GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaD in Escherichia coli BW25113

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 16552 b2453 ethanolamine utilization; homolog of Salmonella enzyme, similar to iron-containing alcohol dehydrogenase (VIMSS)

Query= BRENDA::A4IP64
         (395 letters)



>lcl|FitnessBrowser__Keio:16552 b2453 ethanolamine utilization;
           homolog of Salmonella enzyme, similar to iron-containing
           alcohol dehydrogenase (VIMSS)
          Length = 395

 Score =  219 bits (557), Expect = 1e-61
 Identities = 147/379 (38%), Positives = 213/379 (56%), Gaps = 14/379 (3%)

Query: 9   PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68
           PP++  G G++     + +  G KH+ V+ D  L + G+   +T  L  +G ++ ++   
Sbjct: 27  PPVTLCGPGSVSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLTVKGIAMTLWPCP 86

Query: 69  VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVH-DGSVADYLNLTGTR 127
           V EP +     AVA  R+   D VI  GGGS LD AK   +L  + D ++A+   ++ T 
Sbjct: 87  VGEPCITDVCAAVAQLRESGCDGVIAFGGGSVLDAAKAVTLLVTNPDSTLAE---MSETS 143

Query: 128 TLEKKGLPKILIPTTSGTGSEVTNISVL--SLETTKDVVTHDYLLADVAIVDPQLTVSVP 185
            L+ + LP I IPTT+GTGSE TN++V+  ++   K V+ H  L+ DVAI+D  LT  VP
Sbjct: 144 VLQPR-LPLIAIPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVP 202

Query: 186 PRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMA 245
             VTA TGIDALTHA+EAY ++NA+P +D LA+ AI +I +SL KAV  G D  AR  M 
Sbjct: 203 SHVTAMTGIDALTHAIEAYSALNATPFTDSLAIGAIAMIGKSLPKAVGYGHDLAARESML 262

Query: 246 NGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIF 305
             S +AG+AF +AG+   HA+A+  G   HI HG +NA+LLP VM + R  C +R + I 
Sbjct: 263 LASCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGLANAMLLPTVMEFNRMVCRERFSQIG 322

Query: 306 NALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLL 365
            AL       S+   +   V EL   +A+VGI K LG  G   +   +  + A++   L 
Sbjct: 323 RALRTKK---SDDRDAINAVSEL---IAEVGIGKRLGDVGATSAHYGAWAQAALEDICLR 376

Query: 366 ARSPLPLLEADIRAIYEAA 384
           +      LE  I  +Y AA
Sbjct: 377 SNPRTASLE-QIVGLYAAA 394


Lambda     K      H
   0.318    0.135    0.381 

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: 332
Number of extensions: 13
Number of successful extensions: 3
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
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 (21.7 bits)
S2: 50 (23.9 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 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