GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Cronobacter condimenti 1330

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_007678368.1 BN137_RS04255 pyrroloquinoline quinone-dependent dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000319285.1:WP_007678368.1
          Length = 698

 Score =  398 bits (1023), Expect = e-115
 Identities = 243/660 (36%), Positives = 348/660 (52%), Gaps = 34/660 (5%)

Query: 143 PQEINGTLSADAT-PAEAISPVADQDWPAYGRNQEGQRFSPLKQINADNVHNLKEAWVFR 201
           P + +G   A A+ PA  + P +   W ++      Q++SPL QI  +NV  L + W F 
Sbjct: 64  PDKADGQNVASASQPATPLVP-SSATWDSFHGQLNAQKYSPLTQITPENVGKLTKVWEFH 122

Query: 202 TGDVKQ-PNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKEKWHYDPELKTNESF 260
           TGDV     D        TPI   DT+Y+ T   RL ALD  +GKEKWHYD +       
Sbjct: 123 TGDVSDGKGDTPATVWSATPIFANDTIYIGTPFDRLIALDPGTGKEKWHYDTKSSRKALT 182

Query: 261 QHVTC-RGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAINAENGKLCETFANKGVL 319
           Q V   RGVSY +AK    +P     C + + L   DG+L A++A++GK C  FA+ GVL
Sbjct: 183 QPVLKNRGVSYWQAK----NPVAGEACQKIVYLGTVDGKLFALDADSGKPCTGFADNGVL 238

Query: 320 NL-QSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETSGVIRGFDVNTGELLWA 378
           N+ Q N  + K  L     PP +    +++  +  D        G I   +  TGE  W 
Sbjct: 239 NVNQWNTINAKFPL-SILQPPTVVGNHLLVGWAGKDWAYAEAPPGTIFSINAQTGEREWT 297

Query: 379 FDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQER 438
           F+       AIP +    T  + N W   + D    LVYLP+   +P+ WGGNR  +   
Sbjct: 298 FE-------AIPEEIRKQT-GTANVWTHMSADEANGLVYLPVSSPSPNYWGGNRV-KAIP 348

Query: 439 YASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADITVNGQKVPVIYAPAKTGNIF 498
             +S  AL+  TGK+ WS Q VHHD+WD D+ + PTL DITVNG+ +P +    K G +F
Sbjct: 349 LGTSTTALDINTGKVVWSRQWVHHDVWDYDINSAPTLMDITVNGKAIPALVQATKQGFLF 408

Query: 499 VLDRRNGELVVPAPEKPVPQ--GAAKGDYVTPTQPFSELSFRPTKDLSGADMWG-ATMFD 555
           V++R  GE V P  E+PVPQ  G+ KG+ ++PTQPF              ++W  A +  
Sbjct: 409 VVNRLTGEDVWPIEERPVPQGDGSVKGEVLSPTQPFPTRPAPLLDQSKKPEIWKLADIVG 468

Query: 556 QLVCRVMFHQMRYEGIFTPPSE--QGTLVFPGNLGMFEWGGISVDPNREVAIANPMALPF 613
              C  ++  + YEG++TPP+   +G L +P + G  +WGG++ DP +++AI N   +  
Sbjct: 469 AGQCSRLWDNLTYEGMYTPPTTKGEGALTYPDSAGGVQWGGVAFDPKKQIAIVNTSHIVQ 528

Query: 614 VSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYIS 673
             KL  R      +  K  K  G E+G  PQ G PYG+ L    +  G+PC QP +G I 
Sbjct: 529 YVKLYSR-----EDYDKADKSAGNENGFAPQEGAPYGMRLLVANNWLGMPCWQPPFGEIV 583

Query: 674 ALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVLFIAATADNYL 733
           ALD+ T EV W++ +G  Q    F     +P + G P +GGP  TAG V+FI A+ D  +
Sbjct: 584 ALDMHTGEVKWRRPVGASQQYGFF-----MPESWGSPTIGGPAITAGGVIFIGASMDAKV 638

Query: 734 RAYNMSNGEKLWQGRLPAGGQATPMTYEVNGKQYVVISAGGHGSFGTKMGDYIVAYALPD 793
           RAY++ +GE+LW  ++ A   A P  YE  G+QYV   AGG+     ++GD +V YALP+
Sbjct: 639 RAYSVDSGEELWSDQVEAPAVANPSVYEYKGRQYVAFVAGGNTILKDQVGDQVVVYALPE 698


Lambda     K      H
   0.319    0.137    0.436 

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: 1962
Number of extensions: 122
Number of successful extensions: 17
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: 796
Length of database: 698
Length adjustment: 40
Effective length of query: 756
Effective length of database: 658
Effective search space:   497448
Effective search space used:   497448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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