GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas fluorescens FW300-N1B4

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

Query= BRENDA::Q9RW56
         (523 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417
          Length = 490

 Score =  228 bits (582), Expect = 3e-64
 Identities = 157/491 (31%), Positives = 238/491 (48%), Gaps = 33/491 (6%)

Query: 42  LIIDG--QEVDTEGKIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDA 99
           L IDG   +  ++   ++INP +  EV+ T  +AT  D E A+  A K  + W       
Sbjct: 9   LYIDGGYSDASSDATFEAINPAN-GEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAME 67

Query: 100 RARILLKAAAILKRRRLEACALMSIEVGKNYAEAD-VEVAEAIDFLEYYARSAMKYAGFG 158
           R+RIL +A  IL+ R  E  AL +++ GK Y+E   V++    D LEYYA          
Sbjct: 68  RSRILRRAVDILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPA----- 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 GG+   +    +G ++ PT+  D      + +EEIFGPV+++L  +  ++ +  AN T
Sbjct: 352 LCGGDRLTDGEFAKGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDT 411

Query: 449 EYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPD 508
           E+GL  GV +    R  +   + E G  + N    G      P GGY  SG   +  G  
Sbjct: 412 EFGLAAGVVTKDLNRAHRVIHQLEAGICWIN--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: 30
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 (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