GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Sinorhizobium meliloti 1021

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 SMc00078 SMc00078 Leu/Ile/Val-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|FitnessBrowser__Smeli:SMc00078 SMc00078 Leu/Ile/Val-binding
           protein
          Length = 368

 Score =  349 bits (895), Expect = e-101
 Identities = 172/360 (47%), Positives = 241/360 (66%), Gaps = 1/360 (0%)

Query: 1   MKKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60
           M+ S L+ +AL A +AF+  A AD+ I V  PLTGP AAFG Q++ GAE A   IN+AGG
Sbjct: 1   MRLSRLTGMALAASVAFAPLAHADITIGVITPLTGPVAAFGEQVKNGAEAAVEAINSAGG 60

Query: 61  INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120
           +NGE++ +++ DD  +PKQ +SVAN+ A +G+++V+G   SG S+PAS+V AENGIL   
Sbjct: 61  VNGEKLVVKIVDDAGEPKQAVSVANQLAGEGIQYVVGPVLSGTSMPASDVLAENGILMVT 120

Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180
           P    PDL   GLWN  RTCGRDDQQ  +A  Y+  +FKD ++AV+HDK  YG+GLAD  
Sbjct: 121 PTATTPDLTTRGLWNVLRTCGRDDQQAVVAADYVVKNFKDKRVAVLHDKGAYGKGLADGF 180

Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240
           K A+NA G+TEV+YEG+  G+KDF A++ ++K   V ++Y+GG H E GL+ RQ  DQG+
Sbjct: 181 KAAINAGGITEVVYEGLTPGEKDFGAIVTRLKAENVDVVYFGGYHAEGGLLARQMHDQGV 240

Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLY 300
           KA L+ GDG+ + E  +I G+A +GT+ T   D T NPA   ++E  KA     EA+TL 
Sbjct: 241 KAQLLGGDGLSNTEFWAIGGEAASGTVYTNASDATRNPAAAPVIEALKAKNIPAEAFTLN 300

Query: 301 SYAAMQTI-AGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359
           +YAA+Q + AG  KA  + D  AVA A+K      TV+G +++ E GD   P + +Y+W+
Sbjct: 301 AYAAVQVLKAGIEKAGSTEDATAVATAIKSGEAIDTVIGKLTYGESGDLTSPSFSLYKWE 360


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: 395
Number of extensions: 15
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: 381
Length of database: 368
Length adjustment: 30
Effective length of query: 351
Effective length of database: 338
Effective search space:   118638
Effective search space used:   118638
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 preprint 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