Aligments for a candidate for gdh in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for gdh in Pseudomonas stutzeri RCH2

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate GFF2858 Psest_2914 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__psRCH2:GFF2858
          Length = 776

 Score =  782 bits (2020), Expect = 0.0
 Identities = 386/784 (49%), Positives = 509/784 (64%), Gaps = 23/784 (2%)

Query: 17  LFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLATLA 76
           LF ++ G  + +GG  + ++GG+WY+ I  A  LLT  LL  R   AL VYALL+L  L 
Sbjct: 8   LFCIIVGIALGVGGAKVVSLGGTWYFAIVAAGFLLTGVLLLMRRRTALWVYALLMLGALG 67

Query: 77  WGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGL------YQPGKGALGAMGVALVAS 130
           W V+EVG D+W LAPR  ++  FG+WL+ P++ R L      ++   GA   + +A+   
Sbjct: 68  WAVYEVGLDWWQLAPRGSIIAPFGLWLLTPWIARRLGWQHFGFRAWGGAALPLMLAVGLW 127

Query: 131 AAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLKQINH 190
            A   Y+V +D   + G LPA    AP A    ++  GDW AY R Q G R+SPL QI  
Sbjct: 128 GAATVYAVGHDGHDIKGMLPAPLAQAPAAD--DSVPAGDWHAYGRSQHGQRYSPLAQITP 185

Query: 191 DNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGKQKW 250
            NV  L+  W +QTGD++ P DP E T EVTP+K+ D+LYLCTPH ++ ALDA TG+++W
Sbjct: 186 QNVDRLEPVWHYQTGDLRGPDDPDETTYEVTPLKVDDSLYLCTPHNLVIALDAETGQERW 245

Query: 251 KFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLFALDAETG 310
           +FDP +  +   QH+TCRG+SYH  P   D        C +R+++P  D RL ALDA+TG
Sbjct: 246 RFDPKVPHSVNRQHLTCRGLSYHAAPQGSDVQ-----ACRQRLFMPTADARLIALDAKTG 300

Query: 311 ERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTREPSGAIRG 370
           E CP F +NGE+DL    P    G Y  TSPPV+    +++ GAV DN   +EPSG IR 
Sbjct: 301 EICPGFADNGEIDLWANMPHAKEGFYYSTSPPVVARDLVIIGGAVNDNVRAQEPSGVIRA 360

Query: 371 FDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDI 430
           +DV TG+L W +DPG  D     A   T++ +SPNSW+ +  D  L +VY+P+G   PD 
Sbjct: 361 YDVYTGQLKWNWDPGNPDATEPIAAGQTYSPSSPNSWSISSADEALGMVYVPLGNQVPDQ 420

Query: 431 WGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITDKDGNTVP 490
           WGG R    ER++SS++AL+  +G+L W +QTV HDLWDMD+P+QP+L DI  ++G  VP
Sbjct: 421 WGGRRNENSERFSSSIVALDLDSGQLRWVFQTVRHDLWDMDVPAQPSLVDIQTENG-PVP 479

Query: 491 VIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSELTFRPKQNLTDK 550
            + AP K G+I+VLDRRTG+ ++P  E P PQGAA+GD V+ TQP S L++ P + L  K
Sbjct: 480 AVVAPTKQGDIYVLDRRTGEPILPVREVPAPQGAAEGDWVAKTQPASALSYEPPK-LQGK 538

Query: 551 DMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVDPHRQIAIA 610
           D+WGAT+ DQ++C + F  LRYEG +TPPS QGTLV PGN G+F WGG++VDP RQ+  +
Sbjct: 539 DLWGATLIDQMMCHIQFHSLRYEGRYTPPSTQGTLVHPGNFGVFNWGGVAVDPVRQMVFS 598

Query: 611 NPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFLSPFGLPCK 670
            P  L F SKLIPR            T  S  E  +   +G P+ VEL  F+SP GLPC 
Sbjct: 599 TPAYLAFTSKLIPREDAE-------TTYVSEQEPFLNENFGSPFAVELKAFVSPIGLPCT 651

Query: 671 QPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGKVFFIGATA 730
            P WGYV+  DL+T +  W ++ GTVRD SP+PLPFKMG+P LGGP+ TAG V F+  T 
Sbjct: 652 APPWGYVAGADLRTGKTHWLRKNGTVRDRSPIPLPFKMGVPNLGGPMLTAGGVAFLSGTL 711

Query: 731 DNYLRAFSTDTGELLWQARLPAGGQATPMTYEV-NGKQYVVIAAGGHGSFGTKLGDYVIA 789
           D YLRA+   TG  LW+ARLPAGGQATPMTY+  +G+Q VV+ AGGHGS GTK GD VIA
Sbjct: 712 DYYLRAYDVMTGRELWKARLPAGGQATPMTYQSRSGRQMVVVVAGGHGSLGTKAGDSVIA 771

Query: 790 YALP 793
           YALP
Sbjct: 772 YALP 775


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: 2264
Number of extensions: 151
Number of successful extensions: 14
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: 776
Length adjustment: 41
Effective length of query: 755
Effective length of database: 735
Effective search space:   554925
Effective search space used:   554925
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)
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 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