GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Pseudomonas simiae WCS417

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__WCS417:GFF4494
          Length = 568

 Score =  373 bits (957), Expect = e-107
 Identities = 227/540 (42%), Positives = 315/540 (58%), Gaps = 58/540 (10%)

Query: 1   MWKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMM 60
           M++ F   LQR+G+ALMLP+AILP AGLLL LG+    D L             N+A +M
Sbjct: 1   MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDT---DLL-------------NIA-VM 43

Query: 61  EGAGGIIFDNLAIIFALGVAIGLA-SGDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADA 119
             AG  IF NLA+IFA+G+A+G A   +G A +A  +G++V+  T+         K  D 
Sbjct: 44  HDAGQAIFANLALIFAIGIAVGFARDNNGTAGLAGAIGYLVMVSTL---------KVMDT 94

Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179
           +           +  G+  GI  G +A   YN+F +I LP YL FF G+RFVPI+    +
Sbjct: 95  S-----------INMGMLAGIASGLMAGGLYNRFKDIKLPEYLAFFGGRRFVPIVTGFSA 143

Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239
             L     +IWP IQ G+N+F   L+ S + L  F+FG   RLLI  GLHHI +   WF 
Sbjct: 144 VGLGVIFGLIWPPIQHGINSFGVLLMESGS-LGAFVFGVFNRLLIVTGLHHILNNMAWFV 202

Query: 240 FGSYKN-AAGQIIHGD-QRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAK 297
           FGS+ +   G ++ GD  R F    +       G+FM G FPVM+FGLPAA LA+Y+ A 
Sbjct: 203 FGSFTDPVTGAVVTGDLTRYFAGDPK------GGQFMTGMFPVMLFGLPAACLAMYRNAL 256

Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357
            E +KV+ G+ LS ALTSFLTG+TEP+EF+F+F+AP L+ IHAVL GLS  +  +L++HL
Sbjct: 257 PERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAVLTGLSMAVTNMLNIHL 316

Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKE- 416
           G+TFSGGFID  +LG     T  WLV PVGL YA IYY +F + I  FN KTPGRED + 
Sbjct: 317 GFTFSGGFID-MVLG-WGKSTNGWLVFPVGLAYALIYYSVFNYCIRHFNLKTPGREDTQV 374

Query: 417 VKSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476
           V++  ++ ++     + A+GG  N+  + AC TRLR+++ D+ K    ELK LGA  V+ 
Sbjct: 375 VQAEAMSDNQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKAVDAELKALGAMAVVR 434

Query: 477 VGN--NMQAIFGPKSDQIKHDMQQIMDG------KITSPEETTVTEEGDKETAEIAAAGG 528
            GN  ++Q + GP +D I  +++  M G       + +P E  V     +    + A GG
Sbjct: 435 PGNGGSLQVVVGPMADSIADEIRLAMPGFVAAAPVVVAPVEKPVAVNVQEAEKWLNALGG 494



 Score = 41.2 bits (95), Expect = 1e-07
 Identities = 22/73 (30%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 430 KVLDAMGGKANIKHLDA-CITRLRVEVNDKAKVDVQELKDLGASGVLEVGNNM-QAIFGP 487
           K L+A+GG+ N++ L+A  +TRLRVE+ D + +   +L  LG  GV ++ + +   + G 
Sbjct: 487 KWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLESGVWHLLIGD 546

Query: 488 KSDQIKHDMQQIM 500
           K+  +   +++++
Sbjct: 547 KATGLGEALERLV 559


Lambda     K      H
   0.324    0.143    0.421 

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: 979
Number of extensions: 52
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 675
Length of database: 568
Length adjustment: 37
Effective length of query: 638
Effective length of database: 531
Effective search space:   338778
Effective search space used:   338778
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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