Alignments for a candidate for sdh in Novosphingobium barchaimii LL02

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Novosphingobium barchaimii LL02

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_059151269.1 V474_RS09585 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_001046635.1:WP_059151269.1
          Length = 782

 Score =  471 bits (1212), Expect = e-137
 Identities = 267/650 (41%), Positives = 362/650 (55%), Gaps = 32/650 (4%)

Query: 100 SASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSY--PRPGQTNKWAAE 157
           +A+PA+ DW AYG + +  R+S  ++ITP NA +L+  + + TG     RP +    +  
Sbjct: 158 AANPANADWTAYGANSAGTRHSSAAQITPANAAKLEQVWSFQTGDTRAKRP-EIKSISFM 216

Query: 158 TTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACKGVTYFTSSQVP 217
            TP+ V D +Y CS    +  +D  +G+++W  + +           C+GV+Y      P
Sbjct: 217 ATPLMVDDKVYFCSPTGKVFALDADSGRQVWLRDPHTNI-GNAQMLNCRGVSYHAD---P 272

Query: 218 EGQP-CHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVPGFVSMTTPPP 276
            G   C  RI+  T+D R++A DAATG  C  FG  G VNL  GLG   P     ++PP 
Sbjct: 273 AGAGLCAKRIISMTVDGRMLASDAATGAPCSDFGEMGTVNLDAGLGAVDPLRSYTSSPPV 332

Query: 277 VVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQPTGNNHYSRGT 336
           +V    ++   V D   +  PSGV+R YD +SG+ LWAWD  RP+D   P     ++RG+
Sbjct: 333 IVGNTAILGSYVRDNFTKDDPSGVVRAYDVKSGRLLWAWDSGRPDDAPMPGPGEGWTRGS 392

Query: 337 PNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKTGSPRWVFQTV 396
            N+W+  + D ALGLVY+PTGN+  D+    R+P   + +S++VALDVKTG  RW FQTV
Sbjct: 393 VNAWSVFSADPALGLVYLPTGNATPDHVGTHRNPMLERYASSIVALDVKTGRVRWHFQTV 452

Query: 397 HKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPILPVEERPAPSP 456
           H D+WDYD+ +Q  L D     G  VPAL  PTKRG+ F+LDRR GK +  +EER  P  
Sbjct: 453 HHDIWDYDMPAQPVLFDYTA-GGSKVPALAAPTKRGEIFILDRRTGKSLTGIEERAVPR- 510

Query: 457 GVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRIKFRRANYTGEFTPPSV 516
           G IPG+  SPTQP+  G P+   P L E  MWGM+P+DQ++CRI+FR  +Y+G FTPPS 
Sbjct: 511 GKIPGERYSPTQPYVKGFPSFAPPLLTEASMWGMTPLDQMWCRIRFRSLDYSGNFTPPS- 569

Query: 517 DKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKADELGLMPIDD--P 574
           ++  I++PG  G  +WGSVS DP   ++I N    P   +L       E   +  D   P
Sbjct: 570 ERGMIQWPGTFGVLNWGSVSIDPARNLMIVNSAAIPQEVRLFRHGADTEKPALAKDSHAP 629

Query: 575 NYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAIDMKHGQKVLWQHP 634
            Y P            GT YG+ + P      G+ C  PP+G I A+D+  G K+ W   
Sbjct: 630 GYLP----------QMGTNYGVSLLPMLSP-LGIPCEAPPWGHIAAVDLSTG-KIAWSRT 677

Query: 635 LGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIRAIDEHTGKVVWSA 694
            GT     P G+   +P   G  N GGS  TAGGV FI A  DN +RAID   G+ +W  
Sbjct: 678 FGTTADTAPLGI--AMP---GAFNLGGSANTAGGVTFIGATLDNYLRAIDTTNGRELWRG 732

Query: 695 VLPGGGQANPMTY--EANGHQYVAIMAGGHHFMMTPVSDQLVVYALPDHK 742
            LP GGQA P+TY     G QYV I AGGH +M T   D LV +ALP  K
Sbjct: 733 RLPAGGQATPITYISRKTGRQYVVIAAGGHMYMGTTPGDYLVAFALPKTK 782


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: 1908
Number of extensions: 137
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: 782
Length adjustment: 40
Effective length of query: 703
Effective length of database: 742
Effective search space:   521626
Effective search space used:   521626
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 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