Alignments for a candidate for sdh in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdh in Escherichia coli BW25113

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate 14270 b0124 glucose dehydrogenase (NCBI)

Query= BRENDA::Q70JN9
         (743 letters)



>FitnessBrowser__Keio:14270
          Length = 796

 Score =  471 bits (1213), Expect = e-137
 Identities = 255/666 (38%), Positives = 370/666 (55%), Gaps = 21/666 (3%)

Query: 85  GSMDPNDV-----PQMAPQQSASP-ASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAF 138
           G  DP ++         P ++ SP A  DW AYG +    R+SPL +I   N   LK A+
Sbjct: 139 GFNDPQEINGTLSADATPAEAISPVADQDWPAYGRNQEGQRFSPLKQINADNVHNLKEAW 198

Query: 139 VYHTGSYPRPGQTNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEA 198
           V+ TG   +P    +   E TPIKVGD LY+C+A   +  +D A+GKE W ++   K   
Sbjct: 199 VFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAASGKEKWHYDPELKTNE 258

Query: 199 IPYTAACKGVTYFTS---SQVPEGQP-CHNRILEGTLDMRLIAVDAATGNLCEGFGNGGQ 254
                 C+GV+Y  +   +  PE    C  RI+    D RLIA++A  G LCE F N G 
Sbjct: 259 SFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGRLIAINAENGKLCETFANKGV 318

Query: 255 VNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGKFLWA 314
           +NL   + ++ PG    T+PP + +  +V+   V D       SGVIRG+D  +G+ LWA
Sbjct: 319 LNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFSTRETSGVIRGFDVNTGELLWA 378

Query: 315 WDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSPEENK 374
           +D    + ++ P+  + ++  +PNSWA    D  L LVY+P G +  D +   R+PE+ +
Sbjct: 379 FDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQER 438

Query: 375 VSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTKRGQT 434
            +S+++AL+  TG   W +QTVH D+WD D+ +Q TL D+   +GQ VP +  P K G  
Sbjct: 439 YASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADIT-VNGQKVPVIYAPAKTGNI 497

Query: 435 FVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGMSPID 494
           FVLDRR+G+ ++P  E+P P  G   GD  +PTQP+S  +      DL   DMWG +  D
Sbjct: 498 FVLDRRNGELVVPAPEKPVPQ-GAAKGDYVTPTQPFSE-LSFRPTKDLSGADMWGATMFD 555

Query: 495 QLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNITPMY 554
           QL CR+ F +  Y G FTPPS ++  + +PG  G  +WG +S DP   + IAN    P  
Sbjct: 556 QLVCRVMFHQMRYEGIFTPPS-EQGTLVFPGNLGMFEWGGISVDPNREVAIANPMALPFV 614

Query: 555 DQLVTRKKADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMCNRPP 614
            +L+ R   +     P++ P    G G   G     G PYG+ + PF   + G+ C +P 
Sbjct: 615 SKLIPRGPGN-----PMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFLSPF-GLPCKQPA 668

Query: 615 YGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVVFIAA 674
           +G I+A+D+K  + V+W+  +GT + + P+ +P  +P+ +G P  GG + TAG V+FIAA
Sbjct: 669 WGYISALDLKTNE-VVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPISTAGNVLFIAA 727

Query: 675 ATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEANGHQYVAIMAGGHHFMMTPVSDQLV 734
             DN +RA +   G+ +W   LP GGQA PMTYE NG QYV I AGGH    T + D +V
Sbjct: 728 TADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYEVNGKQYVVISAGGHGSFGTKMGDYIV 787

Query: 735 VYALPD 740
            YALPD
Sbjct: 788 AYALPD 793


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: 2155
Number of extensions: 158
Number of successful extensions: 11
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 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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