GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Galbibacter marinus ck-I2-15

Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_008990590.1 I215_RS03585 aldehyde dehydrogenase

Query= curated2:P39616
         (456 letters)



>NCBI__GCF_000300875.1:WP_008990590.1
          Length = 455

 Score =  402 bits (1032), Expect = e-116
 Identities = 202/449 (44%), Positives = 287/449 (63%), Gaps = 2/449 (0%)

Query: 4   IPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTE 63
           I ++I     +F  G T  + +R  +L+ LK  +   E  ++ A+Y+DL K   EA +TE
Sbjct: 5   ISNLIKGQDVFFKGGGTLAISTRKQLLKALKDTIVNREEVILKAIYKDLKKPTFEALATE 64

Query: 64  IGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALS 123
           I IV+ EI+  +K + KW++PKRV + + +  S S I  EPYG +L+I+PWNYP  LA+ 
Sbjct: 65  INIVIGEINNTLKHIDKWTRPKRVASSILNFPSTSRIHQEPYGRILIISPWNYPFALAII 124

Query: 124 PLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDY 183
           PLIGA+AAGNT+VLKPSE +P  +AI+ ++I  +F  D+V++  G   +S  LL+  +DY
Sbjct: 125 PLIGALAAGNTIVLKPSEMSPNTTAIIQEIIQDIFDQDHVSVVVGDKKISQRLLEFRWDY 184

Query: 184 IFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQT 243
           IFFTGS  VGK V   AA+ L PVTLELGGKSPCIV   A  +  AKRIV+GKF NAGQ+
Sbjct: 185 IFFTGSTEVGKYVYSKAAEHLTPVTLELGGKSPCIVDSTASFKHLAKRIVWGKFLNAGQS 244

Query: 244 CIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIP 303
           CIAPDYL VH  +K +L  E+K  I + Y         Y  I++  H QRLL  + D   
Sbjct: 245 CIAPDYLLVHYKVKDRLINELKEEINKAYPDLCNSTSDYANIINTDHSQRLLKLIQDQEV 304

Query: 304 LTGGQSDPNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKPLA 363
           L GG  D       PT++ +   DSP+MQ+EIFGPILP+  +++  ++ + +    KPLA
Sbjct: 305 LFGGTVD--GQLFVPTLVNEPHIDSPLMQQEIFGPILPIIGFQSFEQIQQIIDRFEKPLA 362

Query: 364 LYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNTFT 423
           LY+F++       V+ + SFGGG +NDT++H A   LPFGGVG SGIG+YHG  +F TF+
Sbjct: 363 LYVFSSENSFTDKVIQSFSFGGGVINDTMVHYADKNLPFGGVGHSGIGAYHGDCTFKTFS 422

Query: 424 HKKSVVKQTNRFDFAFRYPSSKNGLRMIR 452
           H+K++V++++  D   RYP  K  L+ ++
Sbjct: 423 HQKAIVQRSSWLDIPLRYPPYKGKLKWLK 451


Lambda     K      H
   0.320    0.137    0.401 

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: 589
Number of extensions: 23
Number of successful extensions: 2
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: 456
Length of database: 455
Length adjustment: 33
Effective length of query: 423
Effective length of database: 422
Effective search space:   178506
Effective search space used:   178506
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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