GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N1B4

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Pf1N1B4_3270 Alcohol dehydrogenase (EC 1.1.1.1)

Query= BRENDA::P0DJA2
         (383 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3270 Alcohol dehydrogenase
           (EC 1.1.1.1)
          Length = 382

 Score =  514 bits (1323), Expect = e-150
 Identities = 255/381 (66%), Positives = 305/381 (80%)

Query: 3   SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62
           SSTF+IP VN MG G L++A+  +   GF+ ALIV+D  + K+GV   +A+ L  Q I+S
Sbjct: 2   SSTFFIPAVNIMGTGCLDEAMDAIRKYGFRKALIVTDTGLAKAGVATMIAEKLALQDIDS 61

Query: 63  AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEG 122
            ++DG  PNP++  V  GL +LK++  DFV+SLGGGSPHDCAK IAL ATNGG ++DYEG
Sbjct: 62  VIFDGAKPNPSIANVELGLGLLKESRCDFVVSLGGGSPHDCAKGIALCATNGGTIRDYEG 121

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

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

Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKD 302
           MAYAQFLAGMAFNNASLGYVHAMAHQLGG+Y+LPHGVCNAVLLPHV ++NA V A RL D
Sbjct: 242 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNALVCADRLTD 301

Query: 303 VGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDAC 362
           V  AMG DI     +EGA+A I A+RDLA  + IPA L ELGA+  D+P+LA +ALKDAC
Sbjct: 302 VARAMGADIRGFSPEEGAQAAIAAIRDLARDVEIPAGLRELGARLNDIPVLASNALKDAC 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: 514
Number of extensions: 20
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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