GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Pseudomonas fluorescens FW300-N2E3

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04465
          Length = 571

 Score =  366 bits (939), Expect = e-105
 Identities = 226/529 (42%), Positives = 309/529 (58%), Gaps = 61/529 (11%)

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

Query: 61  EGAGGIIFDNLAIIFALGVAIGLA-SGDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADA 119
             AG +IF NLA+IFA+G+A+G A   +G A +A  +G++V+  T+         K  DA
Sbjct: 44  HDAGQVIFANLALIFAIGIAVGFARDNNGTAGLAGAIGYLVMVSTL---------KVLDA 94

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

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

Query: 240 FGSYKN-AAGQIIHGD-QRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAK 297
           FGS+ +   G I+ GD  R F    +       G+FM G FP+M+FGLPAA LA+Y+ A 
Sbjct: 203 FGSFTDPTTGAIVTGDLARYFAGDPK------GGQFMTGMFPMMIFGLPAACLAMYRNAL 256

Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357
            E +KV+ G+ LS ALTSFLTG+TEP+EF+F+F+APLL+ +H +L G++  I   L++HL
Sbjct: 257 PERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVLLTGMAMAITNALNIHL 316

Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGRE---- 413
           G+TFSGG ID  L       T  WLV PVGL YA IYY++F F I +FN KTPGRE    
Sbjct: 317 GFTFSGGAIDMAL--GWGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFNLKTPGREGVVV 374

Query: 414 -DKEVKSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGAS 472
            +K V S N  A       + A+GG  N+  + AC TRLR+E+ D+ K    ELK LGA 
Sbjct: 375 GEKVVLSENQRAG----AYIQALGGAENLITVGACTTRLRLEMVDRNKASDSELKALGAM 430

Query: 473 GVLE--VGNNMQAIFGPKSDQIKHDMQQIMDGKITS-PEETTVTEEGDK 518
            V+    G ++Q + GP +D I  +++Q M    ++      VTEE  K
Sbjct: 431 AVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPK 479



 Score = 37.0 bits (84), Expect = 3e-06
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 430 KVLDAMGGKANIKHLDA-CITRLRVEVNDKAKVDVQELKDLGASGVLEV-GNNMQAIFGP 487
           K L+A+GG  N+  LD   +TR+R+++ D   +   +LKDLG  GV  + G     + G 
Sbjct: 490 KWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDGGVWHLLIGD 549

Query: 488 KSDQIKHDMQQIMD 501
           K+  +   ++ +++
Sbjct: 550 KALSLSEALEGLVN 563


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: 1003
Number of extensions: 53
Number of successful extensions: 8
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: 571
Length adjustment: 37
Effective length of query: 638
Effective length of database: 534
Effective search space:   340692
Effective search space used:   340692
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