GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Dinoroseobacter shibae DFL-12

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__Dino:3608624
          Length = 333

 Score =  326 bits (836), Expect = 5e-94
 Identities = 171/307 (55%), Positives = 218/307 (71%), Gaps = 3/307 (0%)

Query: 1   MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60
           MA L L +++KSFG  DVI GVS+++  GEF+V VGPSGCGKSTLLR++AGLE ++SG +
Sbjct: 1   MATLTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEV 60

Query: 61  AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120
             DG++VN L P  R IAMVFQ+YALYPHM+V++NMA+G+++A   K +   RV  AA++
Sbjct: 61  RIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKL 120

Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180
           LQL PYL R P++LSGGQRQRVA+GRAIVR P VFLFDEPLSNLDA LRV  RLEI  L 
Sbjct: 121 LQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQ 180

Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240
           R +   T +YVTHDQVEAMTLADR+ V+  G+ +QIG PLE+Y  P + FVAGFIGSP  
Sbjct: 181 REL-GVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPPT 239

Query: 241 NFLSGAFAEPYKA-DTIGIRAEHLEIDEQGGEWSGTVIHSEMLGSDSYIYLDIGTGEPVI 299
           NFL         A   +GIR EHL +  Q G     V ++E LG+++ ++L    G  + 
Sbjct: 240 NFLPADMVRAGPAGQQVGIRPEHLRVAPQ-GRLEAHVAYAEALGAETLLHLRASQGTTLT 298

Query: 300 VRESGIA 306
           VR+   A
Sbjct: 299 VRQDAAA 305


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: 343
Number of extensions: 12
Number of successful extensions: 4
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: 333
Length adjustment: 28
Effective length of query: 314
Effective length of database: 305
Effective search space:    95770
Effective search space used:    95770
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