GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gdh in Pseudomonas putida KT2440

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate PP_1444 PP_1444 quinoprotein glucose dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>lcl|FitnessBrowser__Putida:PP_1444 PP_1444 quinoprotein glucose
           dehydrogenase
          Length = 803

 Score =  749 bits (1933), Expect = 0.0
 Identities = 383/808 (47%), Positives = 524/808 (64%), Gaps = 30/808 (3%)

Query: 5   NTGSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAA 64
           N GSR L   + AL   L GL LL GG  L  +GGS YY IAG+       +L   ++ A
Sbjct: 7   NQGSRWLPRLIGALLL-LMGLALLAGGIKLSQLGGSLYYLIAGIGFALSGVLLLAQRQIA 65

Query: 65  LWLYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAAL 124
           L LY  +LLG+ +W ++EVG D+W L PR  I    G+ L+LP+  R L+ PAS A  AL
Sbjct: 66  LGLYGLVLLGSTVWALFEVGLDWWQLVPRLAIWFAIGVVLLLPWARRPLIGPASKANTAL 125

Query: 125 V-VALLISGGILTWAGFNDPQEINGTLSADATPAEAISP-VADQDWPAYGRNQEGQRFSP 182
           + VA++ SG     + F  P E+ G L  D++   + +P + D +W AYGR + G R+SP
Sbjct: 126 LGVAVVASGACALASQFTHPGEVFGELGRDSSEMASAAPAMPDGEWQAYGRTEHGDRYSP 185

Query: 183 LKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAA 242
           L+QI   N + L+EAW  RTGD+   NDP E+TN+ TP+KV   LY CTAH RL ALD  
Sbjct: 186 LRQITPQNAYRLEEAWRIRTGDLPTENDPVELTNQNTPLKVNGMLYACTAHSRLLALDPD 245

Query: 243 SGKEKWHYDPELK----TNESFQHVTCRGVSYHEA------------KAETASPEVMADC 286
           +G E W YDP++K    T + F H+TCRGVSY++             K   A   V   C
Sbjct: 246 TGAEIWRYDPQVKSPTGTFKGFAHMTCRGVSYYDENRYVSRDGSPAPKITDAGQAVAQAC 305

Query: 287 PRRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTI 346
           PRR+ LP  D RLIAINA+NGK+CE FAN+GV++L + +     G Y  TSP  IT   +
Sbjct: 306 PRRLYLPTADARLIAINADNGKVCEGFANQGVIDLTTGIGPFTAGGYYSTSPAAITRDLV 365

Query: 347 VMAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAP 406
           ++ G VTDN ST E SGVIR +DV+ G L+W +D    D     +    ++ NS N W+ 
Sbjct: 366 IIGGHVTDNESTNEPSGVIRAYDVHDGHLVWNWDSNNPDDTKPLAAGKMYSRNSANMWSI 425

Query: 407 AAYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWD 466
           A+ D  L ++YLP+G  TPD WG +RTP  E+Y++ ++AL+  TGK  W+YQ  HHDLWD
Sbjct: 426 ASVDEDLGMIYLPLGNQTPDQWGADRTPGAEKYSAGVVALDLATGKARWNYQFTHHDLWD 485

Query: 467 MDLPAQPTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV 526
           MD+ +QPTL  +  +    P I  P K G+++VLDRR+G  +VP  E P PQGA +GD+ 
Sbjct: 486 MDVGSQPTLVHLKTDDGVKPAIIVPTKQGSLYVLDRRDGTPIVPIREIPTPQGAVEGDHT 545

Query: 527 TPTQPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGN 586
           +PTQ  S+L+     +L+   MWGAT FDQ++CR+ F ++RYEG +TPPSEQG+LV+PGN
Sbjct: 546 SPTQARSDLNLL-GPELTEQAMWGATPFDQMLCRIQFRELRYEGQYTPPSEQGSLVYPGN 604

Query: 587 LGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYG 646
           +G+F WG +SVDP R++   +P  + FVSK++PR      +  + +K     SG+QP  G
Sbjct: 605 VGVFNWGSVSVDPVRQLLFTSPNYMAFVSKMVPR-----EQVAEGSKRESETSGVQPNTG 659

Query: 647 VPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFN 706
            PY V ++PF+SP G+PC+ PAWGY++A+DL TN+VVWK + GT +DS P P+ +PV   
Sbjct: 660 APYAVIMHPFMSPLGVPCQAPAWGYVAAIDLFTNKVVWKHKNGTTRDSTPLPIGLPV--- 716

Query: 707 MGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGK 765
            G+P +GG I TAG V F++ T D YLRAY+++NG++LW+ RLPAGGQATPM+Y   +GK
Sbjct: 717 -GVPSMGGSIVTAGGVGFLSGTLDQYLRAYDVNNGKELWKARLPAGGQATPMSYTGKDGK 775

Query: 766 QYVVISAGGHGSFGTKMGDYIVAYALPD 793
           QYV+++AGGHGS GTKMGDYI+AY L +
Sbjct: 776 QYVLVTAGGHGSLGTKMGDYIIAYKLAE 803


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: 2194
Number of extensions: 124
Number of successful extensions: 13
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: 803
Length adjustment: 41
Effective length of query: 755
Effective length of database: 762
Effective search space:   575310
Effective search space used:   575310
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 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 preprint 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