GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Dyella japonica UNC79MFTsu3.2

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2414
          Length = 358

 Score =  163 bits (413), Expect = 5e-45
 Identities = 107/316 (33%), Positives = 168/316 (53%), Gaps = 17/316 (5%)

Query: 36  LPVLVLLCIGFSVLTENFAGWQ--------NLSIIAQQASINMVLAAGMTFVILTGGIDL 87
           L  L+LL  G  +    F   Q        NL  IA +A+   +++ GMT VI   G+D+
Sbjct: 34  LLTLILLLAGNGLFNPGFLALQWRDGHLYGNLIDIAHRAAPLALVSLGMTLVIALRGLDI 93

Query: 88  SVGSILSISAVVAMLV-------SLMPQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPF 140
           SVG++L+I+A VA           L+P    L++ AAL  G L G+ NG LV    + P 
Sbjct: 94  SVGAVLAIAATVAAWTIGHVSNDGLLPL--WLAIAAALAAGALCGLWNGWLVVGAGMQPI 151

Query: 141 IVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLR 200
           + TL  + A RG+A+ +     +      ++F+GNG VLG+P+ + +  AV A+    LR
Sbjct: 152 VATLILMVAGRGIAQSISGGQILTLYYAPYSFLGNGFVLGLPFSLFVVAAVFALLQLALR 211

Query: 201 RTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLG 260
           +T LGL + A+G N +AA ++G++   + L  Y   G+ A L G++ S+ + +A+    G
Sbjct: 212 KTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSSNVNSADANNAG 271

Query: 261 QSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVI 320
              ELDAI AV LGG+   GG  S+ G+L+GALII  L+  +  +GV       +K +++
Sbjct: 272 LLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIGVPPQVNLAVKAVLV 331

Query: 321 IGAVALDSYRRKGSAR 336
              + L S   +G  R
Sbjct: 332 FAVMLLQSPLCRGQLR 347


Lambda     K      H
   0.325    0.141    0.409 

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: 362
Number of extensions: 19
Number of successful extensions: 2
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: 337
Length of database: 358
Length adjustment: 29
Effective length of query: 308
Effective length of database: 329
Effective search space:   101332
Effective search space used:   101332
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: 49 (23.5 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