Alignments for a candidate for gdh in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Klebsiella michiganensis M5al

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate BWI76_RS13270 BWI76_RS13270 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>FitnessBrowser__Koxy:BWI76_RS13270
          Length = 790

 Score =  641 bits (1653), Expect = 0.0
 Identities = 341/810 (42%), Positives = 491/810 (60%), Gaps = 39/810 (4%)

Query: 1   MAINNT--GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLW 58
           MA +N   G  R+L  L A    + GL + I G  L ++GG++Y+ + GLVM+  A +++
Sbjct: 1   MATDNAPRGFPRILQWLLAGLMLIIGLAIGILGAKLASVGGTFYFALMGLVMVIAAVLIF 60

Query: 59  RSKRAALWLYAALLLGTMIWGVWEVGFDFWALTPRSDIL--VFFGIWLILPFVWRRLVI- 115
           RS+R  + LYA   + +++W + + G+ +W L  R   L  + F   L+ PF+ R+    
Sbjct: 61  RSRRGGIMLYAVAFVASIVWAISDAGWTYWPLFSRLFALGVLAFLCALVWPFLSRQPAKK 120

Query: 116 -PASGAVAALVVALLISGGILTWAGFNDPQEINGTLSADATPAEAISPVA----DQDWPA 170
            PA G  A + VALL+S     W   + P          A+ A  + PVA     ++W  
Sbjct: 121 GPAFGLAAVIAVALLVS---FAWMFKSQPL-------VSASEAVPVKPVAADEQQKNWAH 170

Query: 171 YGRNQEGQRFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLC 230
           +G    G RF+ L QIN  NV  L+ AW+  TGD+ Q N  G   ++ TP+++GDTLY+C
Sbjct: 171 WGNTTHGDRFAALDQINKQNVDQLQVAWIAHTGDIPQSNGSGA-EDQNTPLQIGDTLYVC 229

Query: 231 TAHQRLFALDAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMAD---CP 287
           T + ++ ALD  SGKEKW YD +  T  ++Q   CRG+ Y+E      SP   A    C 
Sbjct: 230 TPYSKVLALDVDSGKEKWRYDSKA-TAPNWQR--CRGLGYYEDSQAQVSPAADAQPAACS 286

Query: 288 RRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIV 347
           RR+ LP  D RLIAI+A+NGKLC+ F + G+++L   M + K G Y+ TS P++    +V
Sbjct: 287 RRLFLPTTDARLIAIDADNGKLCDAFGDHGIVDLSIGMGEIKAGYYQQTSTPLVAGNVVV 346

Query: 348 MAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPA 407
           + G V DNFST E  GV+R +DV+TG+L WA+DPG       P    T+T  +PN W+  
Sbjct: 347 VGGRVADNFSTGEPPGVVRAYDVHTGKLAWAWDPGNPALTGEPPAGQTYTRGTPNVWSAM 406

Query: 408 AYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDM 467
           +YDAKL+L+YLP G  TPD +GG RT   ++Y+SSI+A++ATTG++ W YQT HHDLWD 
Sbjct: 407 SYDAKLNLIYLPTGNATPDFFGGERTALDDKYSSSIVAVDATTGQVRWHYQTTHHDLWDF 466

Query: 468 DLPAQPTLADI-TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV 526
           DLP+QP L D+    G   PV+   +K G IF+L+R  GE V    E+PVP G  KG+  
Sbjct: 467 DLPSQPLLYDLPDGKGGTTPVLVQTSKQGMIFMLNRATGEPVAKVEERPVPAGNVKGERY 526

Query: 527 TPTQPFS-ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPG 585
           +PTQP+S  +     + L+ +DMWGAT  D L+CR+ F +MR++G+FTPP E  +L +PG
Sbjct: 527 SPTQPYSVGMPMIGNETLTESDMWGATPVDLLLCRIQFKEMRHQGVFTPPGEDRSLQYPG 586

Query: 586 NLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQY 645
           +LG   WG +SVDPN  +   N M L   + ++PR      +  KDA  +G E GI P  
Sbjct: 587 SLGGMNWGSVSVDPNNSLIFVNDMRLGLANYMVPRA-----KVAKDA--SGIEMGIVPME 639

Query: 646 GVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPF 705
           G P+G     FLSP G+PC++P +G +SA+DLKT ++VW+  +GT +D+ P  + + +P 
Sbjct: 640 GTPFGAMRERFLSPLGIPCQKPPFGTLSAVDLKTGKLVWQVPVGTVEDTGPLGIRMHMPI 699

Query: 706 NMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTY--EVN 763
            +GMP LG  +ST   +LF A T D YLRA++ +NG+++W+ RLP G Q+ PMTY     
Sbjct: 700 PIGMPTLGASLSTQSGLLFFAGTQDFYLRAFDTANGKEIWKSRLPVGSQSGPMTYVSPKT 759

Query: 764 GKQYVVISAGGHGSFGTKMGDYIVAYALPD 793
           GKQY++I+AGG        GDYI+AYALP+
Sbjct: 760 GKQYIIINAGG-ARQSPDRGDYIIAYALPE 788


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: 2187
Number of extensions: 139
Number of successful extensions: 16
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: 790
Length adjustment: 41
Effective length of query: 755
Effective length of database: 749
Effective search space:   565495
Effective search space used:   565495
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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