GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Thermoactinomyces daqus H-18

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_033099889.1 JG50_RS0104290 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_000763315.1:WP_033099889.1
          Length = 474

 Score =  493 bits (1269), Expect = e-144
 Identities = 249/471 (52%), Positives = 332/471 (70%), Gaps = 5/471 (1%)

Query: 52  FVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSSL 111
           ++ GRW+       V +PA+   +G+V + G  EA+ AV AAY AF  W +   +ER  L
Sbjct: 7   YINGRWIDAINKIDVINPATKKIIGSVPNGGATEAKMAVEAAYPAFQKWSKQPAEERGKL 66

Query: 112 LRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTSA 171
           L KW+DL+ ++KDELA+I+T E GKPL+EA+GEI Y+  F+ W++EE +R+YG+ I  S+
Sbjct: 67  LMKWFDLIEKHKDELAEIMTLEQGKPLQEARGEITYANSFISWYAEEGKRIYGETIPASS 126

Query: 172 KDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQL 231
            DKR  V KQPVGV + ITPWNFP+AMITRKV  ALAAGCTVV+KP+E+TP++AL LA+L
Sbjct: 127 PDKRIFVQKQPVGVIAAITPWNFPAAMITRKVAPALAAGCTVVLKPSEETPFTALKLAEL 186

Query: 232 ANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRV 291
           A+QAGIP GV NV+      A+ +      D  V K++FTGST  GKIL+  AA++VK++
Sbjct: 187 ADQAGIPNGVLNVV---TGDAESIANAWQKDSRVRKLTFTGSTPVGKILMRGAADTVKKI 243

Query: 292 SMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAEA 351
           S+ELGG AP IV   A++D+AV GA+ASKFRNAGQTC+C+NR L    I + F  K AE 
Sbjct: 244 SLELGGHAPLIVTAQADIDKAVDGAIASKFRNAGQTCICTNRILADESIAEEFTVKLAEK 303

Query: 352 MKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKR-HQSGGNFFEP 410
             K L+VGNG EE T  GPLINE+AV+KV KH+ DA  KG  V+TGG R     G F EP
Sbjct: 304 AAK-LKVGNGLEESTDIGPLINEEAVKKVIKHIEDAKQKGGRVLTGGNRLTNQKGYFIEP 362

Query: 411 TLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRVA 470
           T+++N   DMLC+ EETFGP+ PV  F   +EA+  AN +  GLA Y Y+++  +   ++
Sbjct: 363 TVIANAKDDMLCMVEETFGPLIPVATFKTIDEAIERANNSSYGLAAYVYTENLREAVYIS 422

Query: 471 EQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521
           E LE G+VGVN+G  S+ + PFGG K+SGLGREGS+YGI+E+LE+KY+  G
Sbjct: 423 EALEYGIVGVNDGAPSAAQAPFGGFKESGLGREGSRYGIEEFLEIKYISLG 473


Lambda     K      H
   0.318    0.135    0.400 

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: 632
Number of extensions: 24
Number of successful extensions: 4
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: 523
Length of database: 474
Length adjustment: 34
Effective length of query: 489
Effective length of database: 440
Effective search space:   215160
Effective search space used:   215160
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 (21.7 bits)
S2: 52 (24.6 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