GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2E2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf6N2E2_1309 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)

Query= BRENDA::P05091
         (517 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1309
           5-carboxymethyl-2-hydroxymuconate semialdehyde
           dehydrogenase (EC 1.2.1.60)
          Length = 486

 Score =  381 bits (978), Expect = e-110
 Identities = 200/470 (42%), Positives = 284/470 (60%), Gaps = 13/470 (2%)

Query: 50  SRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLA 109
           S+  F   NP+TGE I +VA G  E+V +AV AA+ AF     W    A  R RL+ +L 
Sbjct: 13  SKDVFVNYNPATGEAIGEVASGGAEEVAQAVAAAKEAFP---KWANTPAKERARLMRKLG 69

Query: 110 DLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFS 169
           +LIE++   LA LETLD G P   +  V +        ++A    +  G T P+D    +
Sbjct: 70  ELIEQNVPQLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHTYPVDDQMLN 129

Query: 170 YTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAG 229
           YT ++PVGVC  + PWN P +   WK  P LA GN  V+K++E +PLTA  +  L  EAG
Sbjct: 130 YTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEAG 189

Query: 230 FPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGK 289
            P GV+N++ G+G TAG A+  H DV  ++FTG T  G+ I   AG   LK+ ++ELGGK
Sbjct: 190 IPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG---LKKYSMELGGK 246

Query: 290 SPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVG 349
           SP +I  DAD++ A++ A F +F   G+ C AGSR F+QE +Y +FV    ARAK  +VG
Sbjct: 247 SPVLIFEDADLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIVG 306

Query: 350 NPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG-------GIAADRGYFIQPTV 402
           +P D KT+ G  + +  + K+ GYI  G +EGA LL GG            RG FIQPTV
Sbjct: 307 DPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAHLSRGQFIQPTV 366

Query: 403 FGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQA 462
           F DV + M IA+EEIFGPV+ ++ FK   E +  AN++ YGLA+ ++T+D+ KA+ L+  
Sbjct: 367 FADVNNKMRIAQEEIFGPVVCLIPFKDEAEALHLANDTEYGLASYIWTQDIGKAHRLAHG 426

Query: 463 LQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
           ++AG V++N  +V   + PFGG K SG+GRE G+Y  + + E+K V + +
Sbjct: 427 IEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 476


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: 629
Number of extensions: 29
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: 517
Length of database: 486
Length adjustment: 34
Effective length of query: 483
Effective length of database: 452
Effective search space:   218316
Effective search space used:   218316
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.

Links

Downloads

Related tools

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