GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Desulfovibrio vulgaris Hildenborough

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q8YPM7
         (381 letters)



>MicrobesOnline__882:206177
          Length = 596

 Score =  153 bits (386), Expect = 1e-41
 Identities = 87/204 (42%), Positives = 134/204 (65%), Gaps = 4/204 (1%)

Query: 177 GLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVM 236
           GL  +LLMA I+I +SF IG+++ +GRTS+  + R   +LYIE++RG PLI ++F     
Sbjct: 389 GLAYSLLMAVIAISVSFFIGLVVGIGRTSDNRICRIPCLLYIELIRGNPLIIVIFWIYFF 448

Query: 237 LPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVL 296
           +P+ F  +   +    A   L LF+ AY+AE VR G+Q +  GQVEAA + GL     + 
Sbjct: 449 IPVLF--NTFFNVFWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMR 506

Query: 297 LIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLF 356
            I+LPQAL+ +IPA+VGQFI +FKDTSL  ++G++ELT +A+ I    + +    E+Y  
Sbjct: 507 RIILPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQGI--NNRLMVYPMEIYGT 564

Query: 357 IGLIYWLFCYSMSLASRRLERQLN 380
           +  +Y++ C+SMS+ + RLER+L+
Sbjct: 565 VAFLYFICCWSMSVYAARLERRLS 588



 Score = 91.3 bits (225), Expect = 7e-23
 Identities = 56/164 (34%), Positives = 90/164 (54%), Gaps = 6/164 (3%)

Query: 177 GLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVM 236
           GL +T+ ++ IS  L+  +G +L + R S    +R  +   +E  R  PL+  LF     
Sbjct: 60  GLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFA 119

Query: 237 LPLFFAADVRL------DRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLN 290
            P     ++R            A  GL ++++A+MAE +R GLQ++ +G +EAA + GLN
Sbjct: 120 FPAILPENIRELLFTGNFEFWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLN 179

Query: 291 TFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELT 334
              V+  I+LP A RA+IP L  +F+   K++SL  +VG+ ELT
Sbjct: 180 YVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELT 223


Lambda     K      H
   0.332    0.145    0.452 

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: 671
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 381
Length of database: 596
Length adjustment: 33
Effective length of query: 348
Effective length of database: 563
Effective search space:   195924
Effective search space used:   195924
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 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:

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