GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Shewanella oneidensis MR-1

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__MR1:200788
          Length = 499

 Score =  312 bits (799), Expect = 3e-89
 Identities = 184/503 (36%), Positives = 289/503 (57%), Gaps = 39/503 (7%)

Query: 2   WKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMME 61
           W KF    QR+ +AL++P+AILPAAG++L L          S +PF+     + +  +M 
Sbjct: 24  WFKF---AQRLSQALLIPIAILPAAGVMLGL--------TVSPIPFMP----EVLNVLML 68

Query: 62  GAGGIIFDNLAIIFALGVAIGLASGDGVAAIAAFVGFIVLNKTMGMFLGV--TPEKAADA 119
             G +IF  + I+FA+ VAIG     G+AA  A  G+ V+  T+     +   P +    
Sbjct: 69  AVGKLIFAIMPILFAVAVAIGFCRDQGIAAFTAVFGYGVMTATLAALADLYQLPTQL--- 125

Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179
                 VLG+ TL TG+ GG++IG +  +       I LP+   FF G+R   +++   +
Sbjct: 126 ------VLGMETLDTGIAGGMLIGGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLA 179

Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239
             L + +A IWPS+   +   S+  +     +A  ++G ++RLLIP GLHHI++APF+ E
Sbjct: 180 MGLGYVLAHIWPSLSLLIERVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLE 239

Query: 240 FGSYKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKE 299
            G Y+    +++ G+   ++          AG  + G + + M+GLPAAALAI++ A   
Sbjct: 240 VGQYQLQDAEVVRGEVARYLAGDPQ-----AGN-LAGGYLIKMWGLPAAALAIWRCADNS 293

Query: 300 NKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGY 359
            +  VAG+MLS A  S+LTG+TEP+EF+F+FVAPLLF IH +L GL++ +  +LD+H   
Sbjct: 294 ERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPLLFLIHVMLSGLAYFVCIMLDIHHSI 353

Query: 360 TFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEVKS 419
            FS G +DF LL  L   T W+ V+  G + A IYYI+FR  I+ FN KTPGR    ++S
Sbjct: 354 VFSHGLVDFTLLFSLSRNTGWFAVL--GPLTAVIYYILFRGSILAFNLKTPGR----LQS 407

Query: 420 SNVAASELPFK-VLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLEVG 478
                S+   + ++ A+GG+ NI  L+AC+TRLR+ V+    V+   L  LGA GV+ +G
Sbjct: 408 DGTKGSKESLRAIIAALGGRDNIVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMG 467

Query: 479 NNMQAIFGPKSDQIKHDMQQIMD 501
             +Q ++G K++ ++  +Q+ +D
Sbjct: 468 KGVQIVYGTKAETLRKVLQRYLD 490


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: 805
Number of extensions: 43
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: 675
Length of database: 499
Length adjustment: 36
Effective length of query: 639
Effective length of database: 463
Effective search space:   295857
Effective search space used:   295857
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