GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas fluorescens FW300-N2E3

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate AO353_16045 AO353_16045 glucose dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16045
          Length = 803

 Score =  756 bits (1953), Expect = 0.0
 Identities = 380/804 (47%), Positives = 530/804 (65%), Gaps = 31/804 (3%)

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

Query: 70  ALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAV--AALVVA 127
            +L  + +W +WE+G D+W L PR  +    G+ L+LP+  R L+   +  +  AAL VA
Sbjct: 71  VVLFASTVWALWEIGLDWWQLVPRLSLWFALGVVLLLPWFRRPLLRDGAAPLGTAALSVA 130

Query: 128 LLISGGILTWAGFNDPQEINGTLSADATPAEAISPVADQ-DWPAYGRNQEGQRFSPLKQI 186
           ++++G     + F  P EI G L  D     + +P   + +W AYGR + G R+SPLKQI
Sbjct: 131 VVLAGATAVASQFTHPGEIMGELGRDTADMTSTAPAMPEGEWQAYGRTEFGDRYSPLKQI 190

Query: 187 NADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKE 246
              NV  L+EAW  RTGD+   +DP E+TNE TP+KV   LY CTAH ++ ALD  +GKE
Sbjct: 191 TPANVGKLQEAWRIRTGDLPTADDPVELTNENTPLKVNGMLYACTAHSKVLALDPDTGKE 250

Query: 247 KWHYDPELKTN---ESFQHVTCRGVSYHE----AKAETASPEVMAD--------CPRRII 291
            W +DP++K+    + F H+TCRGVSY++    AKA+ AS  V+++        CPRR+ 
Sbjct: 251 LWRFDPQIKSPVGFKGFAHMTCRGVSYYDENAYAKADNASSAVISEAGKAVAQACPRRLY 310

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

Query: 352 VTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDA 411
           VTDN ST E SGVIR FD+  G L+W +D G  +     +   T+T NSPN W+ A+ D 
Sbjct: 371 VTDNESTNEPSGVIRAFDIRDGHLVWNWDSGNPEATEPLAPGKTYTRNSPNMWSLASVDE 430

Query: 412 KLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPA 471
           KL +VYLP+G   PD WG +RTP  E++++ ++AL+  TGK+ W++Q  HHDLWDMD+ +
Sbjct: 431 KLGMVYLPLGNQMPDQWGADRTPGAEKFSAGMVALDLATGKVRWNFQFTHHDLWDMDVGS 490

Query: 472 QPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQ 530
           QPTL D+ T +G K P + AP K G+++VLDRRNG  +VP  E P PQGA  GD+  PTQ
Sbjct: 491 QPTLLDMKTADGIK-PALIAPTKQGSLYVLDRRNGTPIVPIREVPAPQGAVTGDHTAPTQ 549

Query: 531 PFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMF 590
             S+L+     DL+   MWGA+ FDQ++CR+ F Q+RYEG +TPPS QG+L++PGN+G+F
Sbjct: 550 ARSDLNLL-APDLTEKAMWGASPFDQMLCRIQFKQLRYEGQYTPPSLQGSLIYPGNVGVF 608

Query: 591 EWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYG 650
            WG +S+DP R++   +P  + FVSKLIP+      E    +K     SG+QP  G PY 
Sbjct: 609 NWGSVSLDPVRQMLFTSPNYMAFVSKLIPQA-----EVAAGSKRESETSGVQPNTGAPYA 663

Query: 651 VTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMP 710
           VT++PF+SPFG+PC+ PAWGY++ +DL T++VVWK++ GT +DS P P+ +P+    G+P
Sbjct: 664 VTMHPFMSPFGVPCQAPAWGYVAGIDLTTSKVVWKRKNGTSRDSSPLPIGLPI----GVP 719

Query: 711 MLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGKQYVV 769
            +GG I TAG V F++ T D YLRAY+++NG++LW+ RLPAGGQATPMTY   +GKQYV+
Sbjct: 720 SMGGSIVTAGGVGFLSGTLDQYLRAYDVNNGKELWKSRLPAGGQATPMTYTGKDGKQYVL 779

Query: 770 ISAGGHGSFGTKMGDYIVAYALPD 793
           +  GGHGS GTKMGDY++AY L +
Sbjct: 780 LVVGGHGSLGTKMGDYVIAYKLSE 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: 2182
Number of extensions: 136
Number of successful extensions: 15
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