GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Dinoroseobacter shibae DFL-12

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 3607682 Dshi_1091 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__Dino:3607682
          Length = 424

 Score =  303 bits (776), Expect = 7e-87
 Identities = 168/424 (39%), Positives = 259/424 (61%), Gaps = 6/424 (1%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILL--FSPDSVRSLAIKLFETSEHYTLLA 58
           MTI+ + + LF+L+ +GVP+A +LG  G   ++L  FSP         +  T + + LLA
Sbjct: 1   MTIILILVALFVLLLLGVPVAFALGGMGLAMLILGGFSPLMAPQ---SILSTLDGFILLA 57

Query: 59  IPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAV 118
           +P FLL    +  GGV R L     A VGH  GGLA+A +L+C LFAA+SGSS AT A +
Sbjct: 58  VPLFLLMSNLLLKGGVGRDLFAAVQAWVGHWPGGLAVATILSCALFAAISGSSVATAATI 117

Query: 119 GSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPG 178
           G++AI  M+  GY + F  G++   GTLGILIPPSI M+VY   TE SV  LF+AG+ PG
Sbjct: 118 GTVAIPEMINRGYEKKFVYGLLAAGGTLGILIPPSIPMIVYGFVTEQSVIALFLAGIGPG 177

Query: 179 LLLGLILMVVIYIVARVK-KLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTP 237
           LLL  + ++   + AR+      +P+ ++ E ++++++AL  + L  +++ G+YSGAFTP
Sbjct: 178 LLLVTLFVLFAMLHARLSGTYTPVPKATMAERMSASKRALPSVALAALVIVGLYSGAFTP 237

Query: 238 TEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQI 297
           TEAAA+ +  +  +     R +      + + ES   T  ++ I+A A +F   +   +I
Sbjct: 238 TEAAAIGSAAALAIVTLWLRTLTWVTFWEAVRESAITTAAILLIVAGAKVFGKAIALYRI 297

Query: 298 PQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHL 357
           PQ I++++T++   P MF++VV++VLL+ G   E  ++ILI+ P+  P AM LG DPI  
Sbjct: 298 PQDISAFLTQVIDGPIMFIVVVSLVLLLMGLVFEALSMILIMTPVLLPAAMGLGFDPIWF 357

Query: 358 GIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVS 417
           GI MV+ +E  LITPPVGLNL+V  +V    L    R   P+L+++LV + ++   P ++
Sbjct: 358 GIYMVIMVECALITPPVGLNLYVIQSVARTTLSNVARGVWPFLILMLVTVGVLYAFPQLA 417

Query: 418 LALP 421
           L +P
Sbjct: 418 LYIP 421


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: 511
Number of extensions: 24
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: 424
Length adjustment: 32
Effective length of query: 395
Effective length of database: 392
Effective search space:   154840
Effective search space used:   154840
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