GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Pseudomonas stutzeri RCH2

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate GFF360 Psest_0361 TRAP transporter, DctM subunit

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__psRCH2:GFF360
          Length = 426

 Score =  321 bits (823), Expect = 2e-92
 Identities = 177/424 (41%), Positives = 262/424 (61%), Gaps = 6/424 (1%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60
           + +L  F++L LL    VP+A SLGL+  L    +    + ++ I++      ++LLAIP
Sbjct: 4   VVLLGSFIVLILLR---VPVAYSLGLA-TLVGAWWIDIPLHAVMIQIAGGVNKFSLLAIP 59

Query: 61  FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120
           FF+L+GA M  GG+ARRL+ FA   VG +RGGL++  + A   F A+SGSS A  A+VGS
Sbjct: 60  FFVLAGAIMAEGGMARRLVAFAGVLVGFVRGGLSLVNITASTFFGAISGSSLADTASVGS 119

Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVY--AAATETSVGKLFIAGVVPG 178
           + I  M + GYP+ F   +  +     +L PPS   V+Y  AA    S+  LF+AG+ PG
Sbjct: 120 VLIPEMEKKGYPREFSTAVTISGSVQALLTPPSHNSVIYSLAAGGTVSIAALFVAGIGPG 179

Query: 179 LLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPT 238
           LLL   +  +  + AR +  P    V LR+ L    +ALWGL+ MVIILGGI SG FT T
Sbjct: 180 LLLSATMATLCLLFARKRNYPKGEVVPLRQALKICVEALWGLMTMVIILGGILSGVFTAT 239

Query: 239 EAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIP 298
           E+AAVA V++ FV +F+YRD + SE P++L  + +   ++M +IA A  F +++T  QIP
Sbjct: 240 ESAAVAVVWAFFVTMFIYRDYKWSELPRMLHRTVRTLSIVMILIAFAASFGYIMTLMQIP 299

Query: 299 QSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLG 358
             I +    L  + ++ L+ +N +LL+ G  M+ + +ILIL PI  P+ +  G+DP+H G
Sbjct: 300 SKITTAFLALSDNRYVILMCINFMLLVLGTLMDMAPLILILTPILLPVVVSFGVDPVHFG 359

Query: 359 IIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSL 418
           +IM+VN+ IGLITPPVG  LFV +A+  + +  T++A LP+   L   L+ VTYIP +SL
Sbjct: 360 MIMLVNLGIGLITPPVGAVLFVGAAIGKVTIENTVKALLPFYAALFAVLMAVTYIPMISL 419

Query: 419 ALPN 422
            LP+
Sbjct: 420 WLPS 423


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: 455
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 427
Length of database: 426
Length adjustment: 32
Effective length of query: 395
Effective length of database: 394
Effective search space:   155630
Effective search space used:   155630
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