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_RS11250 HSERO_RS11250 MFS transporter

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



>FitnessBrowser__HerbieS:HSERO_RS11250
          Length = 435

 Score =  296 bits (758), Expect = 9e-85
 Identities = 160/404 (39%), Positives = 235/404 (58%), Gaps = 5/404 (1%)

Query: 20  KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79
           +L+PLL + Y+ S+LDR N+  AK  +  DL  S   YGLGAG+FFL Y + E+PSN+I+
Sbjct: 27  RLLPLLFLCYVASYLDRVNVGFAKLQMLQDLKFSDTVYGLGAGIFFLGYFVFEVPSNMIL 86

Query: 80  HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139
           HKVGAR WIARIM+TWG+IS AMA+V     FY++R LLG+AEAG FPGV+LYLTYW+  
Sbjct: 87  HKVGARLWIARIMITWGIISGAMAYVTTPEMFYIMRFLLGVAEAGFFPGVILYLTYWYPA 146

Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMR-MDGMLGWHGWQWMFMLEGLPAVAFAWVVW 198
            +R + T  F+ G+  + +IGGP+   +M  M G+ G  GWQWMF+LE +P++    +V 
Sbjct: 147 ARRGKITALFMTGIALSGVIGGPLSGWIMHAMPGVWGHTGWQWMFILEAIPSLILGVMVI 206

Query: 199 RKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258
             + DR   A WLS EE R +E  I+   EE   E       +   ++ L   +YFC  +
Sbjct: 207 LYMKDRIRDADWLSEEEKRLLEANISH--EESQKEHLSLGAMFANGRVWLGALIYFCFVM 264

Query: 259 TIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTGL 318
            +Y V F+LP+II   G    ++VGLLT++P+  AA   +LI R A      R  +    
Sbjct: 265 GLYGVSFWLPTIIKATGVSDPLNVGLLTAIPYAFAAAAMVLIGRSADARRERRWHVAIPA 324

Query: 319 LTMALGLGIASVSG--PVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376
               +GL +++  G     ++    L++V       + +  P + L G A A G+  +N+
Sbjct: 325 FIGCIGLLLSTQYGHNTTLAMASLTLASVGILTTLPLFWSLPTAFLSGTAAAAGIALINS 384

Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420
            G L GFV P ++G ++ +T +   G+ V+A  LV+  L  L L
Sbjct: 385 LGNLAGFVSPFLVGWLKDATQSTNAGMYVLAASLVIGGLLTLTL 428


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: 597
Number of extensions: 23
Number of successful extensions: 5
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: 435
Length adjustment: 32
Effective length of query: 406
Effective length of database: 403
Effective search space:   163618
Effective search space used:   163618
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