GapMind for catabolism of small carbon sources

 

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

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_033100857.1 JG50_RS0109305 aldehyde dehydrogenase

Query= SwissProt::O34660
         (495 letters)



>NCBI__GCF_000763315.1:WP_033100857.1
          Length = 499

 Score =  419 bits (1078), Expect = e-122
 Identities = 212/474 (44%), Positives = 305/474 (64%), Gaps = 9/474 (1%)

Query: 22  LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81
           L I G+ VPS SG  F   NPA GE +  + +A  ADVD+AV++AR A    +W     +
Sbjct: 15  LLIGGEHVPSESGEYFTVYNPANGEAIAQVAKATRADVDRAVQSARDALSNSKWARWPAS 74

Query: 82  SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141
            R +++ K+A +M +   +L +LE L++GK ++    G +  AIE    YAG  T I G 
Sbjct: 75  RRGQILNKIASIMRQRFNDLVELEVLNSGKALS-AAKGQVMQAIEDFELYAGAVTTIQGH 133

Query: 142 TIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSAL 201
           T PV   +F+Y+  EPVGV  QI+PWN+PL+M  WK+  ALA GCT++LKPA  TPL+AL
Sbjct: 134 TKPVPNGFFHYSVKEPVGVCAQIVPWNYPLMMTAWKVAPALAAGCTLILKPASLTPLTAL 193

Query: 202 YLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSIK 261
            LA++  +AG PAGVIN+I G G D G  L  H  VDK+AFTG T  GK IM+ A+ ++K
Sbjct: 194 VLADICHEAGVPAGVINVITGSGADVGSYLVEHPGVDKVAFTGETTTGKDIMAKASDTLK 253

Query: 262 RVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEMA 321
           RVTLELGGKSPNI+  DA+L+ A+ G++ G+ +N GQ C A SR+F+H+D YD  +++  
Sbjct: 254 RVTLELGGKSPNIVFADADLEAAVNGSVYGIYYNTGQSCEARSRLFVHEDIYDAFIEKFV 313

Query: 322 SYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCP----FEAGY 377
              + L+ G   +++T +G ++S+ Q + + SY++  + EGA+ + GG  P    F  GY
Sbjct: 314 EQTKKLKLGDPFNEETHVGAVISQGQWDTIDSYVKLAEKEGARVLYGGKRPEGEEFAKGY 373

Query: 378 FVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQA 437
           +  PTV  +  ++M +A+EEIFGPV+  I ++   EV++ AN + YGLAA +WT +  +A
Sbjct: 374 WYMPTVIVDATNDMRVAQEEIFGPVVVVIKFKDEKEVVKLANETMYGLAAAVWTRDFGRA 433

Query: 438 HYIADRLQAGTVWVNCYNVFDA--ASPFGGYKQSGLGREMGSYALDNYTEVKSV 489
           H +A +L+AG V +N  N F A    PFGGYKQSG GRE+   +L+ Y E KSV
Sbjct: 434 HRVASQLKAGVVMIN--NPFSAFPGLPFGGYKQSGFGRELAIESLELYMETKSV 485


Lambda     K      H
   0.316    0.133    0.391 

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: 640
Number of extensions: 25
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: 495
Length of database: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
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: 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