GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Pseudomonas putida KT2440

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate PP_3569 PP_3569 quinate dehydrogenase (quinone)

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__Putida:PP_3569
          Length = 805

 Score =  597 bits (1540), Expect = e-175
 Identities = 340/809 (42%), Positives = 458/809 (56%), Gaps = 50/809 (6%)

Query: 14  LTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLA 73
           L V+ A+L G  +  GG+ LA +GGSWY++IGG AM +   L+ RR  A   +YA+ L+ 
Sbjct: 18  LGVIIALL-GLLLAAGGVKLAGLGGSWYFLIGGLAMAIAGVLIARRKKAGAWLYAVFLVG 76

Query: 74  TLAWGVWEVGTDFWALAPRTDVLVIFG-VWLVLPFVYRGLYQP-----GKGALGAMGVAL 127
           T  W + + G  FW L  R   L +FG + +V+  VY  L +      G+GA G  GV  
Sbjct: 77  TAIWALIDAGLVFWPLFSR---LFMFGAIGMVVALVYPLLARANGASAGRGAYGVAGVMA 133

Query: 128 VASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADG-DWPAYARDQQGTRFSPLK 186
           V     +       P V      A     P   P+    +  DW  Y   + G+RF+ L 
Sbjct: 134 VVLVVAVGNMFVAHPSV------APTGKGPGMTPVETGKEQKDWAHYGNTEGGSRFAALD 187

Query: 187 QINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATG 246
           QIN DNV +L+VAW +QTGD+   SD     D++TP++I   +++CTPH  L ALDA TG
Sbjct: 188 QINRDNVNKLKVAWTYQTGDVAI-SDGNGAEDQLTPLQIGSKVFICTPHNNLIALDADTG 246

Query: 247 KQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQP-------------ALCSRRI 293
           K+ WK +   ++   +Q   CRG++Y +  AA  A  TQP             A C RR+
Sbjct: 247 KELWKNEINAQSK-VWQR--CRGMAYFDATAAI-AQPTQPNSSPITGVSVAAGANCQRRL 302

Query: 294 YLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAG 353
                DGRL A+DA+TGE C  FGNNG++DL+          Y+ +S P++  TT+V+ G
Sbjct: 303 LTNTIDGRLIAVDADTGEFCQGFGNNGQVDLKAGLGDVPDSYYQLSSAPLMAGTTVVVGG 362

Query: 354 AVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYD 413
            V DN  T  P G IRGFDV TG++ W FDPG  +    P  + T+  ++PNSWAP  YD
Sbjct: 363 RVADNVQTDMPGGVIRGFDVITGEMRWAFDPGNPEDRQAPQGDKTYVRSTPNSWAPMSYD 422

Query: 414 PKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLP 473
           P ++ V+LPMG ++ DI+G  R+     Y +SVLAL+ATTG   W +QTVH+DLWD DLP
Sbjct: 423 PAMNTVFLPMGSSSTDIYGVERSKLDHTYGASVLALDATTGNQKWVFQTVHNDLWDFDLP 482

Query: 474 SQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSAT 533
            QP+L D T  DG +VP +    K G I+VLDR TGK +    E PV       +  S T
Sbjct: 483 MQPSLIDFTKDDGQSVPAVVIGTKAGQIYVLDRATGKPLTQVDEVPVKPSNIPNEPYSPT 542

Query: 534 QPYS-ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLG 592
           QP S  +     Q LT+ DMWGAT YDQL+CR+ FK++RY+G +T P    +L FPG+LG
Sbjct: 543 QPKSVGMPQIGAQTLTESDMWGATPYDQLLCRIDFKKMRYDGLYTAPGTDLSLSFPGSLG 602

Query: 593 MFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGI--QPQY 650
              WG IS DP       N M L    ++IP      +     A+GG    TG+   P  
Sbjct: 603 GMNWGSISTDPVHGFIFVNDMRLGLWIQMIP-----SQNKGGAASGGEALNTGMGAVPLK 657

Query: 651 GVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP----VPLPF 706
           G PY V  N FLS  G+PC+ P +G ++A+D+KT +V W+  +GTV D+ P    + LP 
Sbjct: 658 GTPYAVNKNRFLSVAGIPCQAPPFGTLTAIDMKTRQVAWQVPVGTVEDTGPLGIRMHLPI 717

Query: 707 KMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY--EVN 764
           K+G+P LGG ++T G + FI  T D YLRA+ +  G  +W+ARLP G Q  PMTY     
Sbjct: 718 KIGLPTLGGTLSTQGGLVFIAGTQDFYLRAYDSSNGNEIWKARLPVGSQGGPMTYVSPKT 777

Query: 765 GKQYVVIAAGGHGSFGTKLGDYVIAYALP 793
           GKQYVVI AGG     T  GDYVI+YALP
Sbjct: 778 GKQYVVITAGG-ARQSTDRGDYVISYALP 805


Lambda     K      H
   0.319    0.137    0.433 

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: 2229
Number of extensions: 155
Number of successful extensions: 14
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: 805
Length adjustment: 41
Effective length of query: 755
Effective length of database: 764
Effective search space:   576820
Effective search space used:   576820
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