GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Dethiosulfovibrio salsuginis USBA 82

Align Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter (characterized)
to candidate WP_085545458.1 B9Y55_RS11270 dicarboxylate/amino acid:cation symporter

Query= SwissProt::O59010
         (425 letters)



>NCBI__GCF_900177735.1:WP_085545458.1
          Length = 400

 Score =  343 bits (880), Expect = 5e-99
 Identities = 197/411 (47%), Positives = 265/411 (64%), Gaps = 24/411 (5%)

Query: 11  PVLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGA 70
           P++ +I IG +LG   G  LG         + V+P G +F+ LLKML++P+VF+SLVVG 
Sbjct: 9   PLIWRITIGFVLGIAAGAFLG------PKVSIVEPVGKVFITLLKMLIVPLVFSSLVVGV 62

Query: 71  ASIS-PARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPP 129
           +SI  P  LGR+GVK ++ YL+T+A A+ +G+ M   F PG+G+ +  G +    + AP 
Sbjct: 63  SSIGEPKTLGRIGVKTILIYLMTTAVAIVIGLGMGHFFQPGSGMAIE-GVEAAAGRAAPA 121

Query: 130 LVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAING 189
           L ++++ + P NP  ALA G +L  I FA+  GIA   L   + + V       +  +  
Sbjct: 122 LSEVIIGMFPDNPVQALAQGHMLQIIVFALFFGIA-AMLAGDKGKPV-------ISFMES 173

Query: 190 LAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFV 249
           +AE MYK+ + VM  AP GVFALIA  +++ G+ V+   AKV  AVY+G  +  ++VY  
Sbjct: 174 MAETMYKVTDLVMNLAPYGVFALIAVTVSKYGLSVLAPFAKVIGAVYLGCIVHAIVVYSG 233

Query: 250 LLKIYGI-DPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKE-MGISEGIYSFTLPLGA 307
           L+ +     PI F K  ++A LTAFVTRSSS TLPVTM   +E MGISE I SF LPLGA
Sbjct: 234 LVAVVTKKSPIWFFKGIQEASLTAFVTRSSSATLPVTMTCTQENMGISEKISSFVLPLGA 293

Query: 308 TINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVL 367
           TINMDGTALYQGVC  FIA A G  L++G Q+ I++TA LAS+GTAGVPGAG IML +V+
Sbjct: 294 TINMDGTALYQGVCALFIAQAFGIDLSIGAQVGIIVTATLASVGTAGVPGAGLIMLTLVV 353

Query: 368 ESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEGE 418
              GLP+         AM+ GIDA+LDM RT +NVTGD   TA++AKTEGE
Sbjct: 354 TQAGLPM------EGVAMVAGIDAVLDMARTSLNVTGDACVTAVIAKTEGE 398


Lambda     K      H
   0.325    0.141    0.396 

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: 509
Number of extensions: 31
Number of successful extensions: 7
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: 425
Length of database: 400
Length adjustment: 31
Effective length of query: 394
Effective length of database: 369
Effective search space:   145386
Effective search space used:   145386
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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:

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