GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctM in Desulfovibrio vulgaris Miyazaki F

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= reanno::PV4:5208943
         (465 letters)



>lcl|FitnessBrowser__Miya:8501407 DvMF_2137 TRAP dicarboxylate
           transporter, DctM subunit (RefSeq)
          Length = 427

 Score =  270 bits (691), Expect = 5e-77
 Identities = 166/457 (36%), Positives = 254/457 (55%), Gaps = 44/457 (9%)

Query: 6   LFISLFLCMLLGMPIAIALG---FSSMLTILLFSDDSLASV-ALKLYESTSEHYTLLAIP 61
           LF  + L   L  P+A+ALG   F+++L   L     L  + A++   + ++ + LLA+P
Sbjct: 6   LFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFPLLAVP 65

Query: 62  FFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGS 121
            F+L+   +S GG++RRI+  A   VGH+ GGLA  SV++ M FA VSGS+ A  AA+GS
Sbjct: 66  LFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADTAAVGS 125

Query: 122 IVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLM 181
           I+I  M+R GYP   A  V    G +G++IPPSI M+V+ A T  S  R+F  G++PGL+
Sbjct: 126 ILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGVLPGLL 185

Query: 182 MGL-LLMLAIYIVARIKKLPSRPFP--GFRPLAISSAKAMGGLALIVIVLGSIYGGIASP 238
           MG  L+ L +    R  ++P R F      P   S A A+G  A   I+LG+I GG+A+ 
Sbjct: 186 MGASLVALCVVEARRTGRVPERRFDARALWPAIRSGAWALGAPA---IILGTIIGGVATA 242

Query: 239 TEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKE 298
           TE+AA+A  YA  + ++ +R++       WRD                            
Sbjct: 243 TESAAMAVAYALPVGLYAHREL------RWRD---------------------------- 268

Query: 299 IRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLL 358
           +  +       S +++ IIA A LF  V+  ER+P  IA  ++ +       L++VNLLL
Sbjct: 269 LPRLALCAGVTSAVVMLIIAAASLFGWVMALERLPQAIAAWMLSLSGDRIVLLLLVNLLL 328

Query: 359 LAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAG 418
           L  G F+E +A +L+  P+L P+   LGID +HLG+I+VVN+ IGMLTPP+G+ L V+  
Sbjct: 329 LVVGAFLETTAAILLFVPVLVPLLPALGIDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCS 388

Query: 419 ITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFL 455
           I    +  +  + +P L +L+  L L+T+ P + L+L
Sbjct: 389 IARIPLSAISRAIVPMLVVLIVDLLLVTFFPPLVLWL 425


Lambda     K      H
   0.330    0.144    0.424 

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: 610
Number of extensions: 44
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 465
Length of database: 427
Length adjustment: 32
Effective length of query: 433
Effective length of database: 395
Effective search space:   171035
Effective search space used:   171035
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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