GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Klebsiella michiganensis M5al

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate BWI76_RS19985 BWI76_RS19985 MFS transporter

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



>FitnessBrowser__Koxy:BWI76_RS19985
          Length = 429

 Score =  289 bits (740), Expect = 1e-82
 Identities = 151/405 (37%), Positives = 231/405 (57%), Gaps = 5/405 (1%)

Query: 20  KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79
           +L+P ++  Y+L+FLDR+NI  AK    +D G+S  AY LGAG+FF+ YA   +P+NL+M
Sbjct: 16  RLIPFMLALYVLAFLDRSNIGFAKETYQLDTGLSNEAYALGAGIFFVVYAFLGVPANLLM 75

Query: 80  HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139
            K GAR WI    + WGL+SAAMA+   E  F ++R LLG AEAG FPG++   + WF +
Sbjct: 76  RKFGARKWIGCTTLLWGLLSAAMAWADTEAKFLLVRTLLGAAEAGFFPGMIYLTSQWFPQ 135

Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWR 199
           + RA   G F +G   A  +G P+  AL+ M G +G  GW WMF++EGL AV   +  + 
Sbjct: 136 QNRASIMGLFYMGAPLALTLGSPLSGALLEMHGFMGHPGWFWMFIIEGLLAVGAGFFTFF 195

Query: 200 KLPDRPSKAPWLSAEEARGIEQRIA-QETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258
            L D P KA +LSA E + +   +A +E ++       +L+N    Q+ +   +Y   Q+
Sbjct: 196 WLDDTPQKARFLSAAEKQALISELASEEQKKVTSRLSDALRNGRVWQLAI---IYLTIQV 252

Query: 259 TIYTVIFFLPS-IISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTG 317
            +Y +IFFLP+ + +  G        ++T++PW+AA  G  LIPR++   G  R +    
Sbjct: 253 AVYGLIFFLPTQVAALLGTKVGFVASVVTAIPWVAALFGTWLIPRYSDRTGERRNIAAFT 312

Query: 318 LLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNAC 377
           LL  A+G+ ++ +  PV +++  C++AV    VQ + +  P   L G ALA G+GFVN  
Sbjct: 313 LLAAAIGIAVSGLVSPVLAIIALCVAAVGVIAVQPVFWTMPTQLLSGTALAAGIGFVNLF 372

Query: 378 GLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRM 422
           G +GGF+ P +    E    +   GL  +A V +V  +    LR+
Sbjct: 373 GAIGGFLAPIIRVQAETMFASDSAGLVTLACVAIVGVVIIFSLRV 417


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: 512
Number of extensions: 31
Number of successful extensions: 3
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: 429
Length adjustment: 32
Effective length of query: 406
Effective length of database: 397
Effective search space:   161182
Effective search space used:   161182
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