GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Escherichia coli BW25113

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 15507 b1385 phenylacetaldehyde dehydrogenase (VIMSS)

Query= BRENDA::Q97UA1
         (478 letters)



>FitnessBrowser__Keio:15507
          Length = 499

 Score =  280 bits (716), Expect = 8e-80
 Identities = 168/443 (37%), Positives = 254/443 (57%), Gaps = 14/443 (3%)

Query: 41  DVKEAINKAVAKF--DEWSRTPAPKRGSILLKAGELMEQEAQEFALLMTLEEGKTLKDSM 98
           DV  A+  A   F    W+     +R  ILL+  +L+EQ ++E A L TLE+GK++  S 
Sbjct: 58  DVDNAVMSAWRAFVSRRWAGRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISR 117

Query: 99  -FEVTRSYNLLKFYGALAFKISGKTLPSADP-----NTRIFTVKEPLGVVALITPWNFPL 152
            FEV  + N +++   L  KI+GKTL  + P       + +T KEP+GVVA I PWNFPL
Sbjct: 118 AFEVGCTLNWMRYTAGLTTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPL 177

Query: 153 SIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVVGKGSEVGDTI 212
            I +WK+ PALAAG + VIKP+  TPL + ++ E+ S+AG+P+GV N+V G G+  G  +
Sbjct: 178 MIGMWKVMPALAAGCSIVIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAAL 237

Query: 213 VSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSADLTLAAELAV 272
            S  ++A +SFTGST  GK I +     + +TR+ LELGGKN   V K AD     E  +
Sbjct: 238 TSHPHVAKISFTGSTATGKGIARTAA--DHLTRVTLELGGKNPAIVLKDADPQWVIEGLM 295

Query: 273 RGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTEDV-DMGPVVDEGQFK 331
            G F   GQ C A+SR+ I   ++        + VK  +VGPG   V  + P+V      
Sbjct: 296 TGSFLNQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCD 355

Query: 332 KDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTIFEGVTSDMRLFKEEIFGPVLSVTEAK 391
           K   +++  +   A+LI G N   G+GY++ PT+     + +RL +EE+FGPV+++    
Sbjct: 356 KVCSFLDDAQAQQAELIRGSNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVA 415

Query: 392 DLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVGLELQAPFGGFKN 451
           D +EA++L N  +YG TA +   ++    E+  R++AG + VN  T+ ++   PFGG K 
Sbjct: 416 DGEEALQLANDTEYGLTASVWTQNLSQALEYSDRLQAGTVWVNSHTL-IDANLPFGGMKQ 474

Query: 452 SGATTWKEMGEDALEFYLKEKTV 474
           SG  T ++ G D L+ + + K+V
Sbjct: 475 SG--TGRDFGPDWLDGWCETKSV 495


Lambda     K      H
   0.316    0.135    0.389 

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: 623
Number of extensions: 34
Number of successful extensions: 6
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: 478
Length of database: 499
Length adjustment: 34
Effective length of query: 444
Effective length of database: 465
Effective search space:   206460
Effective search space used:   206460
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: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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