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

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417 Betaine aldehyde
           dehydrogenase (EC 1.2.1.8)
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources