GapMind for catabolism of small carbon sources

 

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

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate N515DRAFT_0013 N515DRAFT_0013 aerobic C4-dicarboxylate transport protein

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0013
          Length = 433

 Score =  514 bits (1324), Expect = e-150
 Identities = 258/423 (60%), Positives = 334/423 (78%), Gaps = 1/423 (0%)

Query: 4   SLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAG 63
           + F+  YF VL AI  G L+GH+ PE G  +KPLGDGF+ L+KM+I P+IF TVV GIAG
Sbjct: 3   AFFRHFYFWVLAAIVAGGLIGHYAPETGVALKPLGDGFIALVKMLIGPIIFLTVVLGIAG 62

Query: 64  MESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQ 123
           +  +K VGR GA A+LYFE+VS+ AL+IGL++VN ++PGAG N  PA+LDA AVA YA+ 
Sbjct: 63  VSDVKKVGRVGAKAILYFEVVSSFALVIGLVVVNTLKPGAGFNATPASLDATAVAKYANA 122

Query: 124 AKDQGIVAFIMDVIPASVIGAFAS-GNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFS 182
           A +QG V F++ +IP +   AF+  G++LQVLL A+LFGFA+  LG + + +   +E+ S
Sbjct: 123 AHEQGTVPFLLHLIPKTFSDAFSGDGDLLQVLLLALLFGFAMIHLGERARPVMTFLEALS 182

Query: 183 QVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIA 242
           +V F I+ MIMRLAP+GA GAMAFTIGKYGV +L  L +L+  FY+ CILFVV+VLG+IA
Sbjct: 183 KVFFRIMGMIMRLAPLGAMGAMAFTIGKYGVHSLGPLLKLMGSFYLACILFVVVVLGAIA 242

Query: 243 KATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNL 302
           +ATGFSIFKF+RYIREELL+VLGTSSSESAL  ++ K+E+LGC KSVVGLV+P+GYSFNL
Sbjct: 243 RATGFSIFKFLRYIREELLLVLGTSSSESALVPLMQKLERLGCSKSVVGLVVPSGYSFNL 302

Query: 303 DGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVG 362
           DGT+IYLTMAA+F+AQA   ++ +  ++TLL V +L+SKGA+GVTG+GFI LAATL+ V 
Sbjct: 303 DGTNIYLTMAAIFVAQALGVELTLSQELTLLAVAMLTSKGASGVTGAGFITLAATLAVVP 362

Query: 363 HLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPDGK 422
            +PVAGL+LILGIDRFMSEARA+TN++GNGVAT+VV+ W KELDH  L   L+ R+P   
Sbjct: 363 SVPVAGLSLILGIDRFMSEARAITNIIGNGVATVVVSHWEKELDHASLQAALDGRSPSPA 422

Query: 423 THE 425
             E
Sbjct: 423 ADE 425


Lambda     K      H
   0.327    0.142    0.401 

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: 605
Number of extensions: 26
Number of successful extensions: 3
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: 428
Length of database: 433
Length adjustment: 32
Effective length of query: 396
Effective length of database: 401
Effective search space:   158796
Effective search space used:   158796
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