GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC' in Herbaspirillum seropedicae SmR1

Align RnsD, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate HSERO_RS07090 HSERO_RS07090 ABC transporter permease

Query= TCDB::Q8DU39
         (318 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS07090 HSERO_RS07090 ABC
           transporter permease
          Length = 306

 Score =  126 bits (316), Expect = 8e-34
 Identities = 94/294 (31%), Positives = 135/294 (45%), Gaps = 19/294 (6%)

Query: 6   MLALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFGK 65
           +L  L +  +   TP +F S+G   +E+ G VN+GLEGI+V GA  G      +A SF  
Sbjct: 9   LLLALFAGAIRVGTPFLFVSLGECLTEKGGRVNLGLEGILVCGAMTG------YAASFYS 62

Query: 66  ATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNKGQT 125
            + W+  L  G  GLL  +LH +     R + I  G  L LL   LA F  K        
Sbjct: 63  GSAWLGVLAAGCTGLLLGVLHGVVCSLPRVNDIAFGIALMLLGTGLAFFLGKPFIQPQAP 122

Query: 126 DNISQSFGKFDF-PILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGLRLRSV 184
              S   G +     L H   +  +FF G        VL  V  W  L+ T++GL LR V
Sbjct: 123 MLPSIDLGAWSSNDRLHHALQINALFFIG-------VVLALVLQWG-LSATRWGLALRLV 174

Query: 185 GEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFIALAAM 244
           G+H + A  LG  +   R       G L  +GGA  +     ++      G G +A+A +
Sbjct: 175 GDHAETARALGYRLTGTRIAATAAGGFLAAVGGAYLSLYYPGSWNEGLSSGQGLMAVALV 234

Query: 245 IFGKWNPIGAMLSSLFFGLSQSLAVIGGQLPFLSKIPTVYL-QIAPYALTILVL 297
           IF +W P   +L++L FG + +L   G  L  +      YL   APYALT+L++
Sbjct: 235 IFARWQPWRCLLAALLFGAAGAL---GPALQAVGVTSGYYLFNAAPYALTLLIM 285


Lambda     K      H
   0.328    0.143    0.422 

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: 243
Number of extensions: 14
Number of successful extensions: 4
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: 318
Length of database: 306
Length adjustment: 27
Effective length of query: 291
Effective length of database: 279
Effective search space:    81189
Effective search space used:    81189
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: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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