GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Desulfovibrio vulgaris Hildenborough

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 208042 DVU2545 alcohol dehydrogenase, iron-containing

Query= BRENDA::P0DJA2
         (383 letters)



>MicrobesOnline__882:208042
          Length = 386

 Score =  268 bits (686), Expect = 1e-76
 Identities = 149/368 (40%), Positives = 210/368 (57%)

Query: 15  GEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINSAVYDGVMPNPTV 74
           G G+   A + ++  G    L+V+D  + ++G    V   L A GI  AV+  + PNP  
Sbjct: 18  GNGAARLAGRYVHNLGGTRCLVVTDPGVMRNGHADTVIGSLTAYGIAHAVFQDISPNPRD 77

Query: 75  TAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEGIDKSKKPALPLM 134
             V  G++       D ++++GGGSP DCAK I +VA+NGG +  YEG+D   KP  PL+
Sbjct: 78  VEVQRGVEAYHREGCDAIVAVGGGSPIDCAKGIGIVASNGGSISLYEGVDAIPKPMPPLV 137

Query: 135 SINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPKGLTAATGMD 194
            + TTAG+A+++++F IITD  R VK+AIV +     VS+ DP     M + LTAATG+D
Sbjct: 138 CVPTTAGSAADVSQFAIITDTTRMVKIAIVSKAAVADVSLIDPSTTKSMSRDLTAATGID 197

Query: 195 ALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAYAQFLAGMAF 254
            LTHA EA++S A+ PITD  AL+A S++  +L     +G D  ARE MA A   AG+AF
Sbjct: 198 TLTHAIEAFASNASGPITDMFALEAISLVNTHLPQVLADGDDDTAREGMALACLNAGLAF 257

Query: 255 NNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKDVGVAMGLDIANL 314
           +NA LG VHAMAH LGG  +LPHG CNA+LLP V+  N      R   V  A+G+D+   
Sbjct: 258 SNAILGAVHAMAHSLGGLLDLPHGECNAILLPFVVRRNFDAAPVRYARVANALGIDVGGT 317

Query: 315 GDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDACALTNPRQGDQKE 374
                 +A    +  L  + G    L+  G  +E +  LA  A++D C  TNP   D  +
Sbjct: 318 PATAIRDALFDRLMTLRTAAGFTRGLSAFGVTREQIGRLARLAVEDPCLATNPEALDIAD 377

Query: 375 VEELFLSA 382
           +E L+  A
Sbjct: 378 IESLYAEA 385


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: 400
Number of extensions: 7
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: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
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