GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas fluorescens FW300-N2C3

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate AO356_04765 AO356_04765 lactaldehyde reductase

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_04765
          Length = 382

 Score =  219 bits (557), Expect = 1e-61
 Identities = 130/379 (34%), Positives = 207/379 (54%), Gaps = 6/379 (1%)

Query: 9   PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68
           P ++ +G G LD+ +  ++  G +  L++TD  L K G+  +V   L  +     ++   
Sbjct: 8   PAVNIMGLGCLDEAMTAIRNYGFRKALIVTDVGLAKAGVASKVAELLALQDIDSVIFDGA 67

Query: 69  VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128
            P P +   E  +    + + D V+ +GGGS  D AK  A+ A + G ++DY    G   
Sbjct: 68  KPNPSIANVELGLGLLMENRCDFVVSLGGGSPHDCAKGIALCATNGGQISDY---EGVDR 124

Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLSLET--TKDVVTHDYLLADVAIVDPQLTVSVPP 186
             K  LP I I TT+GT SE+T   +++ ET   K  +    +   +++ DP L V++P 
Sbjct: 125 SSKPQLPLIAINTTAGTASEMTRFCIITDETRHVKMAIVDRNVTPLMSVNDPALMVAMPK 184

Query: 187 RVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMAN 246
            +TAATG+DALTHA+EAYVS  A+P +D  A+ A+ LIS +LR AV +G+D  AR +MA 
Sbjct: 185 GLTAATGMDALTHAIEAYVSTAANPITDACALKAMTLISDNLRLAVRDGNDLVARENMAY 244

Query: 247 GSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFN 306
             +LAG+AF NA +  VHA+A+ LGG + + HG  NAVLLP+V  +    C  R++D+ +
Sbjct: 245 AQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNASVCAARLSDVAH 304

Query: 307 ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLA 366
           A+G ++   S  E +   +  +     DV IP  L   G+  + +  L  +A++    L 
Sbjct: 305 AMGADTRGFSPEEGAREAIATIRSLAHDVDIPAGLRDLGVRLNDVPLLAANALKDACGLT 364

Query: 367 RSPLPLLEADIRAIYEAAF 385
            +P    +  I  I+ +AF
Sbjct: 365 -NPRAADQRQIEEIFRSAF 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: 339
Number of extensions: 15
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 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