GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Paucidesulfovibrio gracilis DSM 16080

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>NCBI__GCF_900167125.1:WP_078716111.1
          Length = 382

 Score =  244 bits (622), Expect = 4e-69
 Identities = 142/354 (40%), Positives = 210/354 (59%), Gaps = 6/354 (1%)

Query: 9   PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68
           PP    G GA+ Q+  E  RLG++ ++V       + G ++ VT+ L + G    ++ +V
Sbjct: 9   PPRIIFGNGAVAQVGRETARLGSRALIVTGKSSSTRTGSLEAVTASLNEAGVHPVLFAEV 68

Query: 69  VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128
             +P ++T E   A AR+ + D+++G+GGGS LD AK   +L  H G + DY +    + 
Sbjct: 69  ESDPSIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRDYTS----QP 124

Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPP 186
            +  G+P I IPTT+GT SE+T  +V++   +  K  +    L+  VA++DPQLTV++P 
Sbjct: 125 ADGPGMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQLTVTMPQ 184

Query: 187 RVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMAN 246
            VTAATG+DALTHA+EAY+S  A+P SD  A+ AIRLI  +L KAV +  +  AR  M  
Sbjct: 185 HVTAATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAAREAMLR 244

Query: 247 GSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFN 306
           G   AGLAF NA VA VH+++ PLG  F IAHG++NA+LLP VM + R +   R   I  
Sbjct: 245 GQMHAGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFNRSAAADRYRHIAE 304

Query: 307 ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQ 360
           ALG N   LS  +A+   V  +E    + G+ + L  +G+ E  +  L KDA++
Sbjct: 305 ALGENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAME 358


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: 359
Number of extensions: 12
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: 382
Length adjustment: 30
Effective length of query: 365
Effective length of database: 352
Effective search space:   128480
Effective search space used:   128480
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 Apr 09 2024. 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