GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Dinoroseobacter shibae DFL-12

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate 3608903 Dshi_2294 Pyrrolo-quinoline quinone (RefSeq)

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__Dino:3608903
          Length = 769

 Score =  560 bits (1444), Expect = e-164
 Identities = 307/791 (38%), Positives = 448/791 (56%), Gaps = 33/791 (4%)

Query: 15  LTALFAA---LCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALWLYAAL 71
           +T LF A   L G  + + G WL+A+GGSWYY +AG  +    +  W+ +    W++ A+
Sbjct: 1   MTKLFGAILVLVGALMFVPGIWLIALGGSWYYSLAGAGLAAAGFYYWKKQLLGAWIFGAV 60

Query: 72  LLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAALVVALLIS 131
             GT +W VWEVGF+ W L PR   LV   +  IL  +    +    G  A+L  A +++
Sbjct: 61  FAGTALWAVWEVGFELWPLVPR---LVAPMVLAILAVLLVPSLNEGRGRTASLAAAGVLA 117

Query: 132 GGILTWA-GFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQEGQRFSPLKQINADN 190
            GI  +  G   PQ +    + D  P  AI+     +W  YGR   G RF+P  QI  +N
Sbjct: 118 LGIAGFFWGMATPQNV--IANTDPVPTRAIA-AESPNWTHYGRTPTGTRFAPFDQITPEN 174

Query: 191 VHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKEKWHY 250
           V  L+ AW F  GD   P+  G+  N  TP+ V   +Y C+ +  + A+DA +G + W Y
Sbjct: 175 VGELEVAWTFNHGDA--PSGTGQDQN--TPLYVDGLVYHCSPNNIVSAIDAVTGAQVWQY 230

Query: 251 DPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAINAENGKLC 310
           DPE  ++  +Q   CRGV+Y+E      +P     C  RI+L   D RLI ++A  G LC
Sbjct: 231 DPEA-SSPLWQR--CRGVTYYEPTPREGAP-ADGTCAARIVLSSVDARLIQLDARTGALC 286

Query: 311 ETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETSGVIRGFDV 370
            TF + G ++L  NM + +PG Y PTS P +    I++ G V D  +  E SGV+R FD 
Sbjct: 287 TTFGDGGAVDLTRNMGEVRPGFYFPTSAPTVMGDRIILGGWVWDGMAVDEPSGVVRAFDG 346

Query: 371 NTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGG 430
            TGE+ WA+D G    + +P +  T+T  +PN W+  A+DA L LVYLP G   PD +G 
Sbjct: 347 RTGEIAWAWDIGNPAIDTVPPEGETYTRGTPNVWSTPAFDAALGLVYLPTGNAQPDFYGS 406

Query: 431 NRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADITV-NGQKVPVIY 489
           +R      + SSI+AL+  TGK+ WS+QT + D+WD D+PAQP L DIT   G+ VP + 
Sbjct: 407 SRIEAANDWNSSIVALDVETGKVVWSFQTTYRDIWDYDVPAQPMLYDITTETGEVVPALI 466

Query: 490 APAKTGNIFVLDRRNGELVVPAPEKPVP-QGAAKGDYVTPTQPFS-ELSFRPTKDLSGAD 547
              K    FVLDRR+G  +    + PVP  G  + DY++P QP+S ++     + L+ A 
Sbjct: 467 QVTKRSQTFVLDRRDGTPIAEVRDLPVPTTGGVEPDYLSPVQPYSVDMPVIGAEPLTEAR 526

Query: 548 MWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDPNREVAIAN 607
           MWGAT  D L CR+ F Q  Y G FTP SEQGTL++PG  G   WG  ++D  R + I N
Sbjct: 527 MWGATPLDHLYCRIRFRQAYYVGDFTPMSEQGTLIWPGYFGGMNWGTGTIDEARGLLIVN 586

Query: 608 PMALPFVSKLIPRGPGNPMEQPKDAKG---TGTESGIQPQYGVPYGVTLNPFLSPFGLPC 664
              +  + +LIPR       Q  DA G    G   G+ PQ G P+G   + F S  G+PC
Sbjct: 587 DTRVAHLLQLIPR-------QEADALGVEVVGPHDGLAPQDGAPFGAMRSNFFSFVGVPC 639

Query: 665 KQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVLF 724
           ++P +G ++A+DL    ++W++ +GT +++ PF +       +G+P++GGPISTA  + F
Sbjct: 640 QEPPYGTMTAIDLADRSILWQRPVGTIEETGPFGIRTGWRMPVGLPLVGGPISTASGLTF 699

Query: 725 IAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY-EVNGKQYVVISAGGHGSFGTKMG 783
            + T D YLRA++   GE+LW+G LP G Q+TPM+Y   +G+QYVV++ GG      + G
Sbjct: 700 YSGTQDYYLRAFSSETGEELWRGALPLGSQSTPMSYIGPDGRQYVVVTVGGLNDIMGR-G 758

Query: 784 DYIVAYALPDD 794
           D ++A+ALP++
Sbjct: 759 DIVMAFALPEE 769


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: 2286
Number of extensions: 169
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: 769
Length adjustment: 41
Effective length of query: 755
Effective length of database: 728
Effective search space:   549640
Effective search space used:   549640
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