GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagPcb in Escherichia coli BW25113

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__Keio:15742
          Length = 530

 Score =  254 bits (648), Expect = 6e-72
 Identities = 161/513 (31%), Positives = 263/513 (51%), Gaps = 74/513 (14%)

Query: 4   FLQKLGKSFMLPIAVLPAVGIILALGRE----DVFNI-------------PFVYQAGTAV 46
           F Q+LGK+FMLP+A+L   GI+L +G      DV  +              ++ + G+  
Sbjct: 14  FFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFA 73

Query: 47  FDHLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATK--------------TIDKTN 92
           F  LP++F I I +G+++++ G A  +G I Y +++ A                 + K N
Sbjct: 74  FSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKAN 133

Query: 93  NM-----------AVFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITII 141
           N+            + G +IAG+I    + RF + +LP+ L FF G R VPI+++++  +
Sbjct: 134 NIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGL 193

Query: 142 LAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGE 201
           +  +  +VWP     I+  G  +   G  G  +FG   RLL+P GLHH+L  +   +F +
Sbjct: 194 VGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHIL--VALIRFTD 251

Query: 202 YNG--------VTGDLARFFAKDPTAGTY----------MTGFFPIMMFGLPAACLAMVV 243
             G        V+G L  F A+     T+            G  P  + GLP A LAM  
Sbjct: 252 AGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYH 311

Query: 244 TAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLG 303
            A+P  R    G++I   +   + G TEP+EF F+F++P+LY +HA+LTGL   +++ LG
Sbjct: 312 CARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLG 371

Query: 304 IRSGFSFSAGAIDYV---LSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGRE 360
           +  G +     ID+V   + +G++ K  ++ +V   +  VY+++F   I   NLKTPGR+
Sbjct: 372 VTIG-NTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRD 430

Query: 361 DDDVDEVLDENTV------QDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEA 414
            +    +  E  V         N   +L+ LGG +N+ ++D+C TRLRL+VKD +LV+  
Sbjct: 431 SEVASSI--EKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQ 488

Query: 415 LLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEEL 447
            LK   A GVV+    ++QV+IGP V+   +E+
Sbjct: 489 ALKDNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521


Lambda     K      H
   0.326    0.144    0.429 

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: 662
Number of extensions: 47
Number of successful extensions: 8
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: 452
Length of database: 530
Length adjustment: 34
Effective length of query: 418
Effective length of database: 496
Effective search space:   207328
Effective search space used:   207328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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