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_069333494.1 C8J29_RS18500 PQQ-binding-like beta-propeller repeat protein

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_003046325.1:WP_069333494.1
          Length = 734

 Score =  506 bits (1303), Expect = e-147
 Identities = 273/647 (42%), Positives = 377/647 (58%), Gaps = 23/647 (3%)

Query: 159 AQPLSNIADGDWPAYARDQQGTRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITD 218
           AQP   +   DWP +  D Q TR+SPL +I  +NV  L+ A+ ++TGDM      G+ + 
Sbjct: 98  AQPQPEVG-ADWPFWGGDAQATRYSPLDEITPENVAGLERAFVYRTGDMPSAEADGKYSP 156

Query: 219 EVTPIKIRDTLYLCTPHQILFALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAA 278
           E TP+KI D L +C+   IL ++DAATG++ W++DPG+         +CRGVS +  PAA
Sbjct: 157 ETTPLKIGDDLLMCSAMNILISIDAATGEENWRYDPGVPAEAIPYGASCRGVSIYTDPAA 216

Query: 279 KDASNTQPALCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEP 338
            + +     LC+ R+     D +L A+DA TG+ C  FG NG +DL        PG Y  
Sbjct: 217 AEGT-----LCATRVIEGTLDAKLVAVDAFTGDPCEGFGENGTVDLWQDIGERVPGWYSV 271

Query: 339 TSPPVITDTTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPN-AIPADEH 397
           T+PP +    +V    V D  +   PSG +RG+D  TG L+W +D  A + N A P    
Sbjct: 272 TAPPAVVRGILVTGAQVKDGQAEDAPSGVVRGYDAVTGDLVWAWDLAAPEANRAGPPAGE 331

Query: 398 TFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLV 457
            +T  +PN W  AV D +L  VYLP+G ++ D +G NR+  +  +A+S++AL+ATTG+ V
Sbjct: 332 VYTRGTPNMWTTAVADEELGYVYLPLGNSSVDYYGSNRSEAENAFATSLVALDATTGEEV 391

Query: 458 WSYQTVHHDLWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPE 517
           W +QTV HD+WD DL SQPTL D         P I  P+K G++++LDR TG+ + P  E
Sbjct: 392 WHFQTVRHDVWDYDLGSQPTLLD-----WQGTPAILLPSKQGDLYILDRATGEPLTPMEE 446

Query: 518 -TPVPQGAAKGDHVSATQPYSELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPF 576
            T +PQG  + D++S TQP S         L  +D WG T  DQL CR+ F R  YEG F
Sbjct: 447 LTGLPQGDVEPDYISPTQPASAWATLRMPPLEPRDAWGFTAIDQLWCRIQFHRANYEGYF 506

Query: 577 TPPS-EQGTLVFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNP---EEP 632
           TPPS ++  + +PG  G  +WG ++VD  R + IAN   +P  ++L+PR         E 
Sbjct: 507 TPPSSDRPWIQYPGYNGGSDWGSVAVDSQRGLIIANYNDVPNYNRLVPRDEVESVPIHEQ 566

Query: 633 PKGATGGSGTETGIQPQYGVPYGVELNPFL--SPFGLPCKQPAWGYVSAVDLKTNEVVWK 690
             GA  G   E    PQ G PYG+ +N        G+PC +P +G++ A+DL+T E VW 
Sbjct: 567 ESGAQAGENAEGAADPQAGSPYGISVNAGWRNEMTGIPCVRPPYGHIRAIDLETGETVWD 626

Query: 691 QRIGTVRDSSP--VP--LPFKMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLW 746
           +  GT R + P  +P  LPF +G P  GG V TAG V F+GA  DN  RA   +TGE LW
Sbjct: 627 RPFGTARRNGPFGIPSYLPFDIGTPNNGGSVVTAGGVIFMGAATDNLFRAIDVETGETLW 686

Query: 747 QARLPAGGQATPMTYEVNGKQYVVIAAGGHGSFGTKLGDYVIAYALP 793
           Q  LPAG QA P+TYEV+G+QYV+IAA GH    T +GD++IAYALP
Sbjct: 687 QDVLPAGAQANPITYEVDGRQYVMIAAVGHHFMETGVGDWMIAYALP 733


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: 2160
Number of extensions: 156
Number of successful extensions: 15
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: 734
Length adjustment: 40
Effective length of query: 756
Effective length of database: 694
Effective search space:   524664
Effective search space used:   524664
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)
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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