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_059150990.1 V474_RS07915 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_001046635.1:WP_059150990.1
          Length = 796

 Score =  705 bits (1820), Expect = 0.0
 Identities = 349/658 (53%), Positives = 447/658 (67%), Gaps = 22/658 (3%)

Query: 91  DVPQMAPQQ---SASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPR 147
           D+P +  +    S +    DW AYG  DS  R+SPL +IT  N   LK A++ HTG  P 
Sbjct: 152 DLPALGAEMGDPSLAATGDDWPAYGGSDSARRFSPLGQITAANVKDLKRAWLVHTGDMPS 211

Query: 148 -PGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAACK 206
            P     +  E TP+KVG+ LY+C+ +N ++ ++PA+GK+IWR +     +AIPYTAAC+
Sbjct: 212 SPKIAKTYGGENTPLKVGNMLYVCTPKNIVLALNPASGKQIWRFDPKVSDDAIPYTAACR 271

Query: 207 GVTYFTSSQVPEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGLGESVP 266
           GV+Y+     P GQPC  R++ GTLD RL A+DA TG  C  FG  G+V+   G+G + P
Sbjct: 272 GVSYYAVPNAPAGQPCAARLIFGTLDARLFAIDARTGARCTAFGANGEVDTKIGMGNTPP 331

Query: 267 GFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPNDHSQP 326
           G+VS+ +PP +V GV V  H+VLDGQ RWAPSGVIRGYDA +GK  WAWD+  P  +  P
Sbjct: 332 GYVSINSPPTIVRGVAVTGHQVLDGQDRWAPSGVIRGYDAVTGKLRWAWDMMHPEWNGYP 391

Query: 327 TGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVALDVKT 386
                + RGTPN W   +GD  LGLVY+P GN+A+DYYS+LR P E + ++++VALDV T
Sbjct: 392 PTGQIWERGTPNMWTIASGDEQLGLVYLPMGNAAADYYSSLRRPLEKEFATSLVALDVTT 451

Query: 387 GSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRDGKPIL 446
           G PRW FQ V  DVWDYD G+QA+L+D  G      PAL++P+K+G  +VLDRR GKP+ 
Sbjct: 452 GKPRWKFQAVRNDVWDYDFGAQASLVDYRG-----TPALVLPSKQGDIYVLDRRTGKPLT 506

Query: 447 PVEERPAPSPGVIPGDPRSPTQP---WSTGMPALRVPDLKETDMWGMSPIDQLFCRIKFR 503
           P+ E  AP  GV P D R+ TQ    W T    LR P L E DMWGMSPIDQ+ CRI+FR
Sbjct: 507 PIGELKAPGGGVEP-DQRAKTQRVSLWHT----LRKPALTERDMWGMSPIDQMVCRIQFR 561

Query: 504 RANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRKKA 563
           +A+Y G FTPP  ++  IEYPGYNGG+DWG V+ DP+ G+++AN+N  P Y +LV R +A
Sbjct: 562 KASYKGFFTPPESERRSIEYPGYNGGTDWGGVAIDPRRGVIVANYNDMPNYVRLVPRAEA 621

Query: 564 DELGLMPIDDPNYKPGGGGAEGNGAMDG-TPYGIVVTPFWD-QYTGMMCNRPPYGMITAI 621
           ++ G  P D    +   GGAEG G     TPY I V   W   +TGM+C +PPYG I AI
Sbjct: 622 NKKGWAPRDQA--RGNIGGAEGAGDPQAHTPYAIDVNAGWRLPFTGMLCKQPPYGGIRAI 679

Query: 622 DMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIR 681
           DMK G + +W  PLGTAR NGP+G+P+ LP+ IGTPNNGGSVVTAGGV+F+AAATDN IR
Sbjct: 680 DMKSG-RTIWDRPLGTARTNGPFGIPSMLPFNIGTPNNGGSVVTAGGVIFVAAATDNLIR 738

Query: 682 AIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQLVVYALP 739
           AID  TGK +WS VLP GGQA PMTY  NG QY+ I+ GGHHFM TP+ D+++ YALP
Sbjct: 739 AIDLKTGKTLWSDVLPAGGQATPMTYSVNGKQYLVIVPGGHHFMETPIGDEVIAYALP 796


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: 2214
Number of extensions: 154
Number of successful extensions: 12
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: 796
Length adjustment: 41
Effective length of query: 702
Effective length of database: 755
Effective search space:   530010
Effective search space used:   530010
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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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:

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:

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:

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:

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