GapMind for catabolism of small carbon sources

 

Aligments 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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