GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Frischella perrara PEB0191

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_052236884.1 FPB0191_RS08270 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>NCBI__GCF_000807275.1:WP_052236884.1
          Length = 803

 Score =  432 bits (1110), Expect = e-125
 Identities = 241/662 (36%), Positives = 355/662 (53%), Gaps = 48/662 (7%)

Query: 104 ASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQTNKWAAETTPIKV 163
           A+ DW AYG  ++ + YS L++I P N  +L+  +   TG  P      +   E TP+KV
Sbjct: 158 AAEDWIAYGGTNAGLHYSALNQIVPNNIHKLQEVWRIRTGDMPTADDPVELTNENTPLKV 217

Query: 164 GDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTAA----------CKGVTYFTS 213
            D LY C+A   ++ ++P TGK +W+ +      AI  + A          C+G++Y+ S
Sbjct: 218 NDKLYTCTAHGWVLALEPETGKTLWKFD-----PAISNSGAGTFKGWAHMTCRGLSYYDS 272

Query: 214 SQV------------PEGQPCHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQVNLMQGL 261
            +              +   C  RI   T D RLIA++A  G LC+ FG  GQV+L QG+
Sbjct: 273 DRYLKQFAKDKIALKVKSSSCPRRIYLPTADARLIALNADNGQLCDSFGVNGQVDLTQGI 332

Query: 262 GESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWAWDVNRPN 321
           G+  PG    T+P  V   +V+V   V D +    PSGV+R +D   G  +W WD   P+
Sbjct: 333 GKFTPGGYYSTSPALVTKQLVIVGGHVTDNESTNEPSGVVRAFDIYDGHLVWNWDSGNPD 392

Query: 322 DHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENKVSSAVVA 381
             +    +  Y+R +PN W+  + D ALGLVY+P GN   D Y   R+P   K ++ +VA
Sbjct: 393 ATTPLPKDKKYTRNSPNVWSITSADEALGLVYLPLGNQTPDQYGGNRTPVVEKYAAGIVA 452

Query: 382 LDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQTFVLDRRD 441
           LD+ +G   W +Q  H D+WD D+ +Q  L+D+    G   PA+I PTK+G  +VL+R+ 
Sbjct: 453 LDITSGKVVWNYQFTHHDLWDMDVPAQPILVDLKTTQGIE-PAVIQPTKQGSLYVLNRKT 511

Query: 442 GKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPIDQLFCRIK 501
           G+PI+P+ E   P  G + GD  SPTQ  +     L  P L+E DMWG +P DQL CRIK
Sbjct: 512 GQPIVPINEVSVPQ-GAVKGDWTSPTQ--ARSQLNLLPPPLREQDMWGATPFDQLSCRIK 568

Query: 502 FRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMYDQLVTRK 561
           F+   Y G++TPPS+    I YPG  G  +WG V+ DP   I+ A+ N      +L+ + 
Sbjct: 569 FKSLRYEGQYTPPSLQGSLI-YPGNVGVMNWGGVAIDPVRKIIFASPNYMAFTSKLIPQA 627

Query: 562 KADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPPYGMITAI 621
           +      +P ++ N   G G     GA    PY + + PF     G  C  P +G +  I
Sbjct: 628 E------VPKNEANASEGAGLQPNQGA----PYAVRIQPFL-SLVGFPCQAPSWGNVAGI 676

Query: 622 DMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAAATDNQIR 681
           ++ +   + W HP GT+R N P+ +P  LP+ +G P  GG + TAGGV F++   D  +R
Sbjct: 677 NLAN-NSIAWIHPNGTSRDNTPF-IP--LPFPVGVPAMGGPMTTAGGVAFLSGTLDQYLR 732

Query: 682 AIDEHTGKVVWSAVLPGGGQANPMTY-EANGHQYVAIMAGGHHFMMTPVSDQLVVYALPD 740
           A D   GK +WS+ LP GGQA PMT+   +  QY+ ++ GGH    T + D ++ YALP 
Sbjct: 733 AYDITNGKEIWSSRLPAGGQATPMTFWGKDNRQYIVLVVGGHGSFGTKMGDYIIAYALPK 792

Query: 741 HK 742
           +K
Sbjct: 793 NK 794


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: 1977
Number of extensions: 125
Number of successful extensions: 9
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: 803
Length adjustment: 41
Effective length of query: 702
Effective length of database: 762
Effective search space:   534924
Effective search space used:   534924
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