GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Acidovorax sp. GW101-3H11

Align MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Ac3H11_2942 Various polyols ABC transporter, permease component 2

Query= TCDB::O30493
         (276 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2942
          Length = 279

 Score =  353 bits (906), Expect = e-102
 Identities = 172/276 (62%), Positives = 218/276 (78%), Gaps = 6/276 (2%)

Query: 7   RRLQSLLLGTLA------WAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL 60
           RR  +  LG LA      W +A+L+FFP+ W+ LT+FKTE+ A A PP F+FTPTLEN+ 
Sbjct: 4   RRRSNFPLGLLALRTAAAWGVALLLFFPLGWLFLTAFKTELQAIAVPPLFVFTPTLENFH 63

Query: 61  HINERSNYFSYAWNSVLISFSATALCLLISVPAAYSMAFYETKRTKSTLLWMLSTKMLPP 120
            + ERS+Y  YA NSV+ S  +T L L+++ PAAY+MAF++ K TK  L+WMLSTKM+P 
Sbjct: 64  EVQERSDYLLYAKNSVITSVLSTVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPA 123

Query: 121 VGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLDGAT 180
           VG L+PIY+LA+   LLDT++ALII++ L NLPI+VWM+Y++FKDIP +ILEAAR+DGAT
Sbjct: 124 VGALVPIYVLAQKSHLLDTQLALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGAT 183

Query: 181 LWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSNAAPLTALIASYSSPEGLF 240
           LWQE+  VLLP+  GGLAST LL L+L WNEAFWSLNL+++ A  L  LIASYSSPEGLF
Sbjct: 184 LWQEVRLVLLPLGMGGLASTGLLCLVLSWNEAFWSLNLSAAKAGTLATLIASYSSPEGLF 243

Query: 241 WAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276
           WAKLSA S +A API++FGW SQKQLV+GL+FGAVK
Sbjct: 244 WAKLSAASLMAIAPIVVFGWFSQKQLVQGLTFGAVK 279


Lambda     K      H
   0.327    0.137    0.426 

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: 344
Number of extensions: 12
Number of successful extensions: 1
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: 276
Length of database: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
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: 47 (22.7 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