GapMind for catabolism of small carbon sources

 

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

Align Histidine transport system permease protein HisM (characterized)
to candidate 3608832 Dshi_2224 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= SwissProt::P0A2I7
         (235 letters)



>FitnessBrowser__Dino:3608832
          Length = 268

 Score =  126 bits (317), Expect = 4e-34
 Identities = 74/209 (35%), Positives = 115/209 (55%), Gaps = 13/209 (6%)

Query: 33  SVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLLVFYSGMYTLEIVKGTD 92
           +++ G  LA  +A+G+ S    +R P   F ++FRG+PL++Q  + Y     L+ V    
Sbjct: 50  ALLFGFFLATAVALGKASDRAVLRVPADWFIFVFRGSPLFIQFFLAYFLFIQLKAVSP-- 107

Query: 93  LLNAF--FRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGFSSFKMYRCI 150
              AF  F S     ++ L LNT AY  EIF GA+RSVP G++EAA AYG + +  +R +
Sbjct: 108 ---AFDPFTSAWAGALVVLFLNTSAYAGEIFYGALRSVPKGDLEAADAYGLAGWTKFRRV 164

Query: 151 ILPSALRIALPAYSNEVILMLHSTALAFTATVP------DLLKIARDINSATYQPFTAFG 204
             P+ LR+A P+Y+NE I + H+T L F A  P      D L  A+     T+ PF  + 
Sbjct: 165 TWPTMLRLAWPSYTNEAIFLFHATTLVFFAGFPAFQQRGDALYYAQYFADKTFNPFIPYP 224

Query: 205 IAAVLYLLISYVLISLFRRAERRWLQHVS 233
           I A  ++L++  +I +F    RR  +H++
Sbjct: 225 IVAFYFILLTLAVIFVFSLINRRLNRHLA 253


Lambda     K      H
   0.330    0.141    0.429 

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: 163
Number of extensions: 9
Number of successful extensions: 2
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: 235
Length of database: 268
Length adjustment: 24
Effective length of query: 211
Effective length of database: 244
Effective search space:    51484
Effective search space used:    51484
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 (21.9 bits)
S2: 46 (22.3 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