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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17535 AO356_17535 PTS
           N-acetyl-D-glucosamine transporter
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources