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

GapMind for catabolism of small carbon sources

Aligments 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources