GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Pseudomonas fluorescens FW300-N2C3

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase

Query= BRENDA::Q1XGK8
         (486 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28685 AO356_28685
           betaine-aldehyde dehydrogenase
          Length = 496

 Score =  352 bits (904), Expect = e-101
 Identities = 190/480 (39%), Positives = 278/480 (57%), Gaps = 5/480 (1%)

Query: 7   FINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAER 66
           FI G +  +A+GR F   NP+    +  V E G  +VDAAV AARAA  G W + S A+R
Sbjct: 21  FIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAAARAAFTGTWAQQSPAQR 80

Query: 67  AEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEAF 126
             +L R+A+ +    +E  +   L+ GKP   A+  +    A   + FA     +     
Sbjct: 81  GLLLFRLAELLDQHREELAQLITLENGKPIG-AARGEAASAANIIRYFAGWPTKIEGSTL 139

Query: 127 EMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPLT 186
            ++   GA  +NY +R P GV  +I PWN PL +  WK+GP LA G   V+KP+E+TPL 
Sbjct: 140 PVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPVLATGCVAVLKPAEQTPLV 199

Query: 187 ATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAAK 246
           A  L ++++AAG PAGV N++ G G  + GA L +HPDVD   FTG T  G +I +AA  
Sbjct: 200 AIRLVQLIEAAGFPAGVVNLLTGLGAQT-GAPLAQHPDVDKIAFTGSTQVGRLIAQAATG 258

Query: 247 GVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEFVA 306
            +++VSLELGGK+  I+  D D+ +A +G     F N GQVC    R+YV   + D+ + 
Sbjct: 259 NMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQGQVCTAGSRLYVHASVLDQVLE 318

Query: 307 RLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPAHL 366
            L+  A + ++GP  D +S+ GPLVS +    V  Y Q+  ++G  +I GG   D PAHL
Sbjct: 319 ELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEEGAELICGG---DRPAHL 375

Query: 367 AGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWTEN 426
             G +++P+++   ++ + V  EEIFGP   +  +   +E +  AN  PYGLA+ +WT +
Sbjct: 376 ERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRANDSPYGLAAGLWTRD 435

Query: 427 GSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICVKL 486
              AHRVA Q++AG VW+N W + D  + FGG KQSG GRE G + ++ YTE K++ V L
Sbjct: 436 LRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNVIDAYTETKSVYVDL 495


Lambda     K      H
   0.318    0.136    0.411 

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: 682
Number of extensions: 34
Number of successful extensions: 4
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: 486
Length of database: 496
Length adjustment: 34
Effective length of query: 452
Effective length of database: 462
Effective search space:   208824
Effective search space used:   208824
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, 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