GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Shewanella oneidensis MR-1

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 203967 SOA0164 iron-containing alcohol dehydrogenase (NCBI ptt file)

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__MR1:203967
          Length = 383

 Score =  220 bits (561), Expect = 5e-62
 Identities = 135/378 (35%), Positives = 212/378 (56%), Gaps = 5/378 (1%)

Query: 9   PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68
           PP+S +G  A+  L  E++       L++TD  LV I LVD++T  L     +  ++  V
Sbjct: 8   PPMSLMGQHAIKLLGTELQARNFNKALIVTDKALVDIKLVDKLTDELSAHDIAFAIFDGV 67

Query: 69  VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128
            P P  +   + +A     K D VI  GGGS+ D AK  A++A + G + DY    G   
Sbjct: 68  KPNPTEKNIVQGLALLEAQKCDFVISFGGGSSHDCAKGIALVAANGGHIRDYSK--GVHL 125

Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLSLET--TKDVVTHDYLLADVAIVDPQLTVSVPP 186
             K  LP + + TT+GT +E+T  ++++ E   TK  +    L   +A+ D +L V++P 
Sbjct: 126 SAKPQLPLVTVNTTAGTAAEMTIFAIVTNEEDETKYPIVDKNLTPIIAVNDSELMVAMPK 185

Query: 187 RVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMAN 246
            +TAATG+DALTHAVEAYVS  A+P +D  A+ AI LI+++L+ AV NG D++AR  M  
Sbjct: 186 FLTAATGMDALTHAVEAYVSTAATPITDASAIKAIELIAQNLKAAVDNGEDREAREAMQY 245

Query: 247 GSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFN 306
           G YLAG+AF NA +  VH++A+ LGG + + HG  NA+LLP V  +      +R A++  
Sbjct: 246 GEYLAGMAFSNASLGYVHSMAHQLGGVYDLVHGLCNAILLPVVSRFNSAEKVERFAEVAK 305

Query: 307 ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLA 366
           A+G ++  ++ ++A+   +  +E+  A VG  + L   G+ E  LE +  +A+     L 
Sbjct: 306 AMGVDTVGMTLIDAAESGILAIEKLSASVGTDQKLSDLGVKEDKLEFMAINALNDACSLT 365

Query: 367 RSPLPLLEADIRAIYEAA 384
            +P      DI  I++ A
Sbjct: 366 -NPRKATTEDIINIFKKA 382


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: 310
Number of extensions: 14
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: 383
Length adjustment: 30
Effective length of query: 365
Effective length of database: 353
Effective search space:   128845
Effective search space used:   128845
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