GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Dyella japonica UNC79MFTsu3.2

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate N515DRAFT_2085 N515DRAFT_2085 Sugar phosphate permease

Query= reanno::WCS417:GFF1429
         (438 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2085
          Length = 434

 Score =  291 bits (744), Expect = 4e-83
 Identities = 158/413 (38%), Positives = 237/413 (57%), Gaps = 5/413 (1%)

Query: 19  VKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLI 78
           ++L+P L I Y+ ++LDR NI  AK  +  DL  S A YGLGAG+FF+ Y L E+PSN++
Sbjct: 21  LRLLPFLFICYVAAYLDRVNIGFAKLQMLSDLHFSEAVYGLGAGVFFIGYFLFEVPSNML 80

Query: 79  MHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFN 138
           +H++GAR WI+RIMV+W L+SAA   V   T+FYVLR LLG+AEAG FPG++LYLTYW+ 
Sbjct: 81  LHRLGARLWISRIMVSWALVSAATMLVTTPTAFYVLRFLLGVAEAGFFPGIVLYLTYWYP 140

Query: 139 REQRARATGYFLLGVCFANIIGGPVGAALMR-MDGMLGWHGWQWMFMLEGLPAVAFAWVV 197
             +R R    F+ G+  A ++GGP+   +M    G+ G   WQW+F+LE LP++A     
Sbjct: 141 SARRGRMNALFMTGIPIAGVLGGPLSGWIMHAFGGVHGLANWQWLFLLEALPSLALGIAT 200

Query: 198 WRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQ 257
              LP+    A WL A E + +E R+A + + G+     S+   +    L AI  YFC  
Sbjct: 201 PFVLPNGIRSASWLDAREKQLLEDRLAGDPQAGSEASLRSVMADVRVWRLAAI--YFCCM 258

Query: 258 ITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTG 317
           + +Y V F+LP++I+  G    + VGLLT++P+  A +  +L+ R +      R  L   
Sbjct: 259 MGLYGVSFYLPTLIAAAGVDDALDVGLLTAIPYAVAVVSMILLARSSDRHNERRWHLAAA 318

Query: 318 LLTMALGLGIASVSGP--VFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVN 375
            +  A GL  +++ G   V  L+   L          + + +P+S L G A A G+  +N
Sbjct: 319 SIAGAAGLYASTLCGSELVLGLIALSLGTAGVLSTMPVFWTWPSSVLAGTAAAAGIAMIN 378

Query: 376 ACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGHEPER 428
           + G L GFV PS++G ++  T +   GL V+A+ L++ A  AL       P R
Sbjct: 379 SIGNLAGFVSPSIIGWMKDLTHSTNAGLWVVAVALLLGAALALLGSAAKAPAR 431


Lambda     K      H
   0.327    0.141    0.438 

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: 559
Number of extensions: 28
Number of successful extensions: 6
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: 438
Length of database: 434
Length adjustment: 32
Effective length of query: 406
Effective length of database: 402
Effective search space:   163212
Effective search space used:   163212
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 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