GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF4494 PS417_23000 PTS
           N-acetyl-D-glucosamine transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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