GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Escherichia coli BW25113

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate 16353 b2246 putative transport protein (VIMSS)

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



>FitnessBrowser__Keio:16353
          Length = 429

 Score =  288 bits (737), Expect = 2e-82
 Identities = 150/406 (36%), Positives = 231/406 (56%), Gaps = 5/406 (1%)

Query: 19  VKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLI 78
           V+L+P ++  Y+L+FLDR+NI  AK    +D G+S  AY LGAG+FF+ YA   +P+NL+
Sbjct: 15  VRLIPFMLALYVLAFLDRSNIGFAKQTYQIDTGLSNEAYALGAGIFFVVYAFLGVPANLL 74

Query: 79  MHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFN 138
           M K+GAR WI    + WG +SAAMA+   E  F ++R LL  AEAG FPG++   + WF 
Sbjct: 75  MRKLGARTWIGTTTLLWGFLSAAMAWADTEAKFLIVRTLLRAAEAGFFPGMIYLTSQWFP 134

Query: 139 REQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVW 198
           +  RA   G F +G   A  +G P+  AL+ M G +G  GW WMF++EGL AV      +
Sbjct: 135 QRNRASIMGLFYMGAPLALTLGSPLSGALLEMHGFMGHPGWFWMFVIEGLLAVGAGVFTF 194

Query: 199 RKLPDRPSKAPWLSAEE-ARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQ 257
             L D P +A +LS +E    I Q  ++E ++       +L+N    Q+ +   +Y   Q
Sbjct: 195 FWLDDTPEQARFLSKQEKTLLINQLASEEQQKVTSRLSDALRNGRVWQLAI---IYLTIQ 251

Query: 258 ITIYTVIFFLPS-IISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVT 316
           + +Y +IFFLP+ + +  G     +  ++T++PW+AA  G  LIPR++   G  R +   
Sbjct: 252 VAVYGLIFFLPTQVAALLGTKVGFTASVVTAIPWVAALFGTWLIPRYSDKTGERRNVAAL 311

Query: 317 GLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376
            LL   +G+G++ +  PV +++  C++A+ F  VQ + +  P   L G ALA G+GFVN 
Sbjct: 312 TLLAAGIGIGLSGLLSPVMAIVALCVAAIGFIAVQPVFWTMPTQLLSGTALAAGIGFVNL 371

Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRM 422
            G +GGF+ P +    E    +   GL  +A V V+ +L    LR+
Sbjct: 372 FGAVGGFIAPILRVKAETLFASDAAGLLTLAAVAVIGSLIIFTLRV 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: 500
Number of extensions: 29
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