GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF 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)



>lcl|FitnessBrowser__Keio:15507 b1385 phenylacetaldehyde
           dehydrogenase (VIMSS)
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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