GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Phaeobacter inhibens BS107

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC

Query= BRENDA::Q93YB2
         (503 letters)



>lcl|FitnessBrowser__Phaeo:GFF3171 PGA1_c32220
           5-carboxymethyl-2-hydroxymuconic semialdehyde
           dehydrogenase HpcC
          Length = 503

 Score =  343 bits (880), Expect = 8e-99
 Identities = 188/458 (41%), Positives = 266/458 (58%), Gaps = 11/458 (2%)

Query: 28  INPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASGAVRARYLRAIAAKVTE 87
           I+P  +++I D+   T  D+D A  AA+ A      A+W       R + L  IA  +  
Sbjct: 42  ISPVDKSVICDVAHGTAADIDAAAQAARQAF-----AEWRDLPAVQRKKILIRIAEGIEA 96

Query: 88  KKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDARQKAPVSLPMDTFKSHV 147
           +  E+A  E  D G+     +      A  F Y+AD  + + AR    +  P  T  +  
Sbjct: 97  RAEEIALCECWDTGQAYKFMSKAALRGAENFRYFAD--QVVQARDGQHLQSP--TLMNVT 152

Query: 148 LREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELASLTCLELGEICKEVGLP 207
            R PIG VG+ITPWN P +++TWK+APALAAGC  + KP+E + LT   L EI +E GLP
Sbjct: 153 TRVPIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLP 212

Query: 208 PGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAAQLVKPVSLELGGKSPL 267
           PGVLN + G G EAG  L  HP +  +AF G S TGS I    A  +K   LELGGK+P+
Sbjct: 213 PGVLNTVNGFGDEAGKALCEHPAIRAIAFVGESRTGSLITKQGADTLKRNHLELGGKNPV 272

Query: 268 VVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFLNRIVKWIKNIKISDPL 327
           +VFED DL++A +  IF  +  NG+ C+++SRL++ +SI  +F  R+++ I NIK+  PL
Sbjct: 273 IVFEDADLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHPL 332

Query: 328 EEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNM 387
           +    +GP+VSE  + K+  +   A  EGATI  GG      ++G+FI PT+ TD   +M
Sbjct: 333 DPTTEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGEPVG--EEGYFIRPTLFTDARNDM 390

Query: 388 QIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLERCERVTKAFKAGIVWV 447
           +I +EE+FGPVL    F+TE EA+ LANDT YGL   + +NDL R  R T   +AG++WV
Sbjct: 391 RIAQEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAGMIWV 450

Query: 448 NCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQV 485
           N         P+GGVK SG GR+ G+W  + Y+  K +
Sbjct: 451 NSENVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQKHI 488


Lambda     K      H
   0.318    0.135    0.416 

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: 653
Number of extensions: 26
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: 503
Length of database: 503
Length adjustment: 34
Effective length of query: 469
Effective length of database: 469
Effective search space:   219961
Effective search space used:   219961
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 (21.7 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