GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfovibrio vulgaris Hildenborough

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 206131 DVU0705 TRAP dicarboxylate transporter, putative

Query= SwissProt::Q9HU16
         (427 letters)



>MicrobesOnline__882:206131
          Length = 427

 Score =  290 bits (742), Expect = 6e-83
 Identities = 164/427 (38%), Positives = 257/427 (60%), Gaps = 4/427 (0%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60
           MTIL LF L  ++MFIGVP+A ++GLS  + I   +   + S+ I ++     Y LLAIP
Sbjct: 1   MTIL-LFGLFAVMMFIGVPLATAMGLSATVAIAA-AKLGLLSVPISVYTGVAKYPLLAIP 58

Query: 61  FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120
            F+ +G      GVA RL++F  A VG +RGGLAIA+++ CM+   +SGS PA  AAV  
Sbjct: 59  MFIFAGMVFERSGVALRLVNFTVALVGPLRGGLAIASIMVCMVLGGISGSGPADAAAVAM 118

Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAAT-ETSVGKLFIAGVVPGL 179
           + I GM  +GYP+AF AG++  AG+  ILIPPSI  ++Y+    + SV  LF AG++PG 
Sbjct: 119 VMIPGMAAAGYPKAFSAGLIAAAGSTAILIPPSIAFILYSVLVPQASVPALFAAGLIPGF 178

Query: 180 LLGLILMVVIYIVARVKKLPAM-PRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPT 238
           L G+ L++  + ++       +    S    L + ++A+WGLL  VIILGGI SG FTPT
Sbjct: 179 LAGIALIIPAWALSVRHGFGLVGDDASCGSILIAFKEAIWGLLAPVIILGGIRSGYFTPT 238

Query: 239 EAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIP 298
           EAA  A  Y  FV  FVYR + L    ++L+ES +++ ++M IIA + +FA   +T    
Sbjct: 239 EAAVAAVFYGLFVGFFVYRTLTLRGIYELLVESAEVSAVVMMIIALSSVFAWAGSTLGAF 298

Query: 299 QSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLG 358
           +++ + +  +  S  M LL V +VL+IAG F++  +I+ I  PI  P+    G + +  G
Sbjct: 299 EAMGNALIGISTSETMTLLAVVLVLIIAGMFLDGVSILFIFIPILLPVMTHFGWNAVWFG 358

Query: 359 IIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418
           +IM + + IG  TPP+ LNL VT+ +  + +  T+   L +++ + + +++V ++P ++ 
Sbjct: 359 VIMTMCLAIGQFTPPLALNLMVTTRIADIGIEETVPWVLWFVLAMTIAMLLVVFVPQLAT 418

Query: 419 ALPNWLG 425
            +P  LG
Sbjct: 419 LVPGHLG 425


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: 32
Number of successful extensions: 3
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.

Links

Downloads

Related tools

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