GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Pseudomonas fluorescens GW456-L13

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833
          Length = 571

 Score =  365 bits (936), Expect = e-105
 Identities = 216/506 (42%), Positives = 304/506 (60%), Gaps = 52/506 (10%)

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+         KA D 
Sbjct: 44  HDAGQVIFANLAMIFAIGIAVGFARDNNGTAGLAGVIGYLVMISTL---------KALD- 93

Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179
                     P++  G+  GI+ G +A   YN+F +I LP YL FF G+RFVPI+    +
Sbjct: 94  ----------PSINMGMLAGIVSGLMAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFAA 143

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

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

Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357
              +KV+ G+ LS ALT+FLTG+TEP+EF+F+F+APLLF +HA+L GLS  I   L++HL
Sbjct: 257 PARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHALLTGLSMAITNALNIHL 316

Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGRE-DKE 416
           G+TFSGGFID  +LG     T  WLV PVGL YA IYY++F F I +F+ KTPGRE   +
Sbjct: 317 GFTFSGGFID-MILG-WGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFDLKTPGRETSAD 374

Query: 417 VKSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476
           V+   VA +E     + A+GG  N+  + AC TRLR+++ D+ K    +LK LGA  V+ 
Sbjct: 375 VEQVAVADNERAGAYIKALGGAENLITVGACTTRLRLDMVDRNKASDTDLKALGAMAVVR 434

Query: 477 --VGNNMQAIFGPKSDQIKHDMQQIM 500
              G ++Q + GP +D I  +++  M
Sbjct: 435 PGKGGSLQVVVGPMADAIADEIRLAM 460



 Score = 34.3 bits (77), Expect = 2e-05
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 432 LDAMGGKANIKHLDA-CITRLRVEVNDKAKVDVQELKDLGASGVLEV-GNNMQAIFGPKS 489
           L+A+GG  N+  LD   +TR+R+++ D   +   +LK LG  GV ++ G     + G K+
Sbjct: 492 LNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDGGIWHLLIGDKA 551

Query: 490 DQIKHDMQQIMD 501
             +   ++ +++
Sbjct: 552 PTLSDALEVLVN 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: 997
Number of extensions: 57
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