Alignments for a candidate for gdh in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Rhodobacter johrii JA192

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_069333644.1 C8J29_RS05030 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_003046325.1:WP_069333644.1
          Length = 781

 Score =  772 bits (1994), Expect = 0.0
 Identities = 391/791 (49%), Positives = 504/791 (63%), Gaps = 30/791 (3%)

Query: 14  LTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLA 73
           LT +   L G  +LI G WLA +GGSW+Y++ GA MLLT + ++RR+S+A  +Y  L+L 
Sbjct: 5   LTAIVLALAGLGLLIPGAWLAVLGGSWFYLVAGALMLLTGWQVFRRSSSAEWIYGGLILG 64

Query: 74  TLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLY-QPGKGALGA-MGVALVASA 131
            L W VWEVG D+W L PR  ++ + G+WL LPF+ R L  + G  A G  + + L+A+ 
Sbjct: 65  ALVWSVWEVGFDWWELIPRGGIIAVLGIWLYLPFMRRQLLTEDGHPAPGLPLALPLLAAI 124

Query: 132 AVLTYSVFNDPQVVNGALP-----ATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLK 186
            V  +S   D     G+LP     A  D  P A P      G+W  Y R Q G R+SPL+
Sbjct: 125 GVAIWSWTGDEAGHAGSLPTEVVSAEPDLGPTAPP------GEWHQYGRTQYGQRYSPLE 178

Query: 187 QINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATG 246
           QIN  NV EL+  WQ+QTGD+K P D  E T +VTP+K+ D LY+CTPH +  ALDAATG
Sbjct: 179 QINIQNVAELEQVWQYQTGDVKLPQDVTETTYQVTPLKVDDRLYICTPHNLAIALDAATG 238

Query: 247 KQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLFALD 306
           K+ W+FD      P  QH TCRGV+Y   PA  +       LC+ R+YLP  D RL ALD
Sbjct: 239 KEAWRFDANSGLEPDRQHQTCRGVTYWRDPARAEGE-----LCAERVYLPTADARLIALD 293

Query: 307 AETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTREPSG 366
           A +G  C  F + G L L+   P T  G Y  TSPPV     I++ GAV DNFS    SG
Sbjct: 294 ARSGAVCTFFADEGTLHLESGMPYTPEGFYYSTSPPVAVGGRIIIGGAVNDNFSVFSQSG 353

Query: 367 AIRGFDVNTGKLLWVFDPGAKDPNAIPAD---EHTFTMNSPNSWAPAVYDPKLDIVYLPM 423
            IR FD NTG LLW +D G  D  A P D     T+T NSPNSW+    D +  +VY+P+
Sbjct: 354 VIRAFDANTGALLWNWDSGNPDETA-PIDWMNGETYTANSPNSWSVFSVDEERGLVYIPL 412

Query: 424 GVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITD 483
           G   PD  G +R+P  E ++SSV+AL+ TTG+  W +QTVHHDLWDMD+P+QP L D+ D
Sbjct: 413 GNQVPDQLGFDRSPAVEEHSSSVVALDVTTGQKAWVFQTVHHDLWDMDVPAQPVLIDL-D 471

Query: 484 KDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQ-GAAKGDHVSATQPYSELTFR 542
            DG TVP +  P K G+I+VL+R TG+ ++P  E P PQ G    +  + TQP S L+F+
Sbjct: 472 IDGQTVPALVQPTKQGDIYVLNRETGEPILPVTEEPAPQEGGLPEESPAPTQPTSALSFK 531

Query: 543 PKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVD 602
           P   L +KDMWG T+YDQL CR+ + RL YEG +TPPS  GT+V+PGN G F WG ++VD
Sbjct: 532 PAA-LREKDMWGVTIYDQLACRIQYHRLNYEGRYTPPSLNGTIVYPGNFGTFNWGSVAVD 590

Query: 603 PHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFL 662
           P RQ+    P  LPF  +L+P      + PP GA   + +E G+    G PYGV + PFL
Sbjct: 591 PERQVMFGMPTYLPFTVELVPA----EDIPPPGANE-TASEQGLNRNEGAPYGVIMGPFL 645

Query: 663 SPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGK 722
            P G+PC  P WGYV+  DL+T ++ +  R GTVRD +P+PLP K+G+P +GGP+ T G 
Sbjct: 646 GPLGVPCSAPPWGYVAGADLRTGDIAYMHRNGTVRDMTPLPLPLKVGVPGIGGPIVTRGG 705

Query: 723 VFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAAGGHGSFGTK 782
           V F+GA  D+YLRA+   TGE LWQARLPAGGQ+TPMTYE +G+Q+VVI AGGHGS GTK
Sbjct: 706 VAFLGAAVDDYLRAYDVTTGEQLWQARLPAGGQSTPMTYEQDGRQFVVIVAGGHGSVGTK 765

Query: 783 LGDYVIAYALP 793
            GDYVIAYALP
Sbjct: 766 PGDYVIAYALP 776


Lambda     K      H
   0.319    0.137    0.433 

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: 2401
Number of extensions: 183
Number of successful extensions: 22
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: 781
Length adjustment: 41
Effective length of query: 755
Effective length of database: 740
Effective search space:   558700
Effective search space used:   558700
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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