GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0461
          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:

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