Alignments for a candidate for sdh in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Rhizobium leguminosarum 3841

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate WP_011651065.1 RL_RS07055 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_000009265.1:WP_011651065.1
          Length = 779

 Score =  483 bits (1243), Expect = e-140
 Identities = 266/660 (40%), Positives = 362/660 (54%), Gaps = 24/660 (3%)

Query: 83  DIGSMDPNDVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHT 142
           D+    P D     P    S   G+W  YG      RYSPL +IT +N   LK A+ Y T
Sbjct: 141 DLAGELPKDTVAANPAFGGSVPDGEWHQYGRTPFGQRYSPLDQITAENVSTLKEAWRYQT 200

Query: 143 GSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYT 202
           G   RP    +   + TP+KV D LY+C+  N  + +D  TGKE W+++ N         
Sbjct: 201 GDVKRPDDVGETTYQVTPLKVKDTLYLCTPHNWAIALDAKTGKEKWKYDANSGMNPDRQH 260

Query: 203 AACKGVTYFTSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLG 262
             C+GVTY+    V  GQPC  R+   T D RLIA+DAA G +C  F + G ++L  G+ 
Sbjct: 261 QTCRGVTYYADPAVAAGQPCAERVYLPTSDARLIALDAADGKVCTSFADQGVLHLETGMR 320

Query: 263 ESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPND 322
            +  G+   T+PP  V G ++V   V D       SGVIR +D  +G  +W WD   P+ 
Sbjct: 321 YNPAGYYYSTSPPVAVAGKIIVGGAVNDNYSTEEQSGVIRAFDINTGALVWNWDSGNPDL 380

Query: 323 HSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVAL 382
            +  T    Y+  +PNSW+  + D ALG+VY+P GN   D     RS    K SS++VAL
Sbjct: 381 TTPITEGQTYTTNSPNSWSVFSVDEALGMVYIPLGNQVPDQIGINRSDNVEKFSSSIVAL 440

Query: 383 DVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDG 442
           D+ TG  RWV QTVH D+WD D+ +Q  L+D+  QDG  VPAL+ PTK+G  +VLDRR G
Sbjct: 441 DIATGQLRWVRQTVHHDLWDMDVPAQPALIDLTKQDGTVVPALVGPTKQGDIYVLDRRSG 500

Query: 443 KPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRIKF 502
           +PI+PV+E PAP  G + GD  SPTQP S          L+E DMWG+S  DQ+ CRI F
Sbjct: 501 EPIIPVKEIPAPG-GAVSGDHTSPTQPISD--LTFSPEPLQEKDMWGVSLFDQMACRIDF 557

Query: 503 RRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKK 562
            R +Y G +TPPS+ K  I YPG  G  +WGSV+ DP+  I+       P Y    +R  
Sbjct: 558 HRYHYEGRYTPPSL-KGTIVYPGNFGTFNWGSVAVDPERQIMFG----MPTYLAFTSR-- 610

Query: 563 ADELGLMPIDD--PNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITA 620
                L+P  D  P  +   G  +G    DG PYG+ + PF      + C  PP+G +  
Sbjct: 611 -----LVPAADIPPRGQDEKGSEQGLNRNDGAPYGVFMGPFLG-LLQIPCQAPPWGYVAG 664

Query: 621 IDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQI 680
           +D++ G K+ + H  GT     P  LP  LP+++G P  GG ++T GGV F+ AA DN +
Sbjct: 665 VDLRTG-KIAYMHKNGTVHDMTP--LP--LPFKVGVPGIGGPMLTKGGVAFLGAAVDNYL 719

Query: 681 RAIDEHTGKVVWSAVLPGGGQANPMTYEANGH-QYVAIMAGGHHFMMTPVSDQLVVYALP 739
           RA D  +G+ +W   LP GGQA PMTY  + + QYV ++AGGH  + T   D ++ Y LP
Sbjct: 720 RAYDVTSGRELWQGRLPAGGQATPMTYMTDDNKQYVVMVAGGHGSVGTTPGDYVIAYTLP 779


Lambda     K      H
   0.315    0.134    0.428 

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: 2142
Number of extensions: 149
Number of successful extensions: 13
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: 743
Length of database: 779
Length adjustment: 40
Effective length of query: 703
Effective length of database: 739
Effective search space:   519517
Effective search space used:   519517
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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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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