GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Shewanella amazonensis SB2B

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  235 bits (600), Expect = 1e-66
 Identities = 134/331 (40%), Positives = 204/331 (61%), Gaps = 17/331 (5%)

Query: 4   VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63
           +++  V K+F +V AV ++SL +  GE   LLG SG GK+T LRM+AG E P+ G+IY+ 
Sbjct: 21  LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLD 80

Query: 64  DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123
            + + D      +PP +R I M+FQSYAL+PHMTV  NIAF LK  K+ + +I QRV+E+
Sbjct: 81  GQDITD------LPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEM 134

Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183
            +L+ + +   RKP +LSGGQRQRVAL R++ ++P++ L+DEP+  LD KLR +M+ E+ 
Sbjct: 135 LKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVV 194

Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243
           ++  ++GVT + VTHDQ EAMTM  RIA+M+ G + QVGSP ++Y+ P +  +A FIG+ 
Sbjct: 195 EILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT- 253

Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGE---LGYVGREVIFGIRPEDLYDAMFA 300
            +N  D  + ED   D    +   LP  F ++G         + V   +RPE     +  
Sbjct: 254 -VNLFDCEIIEDE-ADHAILKSPTLPQPF-LIGHGVTTSLEDKHVWLAVRPE---KTLIT 307

Query: 301 QVRVPGE-NLVRAVVEIVENLGSERIVHLRV 330
           + +  GE N  R  V  +  LG   + ++++
Sbjct: 308 REQPEGEYNWARGKVHDIAYLGGLSVYYIKL 338


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: 352
Number of extensions: 20
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: 372
Length of database: 378
Length adjustment: 30
Effective length of query: 342
Effective length of database: 348
Effective search space:   119016
Effective search space used:   119016
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: 50 (23.9 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