GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8501407
          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 (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