTVFQDYALFPHMSILDNVAYGLMVKGVNKKQRHAMAQEALEKVAL 124

Query: 124 TPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSM 183
               +R P QLSGGQRQRVAI RA+V +P+V L DEPL  LD  LR   +LE+ KL +S+
Sbjct: 125 GFVHQRKPSQLSGGQRQRVAIARALVNEPRVLLLDEPLGALDLKLREQMQLELKKLQQSL 184

Query: 184 HKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKMNFL 243
              T I+VTHDQ EA++++DR+ V  +G +EQ+ +P +LY  P + FVAGF+G+   N  
Sbjct: 185 -GITFIFVTHDQGEALSMSDRVAVFNNGRIEQVDSPRDLYMRPRTPFVAGFVGT--SNVF 241

Query: 244 SGAFAEPY--KADTIGIRAEHLEIDEQGG-EWSGTVIHSEMLGSDSYIYLDIGTGEPVIV 300
            G  AE       +  +R EH+ ++  G  + +GT+   +  G+ +   L +  GE ++V
Sbjct: 242 DGLMAEKLCGMTGSFALRPEHIRLNTPGELQANGTIQAVQYQGAATRFELKLNGGEKLLV 301

Query: 301 RESGIAKHQ------PGQTIRIS 317
            ++ +   +      PGQ + +S
Sbjct: 302 SQANMTGEELPATLTPGQQVMVS 324


Lambda     K      H
   0.321    0.138    0.396 

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: 312
Number of extensions: 13
Number of successful extensions: 2
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: 342
Length of database: 337
Length adjustment: 28
Effective length of query: 314
Effective length of database: 309
Effective search space:    97026
Effective search space used:    97026
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 (21.9 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