GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Pseudomonas fluorescens FW300-N2C3

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17535
          Length = 571

 Score =  370 bits (949), Expect = e-106
 Identities = 224/543 (41%), Positives = 312/543 (57%), Gaps = 60/543 (11%)

Query: 1   MWKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMM 60
           M++ F   LQR+G+ALMLP+AILP AGLLL LG+    D L                 ++
Sbjct: 1   MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDT---DLLD--------------IAII 43

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

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

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

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

Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357
            + +KV+ G++LS ALTSFLTG+TEP+EF+F+F+APLLF +HA+L G+S  +  LL +HL
Sbjct: 257 PQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLFLVHALLTGVSMAVTNLLGIHL 316

Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEV 417
           G+TFSGGFID  +LG     T  WLV+PVGL YAAIYY++F F I +F+ KTPGRE+   
Sbjct: 317 GFTFSGGFID-MVLG-WGKSTNGWLVVPVGLAYAAIYYLVFDFCIRRFDLKTPGREEVPA 374

Query: 418 -KSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476
                +A ++     + A+GG  N+  + AC TRLR+++ D+ K    +LK LGA  V+ 
Sbjct: 375 GDKPAIAENQRAAAYIQALGGADNLITIGACTTRLRLDMVDRNKASDAQLKALGAMAVVR 434

Query: 477 VGN--NMQAIFGPKSDQIKHDMQQIMDGKI--------TSPEETTVTEEGDKETAEIAAA 526
            GN  ++Q + GP +D I  +++  +   +         +P  TT       E  +   A
Sbjct: 435 PGNGGSLQVVVGPMADSIADEIRLAVPSSLRPVTAPVPNAPAPTTPAALSSTEAQQWLDA 494

Query: 527 GGG 529
            GG
Sbjct: 495 LGG 497



 Score = 34.7 bits (78), Expect = 1e-05
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 432 LDAMGGKANIKHLDACIT-RLRVEVNDKAKVDVQELKDLGASGVLEVGNNM-QAIFGPKS 489
           LDA+GG+ N+  L+   T RLRV + D   +    LK LG  G+  + + +   + G K+
Sbjct: 492 LDALGGQDNVLQLECVATSRLRVRLADDKGLSESRLKGLGCQGMSSLEDGVWHLLLGEKA 551

Query: 490 DQIKHDMQQIMDGK 503
            ++   +  +  G+
Sbjct: 552 PRLWQALDGLAHGR 565


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: 1009
Number of extensions: 51
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