GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Dechlorosoma suillum PS

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__PS:Dsui_2060
          Length = 293

 Score =  147 bits (370), Expect = 4e-40
 Identities = 92/285 (32%), Positives = 156/285 (54%), Gaps = 6/285 (2%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGIN--LW 60
           L Q + N + +GS+ AL A+G TL +G+L + N +HG    + +Y    A  S +N  LW
Sbjct: 2   LEQQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAAL-AMVSHLNAPLW 60

Query: 61  LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQN 120
           ++M    V +     + + L+ KP+RAR A     +I +IG+ + L +    ++G     
Sbjct: 61  VAMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFGAEVLR 120

Query: 121 YRVPIVPAQDFM--GIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAK 178
           +   ++PA +FM   +      + ++A+A   M VL  IL+RT++G+A+RA+A++   A 
Sbjct: 121 FPEDVMPAGEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAESPKAAY 180

Query: 179 VSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVILGGIGNPY 237
           + GINVE +   T  + A L  + G + GL    + P MG  ++    A +ILGG+G+  
Sbjct: 181 LLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILGGMGDIR 240

Query: 238 GAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282
           GA+ GG+ +G A+ +S  +  +     VA  L+ +IL +RP GLF
Sbjct: 241 GALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLF 285


Lambda     K      H
   0.329    0.143    0.450 

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: 210
Number of extensions: 13
Number of successful extensions: 4
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: 286
Length of database: 293
Length adjustment: 26
Effective length of query: 260
Effective length of database: 267
Effective search space:    69420
Effective search space used:    69420
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 (21.8 bits)
S2: 48 (23.1 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