GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-transport in Herbaspirillum seropedicae SmR1

Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate HSERO_RS05735 HSERO_RS05735 MFS transporter

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



>FitnessBrowser__HerbieS:HSERO_RS05735
          Length = 442

 Score =  318 bits (815), Expect = 2e-91
 Identities = 165/407 (40%), Positives = 232/407 (57%), Gaps = 4/407 (0%)

Query: 20  KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79
           +++PL +I +I++++DR NI   + HL  D+GI  AAYGLGAGLFF+ YAL E+PSNL++
Sbjct: 29  RVLPLFVIMFIVNYIDRVNIGFVRSHLATDVGIGTAAYGLGAGLFFVGYALFEVPSNLLL 88

Query: 80  HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139
            + GA+ W+ RIM TWGL + AMAFV  ET+FYVLR LLG AEAG FPGV+ Y T W   
Sbjct: 89  QRFGAKAWLTRIMATWGLAATAMAFVNSETTFYVLRFLLGAAEAGFFPGVIYYFTQWLPA 148

Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWR 199
            +R RA   FL G   A+I+ GP+   L+++DG  G  GWQWMF++EG+ +V     VW 
Sbjct: 149 SERGRAMAIFLSGSALASILSGPISGGLLQIDGG-GLQGWQWMFIIEGMASVLLCGFVWF 207

Query: 200 KLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSL---KNWLTPQILLAIFVYFCH 256
            L   P+ A WL+A+E   I + I  E  E        +   +    PQIL+  F+YF  
Sbjct: 208 WLDSMPADAKWLTAQERSAITRAIVDEQAERMKHQPAQVSPRQLLRDPQILIFCFIYFSI 267

Query: 257 QITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVT 316
            +TIY   F+LPSII K G  S   VGL  S+PW+ + +        A      +    T
Sbjct: 268 SLTIYGATFWLPSIIRKMGSFSDFQVGLFNSIPWLISIVAMYAFAALAARFKHQQAWAAT 327

Query: 317 GLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376
            L+  A G+  ++    V++ +  C +AV F    S+ +  P + L     AG +  +N+
Sbjct: 328 ALVIAAAGMFASTFGNSVYAFVSICFAAVGFKAASSLFWPLPQAYLDARIAAGVIALINS 387

Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMG 423
            G LGGFV P+  G +EQ TG+   GL  +A+  +VAA      R G
Sbjct: 388 IGNLGGFVAPTAFGFLEQRTGSIQGGLMGLAITSLVAAGVVFLARSG 434


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: 542
Number of extensions: 33
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: 442
Length adjustment: 32
Effective length of query: 406
Effective length of database: 410
Effective search space:   166460
Effective search space used:   166460
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