GapMind for catabolism of small carbon sources

 

Aligments for a candidate for musK in Dinoroseobacter shibae DFL-12

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)

Query= BRENDA::Q8NMV1
         (376 letters)



>lcl|FitnessBrowser__Dino:3609758 Dshi_3141 ABC transporter related
           (RefSeq)
          Length = 352

 Score =  306 bits (784), Expect = 6e-88
 Identities = 167/317 (52%), Positives = 217/317 (68%), Gaps = 18/317 (5%)

Query: 25  NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84
           +L + D EFLVL+GPSGCGK+TT+RM+AGLE+ TDG I+IGD+ V    P+DRD+AMVFQ
Sbjct: 23  SLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEIWIGDRMVNDDLPKDRDVAMVFQ 82

Query: 85  NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144
           NY LYPHMT+ EN+ + L++ G  + EI  RV  AA  + LT+FL RKPKALSGGQRQRV
Sbjct: 83  NYGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAAEQVELTKFLHRKPKALSGGQRQRV 142

Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204
           A+ RAIVR P+VFLMDEPLSNLDAKLRV  R ++  L R+L +TTVYVTHDQ EA+T+ D
Sbjct: 143 ALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHLSRELQITTVYVTHDQIEAMTLAD 202

Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDG-DATSGHARIKLS 263
           R+AV+K G +QQ+G P E+Y+ PAN+FVAGFIGSPAMNL   SV+DG   T+G  R+   
Sbjct: 203 RVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAMNLINGSVEDGMFVTTGGTRLVKV 262

Query: 264 PETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFL---YGK- 319
           P         D  R  +G R + +++   G+     I + +   E  G  + L   +GK 
Sbjct: 263 PS-------PDRARAILGVRADDMQVHEAGQG---DIDVTIYAFENTGESTLLTVQWGKQ 312

Query: 320 -LVGEGD--LGSSSEDV 333
            ++  GD  L    +DV
Sbjct: 313 RVIARGDRHLRKEQDDV 329


Lambda     K      H
   0.316    0.135    0.380 

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: 368
Number of extensions: 7
Number of successful extensions: 1
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: 376
Length of database: 352
Length adjustment: 29
Effective length of query: 347
Effective length of database: 323
Effective search space:   112081
Effective search space used:   112081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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