GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N2E3

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate AO353_17425 AO353_17425 lactaldehyde reductase

Query= BRENDA::P0DJA2
         (383 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17425
          Length = 382

 Score =  498 bits (1283), Expect = e-146
 Identities = 247/381 (64%), Positives = 303/381 (79%)

Query: 3   SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62
           +STF+IP VN MG G L++A+  +   GF+ ALIV+DA + K+GV   +A+ L  Q I+S
Sbjct: 2   TSTFFIPAVNIMGTGCLDEAMNAIRNYGFRKALIVTDAGLAKAGVAGLIAEKLAMQDIDS 61

Query: 63  AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEG 122
            ++DG  PNP++  V  GL++L+ +  D VISLGGGSPHDCAK IAL ATNGG++ DYEG
Sbjct: 62  VIFDGAKPNPSIANVESGLELLQRSQCDCVISLGGGSPHDCAKGIALCATNGGKIADYEG 121

Query: 123 IDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVG 182
           +D+S KP LPL++INTTAGTASEMTRFCIITDE RHVKMAIVDR+VTP++SVNDP LM  
Sbjct: 122 VDQSAKPQLPLIAINTTAGTASEMTRFCIITDESRHVKMAIVDRNVTPLLSVNDPALMAA 181

Query: 183 MPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREA 242
           MPKGLTAATGMDALTHA EAY STAA PITDACALKA  +I++NL+ A  +G DM ARE 
Sbjct: 182 MPKGLTAATGMDALTHAIEAYVSTAANPITDACALKAIELISRNLRLAVHDGSDMIAREN 241

Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKD 302
           MAYAQFLAGMAFNNASLG+VHAMAHQLGG+Y+LPHGVCNAVLLPHV ++NA+V A RL  
Sbjct: 242 MAYAQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNAAVCAERLAV 301

Query: 303 VGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDAC 362
           V  A+G D   +  +EGA+A I A+R LA  + IP  L +LGAK +D+P+LA +ALKDAC
Sbjct: 302 VAQALGADTLGVSPEEGAQAAIVAIRALARDVEIPGGLRDLGAKLQDIPILAANALKDAC 361

Query: 363 ALTNPRQGDQKEVEELFLSAF 383
            LTNPR  DQ+++EE+F SAF
Sbjct: 362 GLTNPRAADQRQIEEIFRSAF 382


Lambda     K      H
   0.316    0.132    0.373 

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: 499
Number of extensions: 18
Number of successful extensions: 1
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: 383
Length of database: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
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 (21.6 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