GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Pseudomonas fluorescens FW300-N2E3

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AO353_07805 AO353_07805 betaine-aldehyde dehydrogenase

Query= BRENDA::Q9RW56
         (523 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07805 AO353_07805
           betaine-aldehyde dehydrogenase
          Length = 490

 Score =  233 bits (595), Expect = 9e-66
 Identities = 161/491 (32%), Positives = 237/491 (48%), Gaps = 33/491 (6%)

Query: 42  LIIDGQEVDTEGK--IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDA 99
           L IDG   D  G    ++INP +  EV+ T  +AT  D E A+  A K  + W       
Sbjct: 9   LYIDGGYSDASGDATFEAINPAN-GEVLATVQRATFADVERAVVSAEKGQKIWAAMTAME 67

Query: 100 RARILLKAAAILKRRRLEACALMSIEVGKNYAEAD-VEVAEAIDFLEYYARSAMKYAGFG 158
           R+RIL +A  IL+ R  E  AL +++ GK Y+E   V++    D LEYYA          
Sbjct: 68  RSRILRRAVEILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPA----- 122

Query: 159 SSETTWFEGEENGLMSI--------PLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVK 210
                  EGE+  L +         PLG+   I  WN+P  I +  +A  + AGN ++ K
Sbjct: 123 ------IEGEQIPLRTTSFVYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFK 176

Query: 211 PAEDAGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLH 270
           P+E   L    + +I  EAGLPAGV   L G G+EVG +LT H +   I+FTG    G  
Sbjct: 177 PSEVTSLTTLKLAEIYTEAGLPAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKK 236

Query: 271 INEVAAKVQPGQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSR 330
           +   A+        +K V MELGGK  LI+ + AD++ A   A    F  +GQ C+  +R
Sbjct: 237 VMASASGSS-----LKDVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTNGTR 291

Query: 331 LIVVDSVYDEVVNGFVERAKALKMGTGE-ENANVTAVVNQMSFNKIKGYLELAPSEG-KV 388
           + V   +        VER   +++G  E EN N   +V+      + GY+     EG ++
Sbjct: 292 VFVPSHLKAAFEAKIVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARL 351

Query: 389 LLGGEATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANST 448
           L GGE   E    +G ++ PT+  D      + +EEIFGPV+++L  +  ++ +  AN T
Sbjct: 352 LCGGERLTEGEFAKGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDT 411

Query: 449 EYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPD 508
           E+GL  GV +    R  +   + E G  + N    G      P GGY  SG   +  G  
Sbjct: 412 EFGLAAGVVTRDLNRAHRVIHQLEAGICWIN--AWGESDAKMPVGGYKQSGV-GRENGIS 468

Query: 509 YLSNFMQLKTV 519
            L+NF ++K+V
Sbjct: 469 SLNNFTRIKSV 479


Lambda     K      H
   0.317    0.134    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: 636
Number of extensions: 31
Number of successful extensions: 5
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: 490
Length adjustment: 34
Effective length of query: 489
Effective length of database: 456
Effective search space:   222984
Effective search space used:   222984
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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