GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Dyella japonica UNC79MFTsu3.2

Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate N515DRAFT_1367 N515DRAFT_1367 Predicted arabinose efflux permease, MFS family

Query= SwissProt::Q47421
         (501 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1367
          Length = 437

 Score =  217 bits (553), Expect = 6e-61
 Identities = 139/424 (32%), Positives = 231/424 (54%), Gaps = 24/424 (5%)

Query: 26  KAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPG-VQMIAALATFSVPFLIRPLGG 84
           + +  AALG A+E++DF V+ F   ALGQ+FFP   P  +  +     F+  +L RPLGG
Sbjct: 24  RTLALAALGGALEFYDFVVFVFFTKALGQLFFPADMPEWLAQVQVYGIFAAGYLARPLGG 83

Query: 85  VFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGG 144
           +     GD+ GR+++  +++ +M++ T CIGL+P+Y ++G++AP+LLLL ++ QG ++GG
Sbjct: 84  IVMAHFGDRTGRKRMFTLSVFLMALPTLCIGLLPTYAQLGVFAPMLLLLLRVVQGVAIGG 143

Query: 145 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLP 204
           E  GA +FVAE++P  + GF  + L  G  AG ++G+ V   + T +G +  LA+GWRLP
Sbjct: 144 EVPGAWVFVAEHAPPGRVGFACASLTSGLTAGILIGSLVAAGV-TGMGAEKMLAYGWRLP 202

Query: 205 FFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSLLV 264
           F L    G   ++LR  L ETP F +  E+ E      LK         + T H   +L+
Sbjct: 203 FILGGVFGFFAVWLRRWLSETPVFAELRERKELASELPLK--------RVMTGHLGGVLL 254

Query: 265 CIGLVIATNVTYYMLLTYMPSYLSHSLHYSEN---HG-VLIIIAIMIGMLFVQPVMGLLS 320
            + +         +++   P+ +  S H  +    HG  L  + +  G +      G+  
Sbjct: 255 SMLVTWMLTAAVVVVILMTPTLVQSSFHLPQKLAFHGNSLAALMLCFGCI----AGGVAV 310

Query: 321 DRFGRKPFVVIGSVAMFFLAVPSFMLINSDIIGL-IFLGLLMLAVILNAFTGVMASTLPA 379
           DRFGR   +++GSVA   L V +++L      G   F+ L  LA +     GV+ + + A
Sbjct: 311 DRFGRGWSLLVGSVA---LLVTTYLLYRDLGQGAEHFMLLYALAGLCVGVVGVVPAVMVA 367

Query: 380 LFPTHIRYSALASAFNISVLIAG-LTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLF 438
            FP  +R+S L+ ++NI+  + G +TP + A+L  +      PA+Y+ V A IG+L  ++
Sbjct: 368 AFPPAVRFSGLSFSYNIAYAVFGAITPPLIAYLA-AKLGPMAPAHYVAVTAAIGVLCAVY 426

Query: 439 MKET 442
           +  T
Sbjct: 427 LLTT 430


Lambda     K      H
   0.327    0.142    0.427 

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: 582
Number of extensions: 37
Number of successful extensions: 6
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: 501
Length of database: 437
Length adjustment: 33
Effective length of query: 468
Effective length of database: 404
Effective search space:   189072
Effective search space used:   189072
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