GapMind for catabolism of small carbon sources

 

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

Align Possible transporter of polar amino acids including glutamate, glutamine and aspartate, DmeA. It complements a sepJ mutation in Anabaena (TC# 2.A.7.23.2), and SepJ complements a dmeA mutation. Alternatively, and less likely, it could be an activator of an ABC transporter catalyzing uptake of these amino acids (characterized)
to candidate 3609905 Dshi_3287 protein of unknown function DUF6 transmembrane (RefSeq)

Query= TCDB::Q31PG5
         (330 letters)



>lcl|FitnessBrowser__Dino:3609905 Dshi_3287 protein of unknown
           function DUF6 transmembrane (RefSeq)
          Length = 288

 Score = 90.5 bits (223), Expect = 4e-23
 Identities = 85/284 (29%), Positives = 133/284 (46%), Gaps = 37/284 (13%)

Query: 30  LWGGTFTAGRIAVQQLSPLAVACGRYLLATTVLL-LILWQREGWPPLNRRQQLLLFGLGV 88
           +W   FT+ RI V    PL     R+L++  + + + L   + W  L+R Q    F  G+
Sbjct: 16  MWSSAFTSARIIVAAAPPLTTLSLRFLISGLIAVGIALALGQTWR-LSRTQWKATFLFGL 74

Query: 89  SGIALYNWLFFIGLSLIPASRAALIIALNPTAIALGAAIWTGDRLRSWQWAGVGLSLIGA 148
              ALY  L F+ +  + AS AA+I +  P  +AL + +   +RLR     G+   + G 
Sbjct: 75  CQNALYLGLNFVAMQTVQASLAAIIASTMPLVVALASWLVLRERLRPLAMVGLLAGIAGV 134

Query: 149 ILLLGSR-QAGALTLPGWGDLALVGCVLCWTVYSLLARQALRSLSPLTVTTGACCWGSVL 207
           +L++G+R QAG         + LVG + C      LA       + L + T +     ++
Sbjct: 135 VLIMGARLQAG---------VDLVGVLYCGIGVLALA------FATLALRTASSGGNLLM 179

Query: 208 LIGLWLGQGA------QLP---VNVSFSTGSAIAFL------GLGGTALAFCLYANGIER 252
           ++GL +  GA       LP   + V++S    +AF       GL  T + F L    ++R
Sbjct: 180 VVGLQMLVGAVALALVGLPTETLEVTWSWQLVVAFAYTTLVPGLAATFVWFLL----VDR 235

Query: 253 LGAARAGLFINLVPVFGSAIGALLLQEPLSGLTLLGGLLVLAGV 296
           +GA RA  F  L PVFG AI A LL E L    ++G  +V  G+
Sbjct: 236 IGAVRAATFHFLNPVFGVAIAAALLGEALGARDVVGVAIVTLGI 279



 Score = 25.8 bits (55), Expect = 0.001
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%)

Query: 88  VSGIALYNWLFFIGLSLIPASRAALIIALNPT-AIALGAAIWTGDRLRSWQWAGVGLSLI 146
           V G+A   +++F+ +  I A RAA    LNP   +A+ AA+  G+ L +    GV +  +
Sbjct: 220 VPGLAA-TFVWFLLVDRIGAVRAATFHFLNPVFGVAIAAAL-LGEALGARDVVGVAIVTL 277

Query: 147 GAILLLGSR 155
           G + +  SR
Sbjct: 278 GILAVQLSR 286


Lambda     K      H
   0.325    0.142    0.454 

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: 264
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 330
Length of database: 288
Length adjustment: 27
Effective length of query: 303
Effective length of database: 261
Effective search space:    79083
Effective search space used:    79083
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 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