GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Psychromonas ossibalaenae JAMM 0738

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_019613839.1 G327_RS0105925 L-threonine dehydrogenase

Query= BRENDA::P0DJA2
         (383 letters)



>NCBI__GCF_000381745.1:WP_019613839.1
          Length = 382

 Score =  490 bits (1261), Expect = e-143
 Identities = 238/380 (62%), Positives = 294/380 (77%)

Query: 3   SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62
           SS F++P VN MG G L  A+  +   GF   LIV+D  ++  G+VKQV+DLL A  + +
Sbjct: 2   SSAFFMPTVNLMGAGCLSDAVASIKSQGFTQGLIVTDKILSSIGMVKQVSDLLAASEVKT 61

Query: 63  AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEG 122
            V+DG  PNPT+  V  GL+ILKDN  DF+ISLGGGSPHDCAK IALVA NGGE+ DYEG
Sbjct: 62  VVFDGTQPNPTIGNVEAGLQILKDNQCDFIISLGGGSPHDCAKGIALVAANGGEIADYEG 121

Query: 123 IDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVG 182
           +D+S KP LPL+SINTTAGTASEMTRFCIITDE RH+KMAIVD++VTP++SVNDP LM+ 
Sbjct: 122 VDQSPKPQLPLISINTTAGTASEMTRFCIITDEARHIKMAIVDKNVTPLMSVNDPELMLA 181

Query: 183 MPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREA 242
            P  LTAATGMDALTHA EAY S AATPITDA A+KA  +I ++L+TA  +G+ + ARE 
Sbjct: 182 KPASLTAATGMDALTHAVEAYVSIAATPITDAVAIKAIEIIQQSLRTAVKDGQSIEAREQ 241

Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKD 302
           MAYAQF+AGMAFNNASLGYVHAMAHQLGG+Y+LPHGVCNAVLLPHV  +NA V   RLKD
Sbjct: 242 MAYAQFMAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNAVLLPHVQRFNAKVAPARLKD 301

Query: 303 VGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDAC 362
           V  AMG+++ N+ ++EGA+A + A+  L+  +GIPA LT+LG K ED  +L+++ALKDAC
Sbjct: 302 VAKAMGVNVENMSNEEGADAALAAIAQLSTDVGIPAGLTDLGVKAEDFDVLSENALKDAC 361

Query: 363 ALTNPRQGDQKEVEELFLSA 382
             TNP Q    E+ E++  A
Sbjct: 362 GFTNPIQATHAEITEIYRQA 381


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: 507
Number of extensions: 14
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 24 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