GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Algiphilus aromaticivorans DG1253

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_156966509.1 U743_RS02115 iron-containing alcohol dehydrogenase

Query= BRENDA::P0DJA2
         (383 letters)



>NCBI__GCF_000733765.1:WP_156966509.1
          Length = 410

 Score =  244 bits (622), Expect = 4e-69
 Identities = 135/347 (38%), Positives = 203/347 (58%), Gaps = 2/347 (0%)

Query: 15  GEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINSAVYDGVMPNPTV 74
           G G+  +    +  +G K  L+V+DA + + G+VK + + L++ G+    YDGV P+PT+
Sbjct: 41  GAGAAMQLCDAIAATGAKKVLLVTDAMLVELGLVKPIQEKLESLGVGVVTYDGVKPDPTI 100

Query: 75  TAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEGIDKSKKPALPLM 134
             +  G+ I K    + +I++GGGS  D AK IA  A N   V+   G+ +  +   PL 
Sbjct: 101 EQIETGVDIYKGQGCEAIIAVGGGSSIDAAKVIAARARNPHGVRWMAGLFRLLRSPAPLY 160

Query: 135 SINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPKGLTAATGMD 194
           ++ TTAGT SE+T   +++D  +  K AI+D  + P ++  D  LM G+P  +TAATGMD
Sbjct: 161 AVPTTAGTGSEVTIAAVVSDPEKVRKFAIMDFRLVPRMAALDGSLMTGVPAAITAATGMD 220

Query: 195 ALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAYAQFLAGMAF 254
           ALTHA EA+ S  AT  TDA A +A ++I ++L     +GKD+ +R  MA A + AG+AF
Sbjct: 221 ALTHAVEAFISRNATKETDAEAREAVALIMEHLPRVMADGKDLESRSQMAVASYKAGLAF 280

Query: 255 NNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKDVGVAMGLDIANL 314
             A +GYVHA AH  G  Y++PHG  NA+LLP+VL Y+      RL ++    G+   + 
Sbjct: 281 TKAGVGYVHAFAHNFGARYHIPHGKANAILLPYVLEYSKHASRSRLAELARIAGVGEQSA 340

Query: 315 GDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDA 361
            +   A+A I  +RDL    GIPA + EL A   D+P +A +A  +A
Sbjct: 341 SEAALADAFIAHIRDLNQRFGIPARVDELDA--ADIPTIATNARSEA 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: 342
Number of extensions: 11
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: 410
Length adjustment: 31
Effective length of query: 352
Effective length of database: 379
Effective search space:   133408
Effective search space used:   133408
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