GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas fluorescens GW456-L13

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate PfGW456L13_4805 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4805
          Length = 803

 Score =  748 bits (1930), Expect = 0.0
 Identities = 378/807 (46%), Positives = 532/807 (65%), Gaps = 37/807 (4%)

Query: 10  RLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYA 69
           RLL TL  +   L GL +L GG  L  +GGS YY +AG+ +     +L  ++RAAL LYA
Sbjct: 11  RLLPTLLGILLLLMGLAMLAGGIKLSMLGGSLYYLLAGIGIALSGVLLIAARRAALGLYA 70

Query: 70  ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVI--PASGAVAALVVA 127
            +L  + +W +WEVG D+W L PR  +    G+ ++LP+  R L+I  PA     AL VA
Sbjct: 71  LVLFASTVWALWEVGLDWWQLVPRLALWFALGVVMLLPWFRRPLLINGPAPMGTGALSVA 130

Query: 128 LLISGGILTWAGFNDPQEINGTLSADATPAEAISP-VADQDWPAYGRNQEGQRFSPLKQI 186
           ++++G     + F  P E  G L  D     + +P + + DW AYGR++ G R+SPLKQI
Sbjct: 131 VVLAGATAVASQFTHPGETFGELGRDTADMTSTAPQMPEGDWQAYGRSEFGDRYSPLKQI 190

Query: 187 NADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKE 246
              NV  L+EAW  +TGD+   +DP E+TNE TP+K    LY CTAH ++ ALD  +GKE
Sbjct: 191 TPANVGKLQEAWRIQTGDLPTADDPVELTNENTPLKANGMLYACTAHSKVLALDPDTGKE 250

Query: 247 KWHYDPELKTN---ESFQHVTCRGVSYHE----AKAETASPEVMAD--------CPRRII 291
            W +DP++K+    + F H+TCRGVSY++    AK+E+A+  V+++        CPRR+ 
Sbjct: 251 LWRFDPQIKSPVGFKGFAHMTCRGVSYYDEAAYAKSESAASAVISEAGKAVAQACPRRLY 310

Query: 292 LPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGS 351
           LP  D RLIA+NA+ GK+CE F   GV++L   +     G Y  TSP  IT   ++M G 
Sbjct: 311 LPTADARLIALNADTGKICEGFGKNGVVDLTQGIGPFTAGGYYSTSPAAITRDLVIMGGH 370

Query: 352 VTDNFSTRETSGVIRGFDVNTGELLWAFD---PGAKDPNAIPSDEHTFTFNSPNSWAPAA 408
           VTDN ST E SGVIR FDV+ G L+W +D   P A +P  +P  EH ++ NS N W+ A+
Sbjct: 371 VTDNESTNEPSGVIRAFDVHDGHLVWNWDSNNPDATEP--LPEGEH-YSRNSANMWSLAS 427

Query: 409 YDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMD 468
            D KL +VYLP+G  TPD WG +RTP  E++++ ++AL+  TGK+ W+YQ  HHDLWDMD
Sbjct: 428 VDEKLGMVYLPLGNQTPDQWGADRTPGAEKFSAGLVALDLATGKVRWNYQFTHHDLWDMD 487

Query: 469 LPAQPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVT 527
           + +QPTL D+ T +G K P + AP K G+++VLDRR+G  ++P  E P PQGA KGD   
Sbjct: 488 VGSQPTLLDMKTADGVK-PALIAPTKQGSLYVLDRRDGTPIIPIKEIPAPQGAVKGDRTA 546

Query: 528 PTQPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNL 587
           PTQ  S+L+     +L+   MWGA+ FDQ++CR+ F ++RYEG +TPPSEQG+L++PGN+
Sbjct: 547 PTQARSDLNLL-APELTEKAMWGASPFDQMLCRIQFKELRYEGQYTPPSEQGSLIYPGNV 605

Query: 588 GMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGV 647
           G+F WGG+SVDP R++   +P  + FVSK++PR      E   D+K     +G+QP  G 
Sbjct: 606 GVFNWGGVSVDPVRQMLFTSPNYMAFVSKMVPRA-----EVAADSKRESETAGVQPNTGA 660

Query: 648 PYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNM 707
           PY V ++PF+SP G+PC+ PAWGY++ +DL T++VVWK++ GT +DS P P+ +P    +
Sbjct: 661 PYAVIMHPFMSPLGVPCQAPAWGYVAGIDLTTSKVVWKRKNGTSRDSSPLPIGLP----L 716

Query: 708 GMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQ 766
           G+P +GG + TAG V F++ T D YLRAY+++ G +LW+ RLPAGGQATPMTY   +GKQ
Sbjct: 717 GVPSMGGSMVTAGGVGFLSGTLDQYLRAYDVNTGNELWKSRLPAGGQATPMTYTGKDGKQ 776

Query: 767 YVVISAGGHGSFGTKMGDYIVAYALPD 793
           YV++  GGHGS GTKMGDY++AY L +
Sbjct: 777 YVLLVVGGHGSLGTKMGDYVIAYKLSE 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: 2170
Number of extensions: 130
Number of successful extensions: 14
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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