GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::BFirm:BPHYT_RS16105
         (291 letters)



>FitnessBrowser__Dino:3609759
          Length = 275

 Score =  159 bits (401), Expect = 9e-44
 Identities = 82/260 (31%), Positives = 155/260 (59%), Gaps = 3/260 (1%)

Query: 33  VIAWLVALLLFFPIFWMTITAFKTEQQAYASSLFFIPTLDSFREVFARSNYFSFA-WNSI 91
           +IA +  +L+  PI W+ + AFK+    Y   LFF PTL++F  VF          +NS 
Sbjct: 18  IIAAMFVMLV--PILWIFLAAFKSHVDVYQLKLFFTPTLENFGTVFDDPYRLGEKLFNST 75

Query: 92  LISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGL 151
           +++    ++ + +A  AAY+ + F       +L+ +L+T+ +P+V +++P ++++++ GL
Sbjct: 76  VVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQFLPAVVIILPFFIMFRDIGL 135

Query: 152 LDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPG 211
           LD+  GL++V   I +P A+WM   +   IP D  EA  +DG++  Q I  +++PM+ PG
Sbjct: 136 LDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVDGSSRLQVIWNIVLPMAAPG 195

Query: 212 LASTALLLVILSWNEAFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVAPIL 271
           L ++ +   I++WNE  +++ L++ +A  L + +A +   EG  W  LSAA ++ +AP+ 
Sbjct: 196 LLTSGIFCFIIAWNEFLFALILTNKDAVTLPIGLALFKGEEGDLWNLLSAAGIIIMAPMF 255

Query: 272 IVGWLSQKQLVRGLTFGAVK 291
           ++  + +K  V+G+T GAV+
Sbjct: 256 VLALMIRKYFVQGMTMGAVR 275


Lambda     K      H
   0.326    0.136    0.421 

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: 268
Number of extensions: 11
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 291
Length of database: 275
Length adjustment: 26
Effective length of query: 265
Effective length of database: 249
Effective search space:    65985
Effective search space used:    65985
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