GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Escherichia coli BW25113

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)

Query= BRENDA::P45604
         (651 letters)



>FitnessBrowser__Keio:15742
          Length = 530

 Score =  272 bits (695), Expect = 3e-77
 Identities = 172/510 (33%), Positives = 266/510 (52%), Gaps = 55/510 (10%)

Query: 6   FFQRLGRALQLPIAVLPVAALLLRFGQP----DLLNV-------------PFIAQAGGAI 48
           FFQ+LG+   LP+A+L    ++L  G      D++ +              ++++ G   
Sbjct: 14  FFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFA 73

Query: 49  FDNLALIFAIGVASSWSKDNAGSAALAGAVGYFVMTKAM--------------------- 87
           F  L ++F I +    +++N G AA AG +GY VM  A+                     
Sbjct: 74  FSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKAN 133

Query: 88  ----VTINPEINMGVLAGIITGLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLI 143
               +     I+ G+L  +I G++   ++ R+  I+LPD L+FFGG RFVPI +     +
Sbjct: 134 NIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGL 193

Query: 144 LAAIFGYVWPPVQHAIHSGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQ--- 200
           +  +   VWP     I   G  I SAG  G  +FG   RLL+P GLH +L  +  F    
Sbjct: 194 VGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHILVALIRFTDAG 253

Query: 201 -----IGEFTNAAGTVFHGDIN--RFYAGDGTAGMFMS-GFFPIMMFGLPGAALAMYLAA 252
                 G+  + A T+F   ++    +    +A  F+S G  P  + GLPGAALAMY  A
Sbjct: 254 GTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYHCA 313

Query: 253 PKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTGISLFIATALGIH 312
               R  + G+L+S  I   + G TEPLEFLFLF+AP+LY++HA+LTG+   + + LG+ 
Sbjct: 314 RPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLGVT 373

Query: 313 AGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVFFFVYFLLFSAVIRMFNLKTPGREDK 372
            G +     ID+V+   L   S   +M+ V+  ++F VY+++F   I  FNLKTPGR+ +
Sbjct: 374 IG-NTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRDSE 432

Query: 373 AADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLKAIDACITRLRLTVGDSAKVNDAACK 432
            A  + E+A +           + + A+GG DN+ ++D CITRLRL+V D + VN  A K
Sbjct: 433 VASSI-EKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQALK 491

Query: 433 RLGASGVVKLNKQTIQVIVGAKAESIGDEM 462
              A GVV+LN+  +QV++G + +S+ DEM
Sbjct: 492 DNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521


Lambda     K      H
   0.323    0.138    0.406 

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: 783
Number of extensions: 45
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 530
Length adjustment: 37
Effective length of query: 614
Effective length of database: 493
Effective search space:   302702
Effective search space used:   302702
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 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