GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Pseudomonas simiae WCS417

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF5142 PS417_26340 betaine-aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__WCS417:GFF5142
          Length = 490

 Score =  393 bits (1010), Expect = e-114
 Identities = 208/479 (43%), Positives = 287/479 (59%), Gaps = 7/479 (1%)

Query: 38  QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97
           +++I+  + DA S  TF  +NP+ GEV+ QV    KEDV++AV +A    ++   W  M 
Sbjct: 8   KLYIDGGYTDAGSDATFEAINPANGEVLAQVQRATKEDVERAVVSAEKGQKI---WAAMT 64

Query: 98  ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157
           A  R R+L R  D++      LAALETLD GK +  +  VD+      L YYAG      
Sbjct: 65  AMERSRILRRAVDILRERNDELAALETLDTGKAFSETKYVDIVTGADVLEYYAGLVPAIE 124

Query: 158 GKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLT 217
           G+ IP+    F YTR EP+GV   I  WN+P+ +  WK  PALA GN ++ K +E T LT
Sbjct: 125 GEQIPLRDTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLT 184

Query: 218 ALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSS 277
            L +A +  EAG P GV N++ G G   G  +  H  ++KV+FTG T+ G+ +  +A SS
Sbjct: 185 TLKLAEIYTEAGVPAGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSS 244

Query: 278 NLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVE 337
           +LK VT+ELGGKSP I+  DAD+D A + A  A F++ GQ C  G+R FV + +   F  
Sbjct: 245 SLKEVTMELGGKSPLIVFEDADLDRAADIAMMANFYSSGQVCTNGTRVFVPKHLQAAFEA 304

Query: 338 RSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD---- 393
           + V R     VGNP D  T  GP V     + +LGYI  GK+EGA++LCGG    D    
Sbjct: 305 KIVERVARIRVGNPQDDNTNFGPLVSFAHMESVLGYIAKGKEEGARVLCGGDRLTDGEFA 364

Query: 394 RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDL 453
           +G F+ PTVF D  D MTI +EEIFGPVM IL ++T EEV+ RAN++ +GLAA + TKDL
Sbjct: 365 KGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGLVTKDL 424

Query: 454 DKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
           ++A+ +   L+AG  W+N +    A+ P GGYK SG GRE G   L  +T +K+V V++
Sbjct: 425 NRAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483


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: 569
Number of extensions: 32
Number of successful extensions: 3
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: 490
Length adjustment: 34
Effective length of query: 483
Effective length of database: 456
Effective search space:   220248
Effective search space used:   220248
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: 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