GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1444
          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:

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