GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Dechlorosoma suillum PS

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Dsui_1833 Dsui_1833 nitrate transport ATP-binding subunits C and D

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__PS:Dsui_1833
          Length = 266

 Score =  144 bits (364), Expect = 2e-39
 Identities = 78/214 (36%), Positives = 123/214 (57%), Gaps = 16/214 (7%)

Query: 14  GEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADP--E 71
           G+  A+R++ L ++ GEF+ L+G SGCGK+T L +IAGL  P+ G +    + +A P  E
Sbjct: 19  GKFVALRDVDLSIRQGEFIALIGHSGCGKSTLLNLIAGLTRPTDGALICDGREIAGPGPE 78

Query: 72  KGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLK---LRKVPRQEIDQRVREVAELLG 128
           +G+           VFQ+++L P +T +DN+   ++     K  + ++ QR  +   L+G
Sbjct: 79  RGV-----------VFQNHSLLPWLTCFDNVYLAVERVFAAKEGKAKLKQRTHDALALVG 127

Query: 129 LTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQ 188
           LT    + P E+SGG +QRV + RA+  +P+V LMDEP   LDA  R +++ EL K+   
Sbjct: 128 LTHAETKFPHEISGGMKQRVGIARALSMQPKVLLMDEPFGALDALTRAKLQDELMKICDA 187

Query: 189 LGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVG 222
              T + VTHD  EA+ + DRI +M  G    +G
Sbjct: 188 TQATVVMVTHDVDEAVLLSDRIVMMTNGPAATIG 221


Lambda     K      H
   0.323    0.142    0.406 

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: 237
Number of extensions: 10
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: 372
Length of database: 266
Length adjustment: 27
Effective length of query: 345
Effective length of database: 239
Effective search space:    82455
Effective search space used:    82455
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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