GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Shewanella amazonensis SB2B

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= SwissProt::Q57071
         (675 letters)



>FitnessBrowser__SB2B:6936959
          Length = 485

 Score =  321 bits (822), Expect = 6e-92
 Identities = 189/504 (37%), Positives = 290/504 (57%), Gaps = 43/504 (8%)

Query: 3   KKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAK-MME 61
           + +F   QR+ + L++P+AILPAAG+++ +          + +PFI      +VA  +M 
Sbjct: 17  RHWFRFAQRLSQTLLIPIAILPAAGVMIGIAT--------NPLPFIP-----DVANVLML 63

Query: 62  GAGGIIFDNLAIIFALGVAIGLASGDGVAAIAAFVGFIVLNKTMGMFLGV--TPEKAADA 119
             G +IFD + ++FA+ VAIG     G+AA +A  G+ VL  T+     V   P      
Sbjct: 64  SVGKLIFDIMPMLFAIAVAIGFCRDQGIAAFSAAFGYGVLLSTLAAAAKVYHLPSHI--- 120

Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179
                 V G PT+ TG+ GG+++G +          + LP+   FF G+R  P++M    
Sbjct: 121 ------VWGTPTIDTGIAGGMLVGGITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLV 174

Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239
            +LA  +A IWP +   +   S+  +     +A   +G ++RLL+P GLHHI++APF+ E
Sbjct: 175 MLLAVMLAFIWPPLALSIERLSDWAVYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLE 234

Query: 240 FGSYKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKE 299
            G Y +  G+I+ G+   +          +AG  + G + + M+GLPAAALAI++ A + 
Sbjct: 235 VGQYAHD-GEIVRGEMARYFAG-----DPSAGN-LAGGYLIKMWGLPAAALAIWRCADRN 287

Query: 300 NKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGY 359
            +  VAG+MLS A  S+LTG+TEP+EF+FLFVAPLL+  HA+L GL++ I  LLD+H   
Sbjct: 288 QRNRVAGVMLSAATASWLTGVTEPIEFAFLFVAPLLYLCHALLTGLAYSIAILLDMHHSV 347

Query: 360 TFSGGFIDFFLLGILPNKTQW-WLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEV- 417
            FS G +DF LL    + T W W + P+  V   IYYI+FR  I+ FN KTPGR + +  
Sbjct: 348 VFSHGLVDFVLLFPQSSNTHWIWFLGPLTFV---IYYILFRASILAFNLKTPGRFEADTG 404

Query: 418 KSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLEV 477
           +  N+ A      ++ A+GG  NI  L AC+TRLR+ V D ++VD Q L  LGA GV+ V
Sbjct: 405 QKRNLIA------IVSALGGGGNIADLSACLTRLRISVADPSQVDRQRLMSLGAKGVIVV 458

Query: 478 GNNMQAIFGPKSDQIKHDMQQIMD 501
           G+ +Q +FG K++ ++  +Q+ +D
Sbjct: 459 GSGVQLVFGTKAETLRKLLQRYLD 482


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: 774
Number of extensions: 35
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: 485
Length adjustment: 36
Effective length of query: 639
Effective length of database: 449
Effective search space:   286911
Effective search space used:   286911
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