GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Thermoactinomyces daqus H-18

Align lysine-specific permease (characterized)
to candidate WP_033100257.1 JG50_RS0106285 amino acid permease

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_000763315.1:WP_033100257.1
          Length = 446

 Score =  280 bits (716), Expect = 7e-80
 Identities = 159/410 (38%), Positives = 237/410 (57%), Gaps = 25/410 (6%)

Query: 13  LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72
           L+++L  RH+ M+A+GG+IG G+F  S  TIS AGPG  + SY L G+++Y +M+++ E+
Sbjct: 5   LQKQLLPRHVQMMALGGAIGAGIFQGSAETISAAGPG-VIFSYALAGILLYIVMSAMAEM 63

Query: 73  AAYMPVSGSFATYGQNYVEEGFG----FALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDT 128
           A      G   T  +  V + FG    F LGW Y+  W + +AV++V A   + +WF   
Sbjct: 64  AL-----GFAGTDLRGLVHKAFGTRVSFILGWLYFIQWVLVMAVEIVTAGTFLQYWF-SV 117

Query: 129 PGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPA 188
           P W+ S +   VI  +N  SVR FGE EYW + +K+ T+IVF+I+G L++ GI   AQ  
Sbjct: 118 PVWLLSLIVTLVIIAINLFSVRLFGEIEYWLTSVKIVTLIVFVILGALLLFGIIPSAQAP 177

Query: 189 GWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWR 248
           G +N+ +    F  G+  ++   +IV FS+ GTE+IG+   E +D  K +PR ++ V  R
Sbjct: 178 GLTNYRVHGGFFPLGWQGVLSSLLIVIFSYGGTEMIGLTITEMKDAKKTLPRVIKGVILR 237

Query: 249 ILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAV 308
           I LFYV  +LII+ +IP+        D    S SPF  V    GL   A +MN ++LTAV
Sbjct: 238 ICLFYVLPLLIITGLIPW--------DQVKSSGSPFVEVLSAVGLKGVANIMNFILLTAV 289

Query: 309 LSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQ 368
           +SA NSGMYA+TRMLY+LA + +AP  F +L + GVP  AL A++V   L  L +    +
Sbjct: 290 ISAANSGMYATTRMLYSLAGEKEAPAFFTRLGKRGVPIYALAASSVCLFLGSLVAFIAPE 349

Query: 369 TVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFP 418
           +V+ +L+   G T  + W+ I +SH + R  Y           +R  FFP
Sbjct: 350 SVFQYLMGIPGYTVILTWILICLSHLKLRGKYE------RTPDFRLSFFP 393


Lambda     K      H
   0.327    0.142    0.451 

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: 660
Number of extensions: 47
Number of successful extensions: 5
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: 489
Length of database: 446
Length adjustment: 33
Effective length of query: 456
Effective length of database: 413
Effective search space:   188328
Effective search space used:   188328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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