GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:16552
          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:

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