GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__MR1:200788 SO1623 PTS system, glucose-specific
           IIBC component (NCBI ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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