GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Dechlorosoma suillum PS

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate Dsui_0630 Dsui_0630 ABC-type branched-chain amino acid transport system, periplasmic component

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|FitnessBrowser__PS:Dsui_0630 Dsui_0630 ABC-type branched-chain
           amino acid transport system, periplasmic component
          Length = 434

 Score =  189 bits (479), Expect = 2e-52
 Identities = 127/345 (36%), Positives = 171/345 (49%), Gaps = 16/345 (4%)

Query: 25  VLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GINGEQIKIEL--GDDVSDPKQGI 81
           V I  A PLTGP A  G   + GA  A  ++NA G  I G ++K EL   DD +DPKQG 
Sbjct: 46  VKIGHASPLTGPQAHIGKDNEYGATLAIEELNAKGLEIGGAKVKFELISDDDQADPKQGT 105

Query: 82  SVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPDLHGTGLWNTFRTCG 141
           +VA KF    V  VIGH NSG +IPAS++Y + GI +       P     G    FR   
Sbjct: 106 TVAQKFVDAKVNGVIGHLNSGTTIPASKIYFDAGIPQISGSATNPTYTKQGFATAFRVMA 165

Query: 142 RDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAAGVTEVIYEGINVGD 201
            D+QQG    ++ A       +A++ D+T YGQGLADE KKA  AAG+  V  E  N   
Sbjct: 166 NDEQQGKALAQFAAKTLAAKSVAIIDDRTAYGQGLADEFKKAAEAAGLKVVASEYTNDKA 225

Query: 202 KDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVSGDGIVSNELASIAGD 261
            DF A++ K+K     +I++GG+  + G + +Q  + GLKA  ++GDG  +    ++AG 
Sbjct: 226 TDFKAILTKIKSKKPDLIFYGGMDPQGGPMAKQMKELGLKAKFLTGDGGCTPNFITLAGA 285

Query: 262 AVAGTLNT-----FGPDPTANPANKELVEKFKAAGFNPEAYTLYSYAAMQTIAGAAKAAG 316
           A  G   +         P       + V KFK      + Y  Y Y A   +  A K A 
Sbjct: 286 AAEGQYCSLPGVPLDKMPGGTVFKDKFVGKFKT---EIQLYAPYVYDATMVLVDAMKRAN 342

Query: 317 SLDPEAVAKAMKE--KGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359
           S++P   AK + E  K  F  V   I FDE GD K      YE+K
Sbjct: 343 SVEP---AKYLPEIGKTSFQGVTAKIGFDEFGDLKDGAISFYEYK 384


Lambda     K      H
   0.314    0.132    0.383 

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: 453
Number of extensions: 24
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: 381
Length of database: 434
Length adjustment: 31
Effective length of query: 350
Effective length of database: 403
Effective search space:   141050
Effective search space used:   141050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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 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