Alignments for a candidate for gdh in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Halomonas desiderata SP1

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_086511089.1 BZY95_RS17045 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_002151265.1:WP_086511089.1
          Length = 812

 Score =  585 bits (1508), Expect = e-171
 Identities = 316/817 (38%), Positives = 460/817 (56%), Gaps = 41/817 (5%)

Query: 7   GSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAALW 66
           G+    VT+ A+   L GL + +GG +L+ +GG++Y+ +AG+  L  A ML     A +W
Sbjct: 8   GAAGWAVTVFAIVLLLLGLAMSLGGAYLIYLGGTFYFLLAGIGTLVAAVMLKLGLPAGVW 67

Query: 67  LYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIW--------LILPFVWRR-LVIPA 117
           +YAA + GT +W +WE+    W      D++   G+         L+LP ++RR    PA
Sbjct: 68  VYAATVAGTFLWSLWEIAMKGWMPVWHIDLMARTGLMAGLLAVALLLLPVLYRRGYYQPA 127

Query: 118 SGAVAALVVALLISG--GILTWAGFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQ 175
               + L+  L++ G  G + W  F+   +   T +A+A P +      D DW AYG   
Sbjct: 128 LPYASPLLGMLIMVGYAGTVLWLIFDSGPDAPTTAAAEAIPQQ--DAPNDTDWVAYGGTN 185

Query: 176 EGQRFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQR 235
             QRFSP  +I   N   L+ AW F TGD + P+D      + TP+K+G++LY+CT   +
Sbjct: 186 LAQRFSPADRITPHNADQLEVAWEFNTGD-EPPSDAAPYAFQNTPLKIGNSLYVCTQSNQ 244

Query: 236 LFALDAASGKEKWHYDPELKTNESFQHV---TCRGVSYHEAKAETASPEVMADCPRRIIL 292
           +FALD  +G+++WH+DPE+   E+ +HV   TCR V+Y EA      P+ + +CPRR++L
Sbjct: 245 VFALDPGTGEQQWHFDPEVAV-EAQEHVFSTTCRAVAYFEA------PDPVEECPRRLLL 297

Query: 293 PVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSV 352
              DGRL+A+NAE+G LC +F + G ++L   M     GL   TS PI+ +  +V+   V
Sbjct: 298 GTLDGRLMALNAEDGSLCNSFGDNGTVDLNDRMDPQALGLLSNTSGPIVVNGIVVVGHQV 357

Query: 353 TDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAK 412
           TDN      SG +R +D  TGE  W +D     P+  P +   +   +PN W   + D +
Sbjct: 358 TDNQRRDAPSGAVRAYDAITGEWQWTWDSVWTTPDQQPPEGELYPRGTPNVWTAISADEE 417

Query: 413 LDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQ 472
           L LVYLP G  T D +GG+R+PE++ + S+++A+ A +G++ W + TV HDLWD DL AQ
Sbjct: 418 LGLVYLPTGNPTNDQYGGDRSPEEDEFTSTLVAVEADSGEVRWKFTTVLHDLWDYDLGAQ 477

Query: 473 PTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPF 532
           P L D   +    P +    K G +FV DR  GE ++P  E+PVPQGA +GD+    Q F
Sbjct: 478 PALIDFPTDDGPRPAVVQATKYGQVFVFDRETGEPLLPIEERPVPQGAIEGDWTAEVQRF 537

Query: 533 S-------ELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPS---EQGTLV 582
           S        +  +  +  +GA  WGAT  D L CR+ F +MRYEG+FTPP+     G L 
Sbjct: 538 SPSMPNFGSIPGQEVEHFTGAHTWGATPIDHLYCRIQFERMRYEGMFTPPTLDHAGGMLQ 597

Query: 583 FPGNLGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQ-----PKDAKGTGT 637
           FP  LG   WG  + D +  + I N   +P    L PR   + ME       +DA     
Sbjct: 598 FPAILGGINWGSAAFDLDNGLMIVNNNRMPSRVVLYPREEADEMENIAPIGEEDASYIDQ 657

Query: 638 ESGIQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPF 697
           E+  QP  G P       +LSP  +PC  P WG++SA DL + E+VW + IGT  D  P+
Sbjct: 658 EA--QPMLGAPVAAQRGAWLSPLDMPCAAPPWGFLSATDLASGELVWSRPIGTSFDQGPW 715

Query: 698 PMPVPVPFNMGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATP 757
            +P  +   +G P   GP++TAG V FI AT D+Y+RA+N + G+ LW+ RLPAGGQATP
Sbjct: 716 GIPARLKMTVGAPTSAGPVTTAGGVTFIGATMDDYIRAFNNTTGDMLWEARLPAGGQATP 775

Query: 758 MTYEVNGKQYVVISAGGHGSFGTKMGDYIVAYALPDD 794
           MTY   G+QYVVI+AGG     T +GD ++AYALP++
Sbjct: 776 MTYMHEGRQYVVIAAGGAFQAETSLGDSVMAYALPEE 812


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: 2239
Number of extensions: 157
Number of successful extensions: 10
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: 812
Length adjustment: 41
Effective length of query: 755
Effective length of database: 771
Effective search space:   582105
Effective search space used:   582105
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 24 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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
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