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 GFF2081 Psest_2124 TRAP transporter, DctM subunit

Query= SwissProt::Q9HU16
         (427 letters)



>FitnessBrowser__psRCH2:GFF2081
          Length = 425

 Score =  280 bits (715), Expect = 8e-80
 Identities = 151/424 (35%), Positives = 250/424 (58%)

Query: 1   MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60
           MT++     L   M +G+PIA +L L+G++ +       V+ LA  L   ++ + LLA+P
Sbjct: 1   MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVP 60

Query: 61  FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120
           FF+L+G  M  GG++RR+I  A A  GH RGGL   A+ A +L A++SGS+ A  AA+ +
Sbjct: 61  FFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALAT 120

Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180
           + +  M   GYP +  +G+V   G +  +IPPS+  V+Y   T TS+ +LF+AG+VPGL+
Sbjct: 121 LLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVPGLI 180

Query: 181 LGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240
           +G+ L+V   ++AR    P   + S  E           L+L VII+GG+  G FTPTEA
Sbjct: 181 MGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPTEA 240

Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300
           A VAAVY+  V+  +YR++  +   +VL  + + T  +MF+ A A + A+++T  Q+P  
Sbjct: 241 AVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLPDE 300

Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGII 360
           IA+ +  L   P + ++ + ++++  G  ++ +  ILIL P+  PIA++ GIDP++ G++
Sbjct: 301 IAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVM 360

Query: 361 MVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLAL 420
            V+   IGLITPPVG  L V   +  + +   +R  +P+ +I LV + ++  +P++    
Sbjct: 361 FVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSIITVP 420

Query: 421 PNWL 424
             WL
Sbjct: 421 LAWL 424


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: 458
Number of extensions: 19
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: 425
Length adjustment: 32
Effective length of query: 395
Effective length of database: 393
Effective search space:   155235
Effective search space used:   155235
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