GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Collinsella tanakaei YIT 12063

Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate WP_009141894.1 HMPREF9452_RS09360 PTS transporter subunit EIIC

Query= SwissProt::Q57071
         (675 letters)



>NCBI__GCF_000225705.1:WP_009141894.1
          Length = 530

 Score =  266 bits (679), Expect = 2e-75
 Identities = 172/541 (31%), Positives = 279/541 (51%), Gaps = 62/541 (11%)

Query: 8   QLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLM--PFIKAEGFQNVAKMMEGAGG 65
           ++Q+ G A+  PV +   AG+++  G  F  + +   +  P     G  NV  +++G G 
Sbjct: 4   KIQKFGGAMFTPVMLFAFAGVVIGFGTLFTTEVIFGPLAAPGTMWYGVWNV--ILQG-GW 60

Query: 66  IIFDNLAIIFALGVAIGLASGDGV-AAIAAFVGFIVLN---KTM----GMFLGVTPEKAA 117
            +F+ L ++FA+ + IGLA+       + A VG++       TM    G F GV      
Sbjct: 61  TVFNQLPLLFAVSLPIGLANKQNARCCMEALVGYLTFQYFVSTMLSQWGGFFGVDFAAEV 120

Query: 118 DAATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMAT 177
              +G A +  I TL  G+ G + +  +    +NKFY + LP +LG FAG  FV I+   
Sbjct: 121 GGTSGLAMIASIKTLDMGMIGALAVSGIIIAIHNKFYEVELPEWLGVFAGSTFVYIITFF 180

Query: 178 CSFILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFW 237
               +AF   + WP +Q G+ AF +G +A+   L V +F F++R LIPFGLHH+ ++PF+
Sbjct: 181 VMLPVAFVACLGWPHVQDGIRAF-QGFVATTGTLGVGVFAFLERALIPFGLHHLMYSPFY 239

Query: 238 FE--------FGSYKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAA 289
           ++        + ++  A  QI      +  +++      T   + +      +FG P  A
Sbjct: 240 YDNAVVDGGIYTAFATALPQIAASTDSL--KELAPYAAFTCSTWSK------IFGCPGIA 291

Query: 290 LAIYQTAKKENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLI 349
           LA + TAK E KK +  L++   LT+   G+TEP+EF+FLF+AP LF +H VL  L  + 
Sbjct: 292 LAFFVTAKPEKKKELLSLLIPITLTAVFCGVTEPIEFTFLFIAPPLFIVHCVLAALLAMA 351

Query: 350 LYLLDLHLGYTFSGGFIDFFLLGILPNKTQWW----LVIPVGLVYAAIYYIIFRFLIVKF 405
           + ++   +G  F+GG I+   L  +P     W    + + VGLV+  I++++FRFLIVKF
Sbjct: 352 INMVGC-VG-VFAGGIIEISSLNFIPLMANHWQQYAMALVVGLVFTVIWFVVFRFLIVKF 409

Query: 406 NFKTPGRED-------------KEVKSSNVAASE------------LPFKVLDAMGGKAN 440
           +FKTPGRED             +  K+  +A+ E            +  +VL+ +GG  N
Sbjct: 410 DFKTPGREDDDEQVKFRSKAEYRAAKNGELASGEGAKVDESDPYAVMAAEVLELLGGADN 469

Query: 441 IKHLDACITRLRVEVNDKAKV-DVQELKDLGASGVLEVGNNMQAIFGPKSDQIKHDMQQI 499
           I  +  C+TRLRV V D+  V D  + K +G SG+ + G  MQ I G K  +++   + +
Sbjct: 470 IVDVTNCVTRLRVNVKDETLVADDPDFKSIGTSGIAKNGKGMQVIIGLKVPKVRDRFEAL 529

Query: 500 M 500
           +
Sbjct: 530 L 530


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: 850
Number of extensions: 47
Number of successful extensions: 6
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: 530
Length adjustment: 37
Effective length of query: 638
Effective length of database: 493
Effective search space:   314534
Effective search space used:   314534
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 24 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