GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Burkholderia phytofirmans PsJN

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__BFirm:BPHYT_RS02745
          Length = 591

 Score =  365 bits (936), Expect = e-105
 Identities = 226/552 (40%), Positives = 309/552 (55%), Gaps = 77/552 (13%)

Query: 6   FGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMMEGAGG 65
           F ++QR+G+ALMLP+A+LP AGLLL LG   Q D                  KM+  AGG
Sbjct: 6   FLKIQRLGRALMLPIAVLPVAGLLLRLG---QPDVFN--------------IKMIADAGG 48

Query: 66  IIFDNLAIIFALGVAIGLAS-GDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADAATGFA 124
            IFDNL ++FA+GVA+G A   +GVA +A  +G+++    + +   +  +          
Sbjct: 49  AIFDNLPLLFAIGVAVGFAKDNNGVAGLAGAIGYLI---EVAVMKDINDK---------- 95

Query: 125 NVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCSFILAF 184
                  L  GV  GI+ G +A   YN++ +I LP YL FF GKRFVPI+      +L  
Sbjct: 96  -------LNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGI 148

Query: 185 PMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFEFGSYK 244
               +W  +Q  ++     L  +   L  F+FG + RLL+  GLHHI ++  WF FG++ 
Sbjct: 149 AFGYVWQPVQAVIDTAGHWLTTAGA-LGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFT 207

Query: 245 NAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKENKKVV 304
              G  + GD   F          TAG FM G FPVMMFGLPAA LA++  A KE + VV
Sbjct: 208 PPGGAAVTGDLHRFFAG-----DPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVV 262

Query: 305 AGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGYTFSGG 364
            GL+ S ALTSFLTG+TEP+EFSF+F+AP+L+ IHA+L G+S  I   L +HLG+TFS G
Sbjct: 263 GGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAG 322

Query: 365 FIDFFL-LGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGRE----DKEVKS 419
            ID+ L  G+    T+ W  IP+GLVY  +YY +FRF I KFN  TPGRE    D++V S
Sbjct: 323 AIDYVLNYGL---STRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVDS 379

Query: 420 -------SNVAASELP--FKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLG 470
                  S VA + +P   + + A+GG +N+  +DAC TRLR+ V D  KV   ELK +G
Sbjct: 380 FAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIG 439

Query: 471 ASGVLEVGN-NMQAIFGPKSDQIKHDMQQIMDGKITSPEETTVTEEGDKETAEIAAAGGG 529
           A GVL+ G+ N+Q I GP++D             I + E  TV  +G  +  + AAA   
Sbjct: 440 ARGVLKRGSTNVQVIIGPEAD-------------IIADEIRTVIAQGGGDAVKPAAAAPA 486

Query: 530 --VVYAPIKGEV 539
             V  AP+   V
Sbjct: 487 QVVAAAPVAASV 498


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: 1061
Number of extensions: 56
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: 675
Length of database: 591
Length adjustment: 38
Effective length of query: 637
Effective length of database: 553
Effective search space:   352261
Effective search space used:   352261
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: 54 (25.4 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