GapMind for catabolism of small carbon sources

 

Alignments 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 SMc01946 SMc01946 leucine-specific binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__Smeli:SMc01946
          Length = 372

 Score =  576 bits (1485), Expect = e-169
 Identities = 281/360 (78%), Positives = 315/360 (87%)

Query: 1   MKKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60
           MKKSLLSAVALTAM+AFSG AWAD+L+ V GPLTGPNAAFGAQLQKGAEQAA DINAAGG
Sbjct: 1   MKKSLLSAVALTAMVAFSGTAWADILVGVGGPLTGPNAAFGAQLQKGAEQAAEDINAAGG 60

Query: 61  INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120
           INGEQIK+ LGDDVSDPKQG+SVA KF ADGVKFV+GHFNSGVSIPASE+YAENGIL+  
Sbjct: 61  INGEQIKVVLGDDVSDPKQGVSVAQKFVADGVKFVVGHFNSGVSIPASEIYAENGILQVT 120

Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180
           P    P     GLWNTFRTCGRDDQQGA+AG Y+A +FKDAK+AV+HDKTPYGQGLADET
Sbjct: 121 PASTNPQFTERGLWNTFRTCGRDDQQGAVAGAYIAANFKDAKVAVIHDKTPYGQGLADET 180

Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240
           KK+MN AGVTE +YEGIN GDKDFSALIAKMK+AGVSI+Y+GGLHTEAGLI+RQ  DQGL
Sbjct: 181 KKSMNEAGVTEALYEGINTGDKDFSALIAKMKQAGVSIVYYGGLHTEAGLIMRQMKDQGL 240

Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLY 300
           KAT++SGDGIVSNELASIAGDAV GTL TF PDP  +PA K+LVEKF+AAGF PEAYTLY
Sbjct: 241 KATMMSGDGIVSNELASIAGDAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEAYTLY 300

Query: 301 SYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWKK 360
           +YAA+Q IA  AKAAG+ DP+AVA+A+K KGPF T +G++ FDEKGD   P Y+MY WKK
Sbjct: 301 AYAALQVIAEGAKAAGNTDPQAVAEAIKAKGPFKTAIGELGFDEKGDITRPDYVMYTWKK 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: 591
Number of extensions: 11
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: 381
Length of database: 372
Length adjustment: 30
Effective length of query: 351
Effective length of database: 342
Effective search space:   120042
Effective search space used:   120042
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.

Links

Downloads

Related tools

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