GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_3569 PP_3569 quinate dehydrogenase
           (quinone)
          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 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