GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas fluorescens FW300-N2E3

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate AO353_07245 AO353_07245 alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07245
          Length = 382

 Score =  318 bits (814), Expect = 2e-91
 Identities = 176/373 (47%), Positives = 246/373 (65%), Gaps = 7/373 (1%)

Query: 15  GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPL 74
           G GA++QL  E+ RL   + L++TD  LVK G V+   + L   G +  ++  V+P+P +
Sbjct: 15  GAGAIEQLAAELTRLDVDNPLIVTDAALVKSGTVELALAQLG--GRTYEIFDRVLPDPEI 72

Query: 75  ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134
              E  +   R+G  D +IG+GGGSA+D+AK  A  A + G++ D   L G   + +KG 
Sbjct: 73  AIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALED---LFGIDQVPRKGP 129

Query: 135 PKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAAT 192
           P I IPTT+GTGSEVTN+++LS  +   K  +  DYLL DVA+V PQ+T++ P  VTAA+
Sbjct: 130 PLIAIPTTAGTGSEVTNVAILSDRVAQLKKGIISDYLLPDVALVSPQMTLTCPRSVTAAS 189

Query: 193 GIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAG 252
           G+DAL HAVE+Y+S+NASP +D LA+ AI+LI ++L KA  N S+ QAR DMA  S +AG
Sbjct: 190 GVDALVHAVESYLSLNASPITDALAIGAIKLIIKALPKAYTNPSNLQAREDMATASLMAG 249

Query: 253 LAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNS 312
           +AF NAGV  VHALAYPLGG+F++ HG SNA+LLPYVM + + +C +RM DI  ALG  +
Sbjct: 250 MAFGNAGVGAVHALAYPLGGRFNVTHGVSNALLLPYVMAWNKMACIERMQDIAEALGVKT 309

Query: 313 SFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPL 372
           + LS  EA+ + VE + R  A V IP+ L   GIPE A+ ++  +A   +RL+  +P  L
Sbjct: 310 AQLSAEEAADKAVEAMARLCAAVEIPQGLHSLGIPEDAIPAMAVEAAGIERLMRNNPRKL 369

Query: 373 LEADIRAIYEAAF 385
             ADI  IY AA+
Sbjct: 370 STADIEKIYRAAY 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: 421
Number of extensions: 23
Number of successful extensions: 4
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