GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Geobacter daltonii FRC-32

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012647687.1 GEOB_RS12935 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000022265.1:WP_012647687.1
          Length = 1004

 Score =  238 bits (607), Expect = 8e-67
 Identities = 151/454 (33%), Positives = 241/454 (53%), Gaps = 23/454 (5%)

Query: 55  PTVNPST-GEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIE 113
           P++NPS   E++  V +   ++V +A+ AAR +F+    WR +    R   L +   ++ 
Sbjct: 524 PSMNPSDPSEIVGWVCQAGTDEVAQAIGAARKSFET---WRDITPEIRAEFLLKACTVVR 580

Query: 114 RDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAG-----WADKYHGKTIPIDGDFF 168
           R    L+AL+ L+ GK +  +Y  D+   +  L YYA       + +  GK       +F
Sbjct: 581 RRIYELSALQVLEIGKQWDQAY-ADVTEAIDFLEYYAREMIRLGSPRSMGKVAGETNQYF 639

Query: 169 SYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEA 228
               +EP GV   I PWNFPL +    +  A+ TGN VV K +  T +    + ++ +E 
Sbjct: 640 ----YEPKGVAAVIAPWNFPLAISMGMVSAAIVTGNCVVFKPSGLTSIIGWQLVDIFREV 695

Query: 229 GFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG-RVIQVAA----GSSNLKRVT 283
           G P GV N VPG     G  +  H  V  +AFTGS E+G R+I+ AA    G   +K+V 
Sbjct: 696 GLPDGVFNFVPGRSGIMGDYLVDHPHVSLIAFTGSMEVGLRIIERAAKVQPGQEMVKKVI 755

Query: 284 LELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARA 343
            E+GGK+  II  DAD+D AV     + F  QGQ C A SR  V + IYD+FV+R  A A
Sbjct: 756 CEMGGKNAIIIDDDADLDEAVPHVFNSAFGFQGQKCSACSRVIVLDGIYDKFVQRLTALA 815

Query: 344 KSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVF 403
           ++  VG   D     G   +E   K+I+ YI  G+QEG +LL  G +  + G+F+  T+ 
Sbjct: 816 EAVPVGPVEDPANLIGAVAEENAQKRIMNYIEVGRQEG-RLLYQGHV-PEVGFFVPLTII 873

Query: 404 GDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQAL 463
           GD++    +A+EEIFGP++ +++ +   E +  AN++ Y L   +F++  +     ++  
Sbjct: 874 GDIRPEHRLAQEEIFGPLLAVMRARDFNEALVWANSTRYALTGGLFSRSPEHIAIATKRF 933

Query: 464 QAGTVWV--NCYDVFGAQSPFGGYKMSGSGRELG 495
           + G +++  NC      + PFGG+++SG+G + G
Sbjct: 934 RVGNLYLNRNCTGALVGRQPFGGFRLSGAGTKAG 967


Lambda     K      H
   0.319    0.136    0.409 

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: 1159
Number of extensions: 49
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: 517
Length of database: 1004
Length adjustment: 40
Effective length of query: 477
Effective length of database: 964
Effective search space:   459828
Effective search space used:   459828
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: 55 (25.8 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