GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gdh in Dyella japonica UNC79MFTsu3.2

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate N515DRAFT_0461 N515DRAFT_0461 quinoprotein glucose dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0461 N515DRAFT_0461
           quinoprotein glucose dehydrogenase
          Length = 816

 Score =  795 bits (2054), Expect = 0.0
 Identities = 404/814 (49%), Positives = 531/814 (65%), Gaps = 48/814 (5%)

Query: 15  LTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYAALLLG 74
           +TA      GL LL GG WL+ +GGS YY +AG +++   W+ WR    AL L+A LLL 
Sbjct: 13  ITAALFVFLGLGLLAGGAWLLVLGGSPYYVLAGAMLIATGWLAWRGSGLALGLHALLLLA 72

Query: 75  TMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIP-------ASGAVAA-LVV 126
           T++W ++EV FD+W L PR  +    G+WL+LP+V RRL          A+G +   LV+
Sbjct: 73  TLLWAIYEVRFDWWQLVPRVAVWFVLGVWLLLPWVSRRLEPDPEPTLRWATGTLPLWLVL 132

Query: 127 ALLISGGILTWAGFNDPQEINGTL-SADATPAEAISPVADQDWPAYGRNQEGQRFSPLKQ 185
           A  ++ G + +  F D   + G    A A PA+A       DW AYGR+  G R +P  Q
Sbjct: 133 AASVALGAVAY--FTDYYTLAGEAPEAGAPPADATG-TPPNDWIAYGRSGHGDRHAPAAQ 189

Query: 186 INADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGK 245
           I   NV  L+ AW F TGD K P DP EI NEVTP+K    LYLCT H  + ALD  +GK
Sbjct: 190 ITPANVAKLQVAWTFHTGDFKGPGDPTEIANEVTPLKANGMLYLCTPHDIVIALDPDTGK 249

Query: 246 EKWHYDPELKTN-ESFQHVTCRGVSYHE-----AKAETASPEVMA--------------- 284
           E+W YDP++  + + +QH+ CRGV+YH+     A+A TA     A               
Sbjct: 250 ERWRYDPKINRDAKGYQHMICRGVAYHDSGAYAAQAATAGVAPAAPPPTPKGAVAAEAIH 309

Query: 285 --DCPRRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIIT 342
              CPRRI  P  D  ++A+NA+NG+ C  F + GV+ L   M   + G   PTSPP +T
Sbjct: 310 FDSCPRRIFAPTADATVVALNADNGQPCTDFGDHGVIGLYQGMAMKRRGFLNPTSPPTVT 369

Query: 343 DKTIVMAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNA-IPSDEHTFTFNSP 401
              ++++ SVTDN ST E SGVIRG+DV TG+LLW +D  A D  A +P+ +H +  NSP
Sbjct: 370 RNVLIVSASVTDNESTDEPSGVIRGYDVTTGQLLWNWDAAAPDSTAPLPAGQH-YKRNSP 428

Query: 402 NSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVH 461
           NSW+ ++ D KL LVY+PMG  TPD+WGG R PE ER+ S+I+AL+  TGKL W YQTVH
Sbjct: 429 NSWSVSSVDEKLGLVYIPMGNQTPDMWGGERYPEGERFNSAIVALDIATGKLRWVYQTVH 488

Query: 462 HDLWDMDLPAQPTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAA 521
           HDLWDMD+  QP+L D+     KVP + A  K G+I+VLDRR+G+ VVPAPE+PVPQGAA
Sbjct: 489 HDLWDMDIGGQPSLVDLDTPQGKVPALVASTKRGDIYVLDRRDGKPVVPAPERPVPQGAA 548

Query: 522 KGDYVTPTQPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTL 581
            GD  +PTQPFS LSF P   L  ADMWG   +DQLVCR+ F ++RY+GIFTPPSEQG+L
Sbjct: 549 TGDRTSPTQPFSALSFAPEHPLREADMWGTNPYDQLVCRIKFRRLRYDGIFTPPSEQGSL 608

Query: 582 VFPGNLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKG-TGTESG 640
           V+PGN G+F+WGG++VDP R++ I NP  + F+S+LI R      E+ + AKG TG E G
Sbjct: 609 VYPGNYGVFDWGGVTVDPQRQLLIGNPNYMAFMSRLITR----ETEEARSAKGSTGIEHG 664

Query: 641 IQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMP 700
           +QP  G P+ V L P LSP G+PC+ P WGY++A+DL+T   +W  R GT  DS P P+P
Sbjct: 665 LQPMQGTPFAVDLRPLLSPLGIPCQAPPWGYVAAVDLRTMRKLWMHRNGTVVDSAPLPIP 724

Query: 701 VPVPFNMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY 760
           +P    +G+P LGG I+T G V F++A+ D YLRAY++ NG++LW+ RLPAGGQATPM+Y
Sbjct: 725 LP----LGVPSLGGMITTGGGVAFMSASLDYYLRAYDVRNGKQLWEARLPAGGQATPMSY 780

Query: 761 --EVNGKQYVVISAGGHGSFGTKMGDYIVAYALP 792
             +  G+QYVVI AGGHGS GTKMGD ++AYALP
Sbjct: 781 VSDQTGRQYVVIMAGGHGSLGTKMGDALIAYALP 814


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: 2448
Number of extensions: 137
Number of successful extensions: 12
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: 816
Length adjustment: 41
Effective length of query: 755
Effective length of database: 775
Effective search space:   585125
Effective search space used:   585125
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: 56 (26.2 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