GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfovibrio vulgaris Miyazaki F

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__Miya:8501407
          Length = 427

 Score =  317 bits (813), Expect = 3e-91
 Identities = 171/430 (39%), Positives = 264/430 (61%), Gaps = 9/430 (2%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTIL---LFSPDSVRSLAI--KLFETSEHYT 55
           M  L LF  + LL  +  P+AV+LG +    +L   L  P  +  +    +L+  ++ + 
Sbjct: 1   MVGLILFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFP 60

Query: 56  LLAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATV 115
           LLA+P F+L+G  M+ GG++RR++  A+A VGH+ GGLA  +V++ M FA +SGS+ A  
Sbjct: 61  LLAVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADT 120

Query: 116 AAVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGV 175
           AAVGSI I  M+R GYP      +    G +G++IPPSI M+V+ A T  S+G+LF  GV
Sbjct: 121 AAVGSILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGV 180

Query: 176 VPGLLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAF 235
           +PGLL+G  L+ +  + AR        R   R    + R   W L    IILG I  G  
Sbjct: 181 LPGLLMGASLVALCVVEARRTGRVPERRFDARALWPAIRSGAWALGAPAIILGTIIGGVA 240

Query: 236 TPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTE 295
           T TE+AA+A  Y+  V L+ +R++R  + P++ L +G  + ++M IIA A LF  V+  E
Sbjct: 241 TATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWVMALE 300

Query: 296 QIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPI 355
           ++PQ+IA+W+  L     + LL+VN++LL+ G F+E +A IL+  P+  P+   LGID +
Sbjct: 301 RLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALGIDLV 360

Query: 356 HLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPA 415
           HLG+I+VVN+ IG++TPP+G+ L V+ ++  +PL A  RA +P L++L+V L++VT+ P 
Sbjct: 361 HLGVIVVVNLAIGMLTPPLGVCLVVSCSIARIPLSAISRAIVPMLVVLIVDLLLVTFFPP 420

Query: 416 VSLALPNWLG 425
           + L    WLG
Sbjct: 421 LVL----WLG 426


Lambda     K      H
   0.330    0.144    0.425 

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: 531
Number of extensions: 31
Number of successful extensions: 4
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: 427
Length of database: 427
Length adjustment: 32
Effective length of query: 395
Effective length of database: 395
Effective search space:   156025
Effective search space used:   156025
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: 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