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_RS22270 HSERO_RS22270 MFS transporter

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



>FitnessBrowser__HerbieS:HSERO_RS22270
          Length = 445

 Score =  299 bits (766), Expect = 1e-85
 Identities = 167/417 (40%), Positives = 246/417 (58%), Gaps = 3/417 (0%)

Query: 6   SARTPQALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFF 65
           +A +  A  K +  +L+P +++ Y++S+LDR N+  A   ++ DLG++ + +GLGAGLFF
Sbjct: 16  AAVSEDATMKKVMRRLIPFILLCYVVSYLDRINVGFAALTMNKDLGLTPSQFGLGAGLFF 75

Query: 66  LTYALSEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGL 125
           + Y   EIPSNL +H+ GAR WI+RIM++WGLIS A AFV G  SF + R LLG+AEAG 
Sbjct: 76  IGYFFFEIPSNLALHRFGARMWISRIMISWGLISMATAFVVGPKSFALARFLLGMAEAGF 135

Query: 126 FPGVMLYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFML 185
            PG+ LY T WF    R +AT +FL+G+  ANIIG P+  ALM + GM G+ GWQ + +L
Sbjct: 136 TPGIYLYFTQWFPGAWRGKATAFFLIGIPVANIIGSPLSGALMELHGMWGFKGWQVLLLL 195

Query: 186 EGLPAVAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQ 245
           E LPAV    +    LPDRP+KA WLSA+E + +E  ++ E    A   G+ LK+  T  
Sbjct: 196 EALPAVLLGVMCLFLLPDRPAKAKWLSADEKQWLENELSTEQNVLAARHGNKLKDAFTNW 255

Query: 246 ILLAIF-VYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA 304
            + A+    FC  I   ++  +LP II ++G L +  VGL+ ++P++  A+   L  R A
Sbjct: 256 RVFALAGANFCGIIGSLSIGLWLPQIIREFG-LPSHQVGLVAAIPYLVGAVAMTLWARLA 314

Query: 305 TTPGRCRRLLVTGLLTMALGLGI-ASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLK 363
               R    +   ++  AL LGI A +  P+  +L   ++       Q+  +  P+  L 
Sbjct: 315 NRSERRLFFVAGAIVLAALSLGISAFLHTPLLKMLAITVAVASILSFQATFWAIPSGFLT 374

Query: 364 GVALAGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420
           G A AGGL  + + G LGGFVGPSV+G I ++T      L  +A  L++ A+  L L
Sbjct: 375 GRAAAGGLALIVSIGNLGGFVGPSVIGFIREATQGFTYPLIFVAGALLLGAVITLAL 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: 581
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: 445
Length adjustment: 32
Effective length of query: 406
Effective length of database: 413
Effective search space:   167678
Effective search space used:   167678
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