GapMind for catabolism of small carbon sources

 

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

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__Dino:3609758
          Length = 352

 Score =  346 bits (888), Expect = e-100
 Identities = 185/371 (49%), Positives = 246/371 (66%), Gaps = 21/371 (5%)

Query: 1   MAGVRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQI 60
           MA V L D+ K +G+   V   SL V+D EF++LLGPSGCGKTTT+RMIAGLE+P+ G+I
Sbjct: 1   MAEVILKDLTKRWGDFVGVDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEI 60

Query: 61  YIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRV 120
           +IGD++V D        PKDRD+AMVFQ+Y LYPHMT+++NIA+PL++R V + EI  RV
Sbjct: 61  WIGDRMVNDDL------PKDRDVAMVFQNYGLYPHMTIFENIAYPLRVRGVDKAEIPPRV 114

Query: 121 REVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRA 180
           +  AE + LT+ L+RKP+ LSGGQRQRVAL RAIVRKP+VFLMDEPLSNLDAKLRV MRA
Sbjct: 115 QRAAEQVELTKFLHRKPKALSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRA 174

Query: 181 ELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFI 240
           ELK L R+L +TT+YVTHDQ+EAMT+ DR+AVM  GV+QQ+G+PDE+Y+ PAN FVAGFI
Sbjct: 175 ELKHLSRELQITTVYVTHDQIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFI 234

Query: 241 GSPPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFA 300
           GSP MN ++  V +  FV  G  RL  +P                I G+R +D+      
Sbjct: 235 GSPAMNLINGSVEDGMFVTTGGTRLVKVPSPDRA---------RAILGVRADDM------ 279

Query: 301 QVRVPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRSESRVREGVEVDVVFDMKKI 360
           QV   G+  +   +   EN G   ++ ++ G    +       R  +   V +  +   +
Sbjct: 280 QVHEAGQGDIDVTIYAFENTGESTLLTVQWGKQRVIARGDRHLRKEQDDVVGISLNTDHL 339

Query: 361 HIFDKTTGKAI 371
           ++FD  T + I
Sbjct: 340 YLFDPDTEERI 350


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: 419
Number of extensions: 21
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: 352
Length adjustment: 29
Effective length of query: 343
Effective length of database: 323
Effective search space:   110789
Effective search space used:   110789
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: 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