GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Dechlorosoma suillum PS

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Dsui_1262 Dsui_1262 TRAP transporter, DctM subunit

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__PS:Dsui_1262
          Length = 488

 Score =  187 bits (475), Expect = 6e-52
 Identities = 130/429 (30%), Positives = 223/429 (51%), Gaps = 18/429 (4%)

Query: 3   ILFLFLLLFLLMFIGVPIAVSLGLSG------ALTILLFSPDSVRSLAIKLFETSEHYTL 56
           ++F  L+LFLL   G P+A +L  +G       + + L  P   ++L  ++F    + TL
Sbjct: 11  VMFGALVLFLLF--GYPVAFALAANGMVFGFIGMELGLLHPALFQALPERVFGIMANDTL 68

Query: 57  LAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVA 116
           LAIPFF   G  +   G+A  L+D      G +RGGLA A +    L AA +G   A+V 
Sbjct: 69  LAIPFFTFMGLVLERSGMAEDLLDTIGQLFGPMRGGLAYAVIFVGALLAATTGVVAASVI 128

Query: 117 AVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVV 176
           ++G I++  M+R GY +   +G++  +GTL  +IPPS+V+++ A     SVG ++   +V
Sbjct: 129 SMGLISLPIMLRYGYDKRLASGVIAASGTLAQIIPPSLVLIIMADQLGKSVGDMYEGAMV 188

Query: 177 PGLLLGLILM--VVIYIVARVKKLPAMP--RVSLREWLASAR---KALWGLLLMVIILGG 229
           PGL+L  + +  VVI  + +    PA+P    SLR      R     +  L+L+ ++LG 
Sbjct: 189 PGLILTSLYVGYVVILTLIKPNAAPALPLEARSLRGAKLLMRVLTSLVPPLVLIFLVLGT 248

Query: 230 IYSGAFTPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFA 289
           I+ G  TPTE  A+ A  +  +AL   R + +S   + +  + KL+  ++FI+  + +F 
Sbjct: 249 IFMGIATPTEGGAMGASGALILALMRKR-LSVSLLKQAMDTTAKLSSFVVFILVGSTVFG 307

Query: 290 HVLTTEQIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAME 349
            V         +   +T L      FL+VVNI++ +   F++   +  I+ P+  P+A +
Sbjct: 308 LVFRAVNGDLWVEHLLTSLPGGQLGFLIVVNILVFVLAFFLDFFELSFIIVPLLGPVAEK 367

Query: 350 LGIDPIHLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGAT--IRAALPWLMILLVFL 407
           LGID I  G+++ VNM+   + PP G  LF   +V    +  T     A+P++ I ++ +
Sbjct: 368 LGIDLIWFGVLLGVNMQTSFMHPPFGFALFYLRSVAPASIKTTDIYWGAVPFVCIQIIMV 427

Query: 408 IIVTYIPAV 416
            ++   P +
Sbjct: 428 ALIIIFPGI 436


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: 461
Number of extensions: 22
Number of successful extensions: 2
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: 488
Length adjustment: 33
Effective length of query: 394
Effective length of database: 455
Effective search space:   179270
Effective search space used:   179270
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