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 GFF3619 PGA1_262p00230 betaine aldehyde dehydrogenase BetB

Query= BRENDA::C0P9J6
         (505 letters)



>lcl|FitnessBrowser__Phaeo:GFF3619 PGA1_262p00230 betaine aldehyde
           dehydrogenase BetB
          Length = 494

 Score =  318 bits (816), Expect = 2e-91
 Identities = 195/481 (40%), Positives = 265/481 (55%), Gaps = 12/481 (2%)

Query: 10  RQLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWA 69
           R  F+DG    P  G R+   +P       +  AG A DVD AV +A A  +      W+
Sbjct: 21  RDHFIDGRAVAPGAGGRMESFDPGRGTAFDDFAAGDAADVDHAVTSAVAGFEI-----WS 75

Query: 70  RAPGAVRAKYLRAIAAKVIERKPELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEA 129
             P A R   L   A  +      LA +E +D GK   EA  D+   A   EY+A  A+ 
Sbjct: 76  ATPPARRCAILNEAARLMRHEAEHLAVVECVDSGKTLAEARGDIAGSARLLEYYAGAADK 135

Query: 130 LDKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKIAPALAAGCTAVLKPS 189
           LD R    V+L  +     LR EP+GV   I PWNYP       IAPALAAGC+AV+KP+
Sbjct: 136 LDGRS---VNLGNDNAAFTLR-EPVGVTAHIVPWNYPSSTLVRGIAPALAAGCSAVVKPA 191

Query: 190 ELASVTCLELADICKEVGLPSGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIM 249
           E    T L +AD+    GLP+GV+N+VTG G  AGAPL   P V  V FTGS  TG  +M
Sbjct: 192 ETTPFTALMIADLLIRAGLPAGVVNVVTGTGIAAGAPLVRDPRVRHVTFTGSVATGVGVM 251

Query: 250 ASAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLIHTKIA 309
            S AP V  +TLELGGKSP+V F D ++D  VE  L+  F   GQICSA SRL+IH  + 
Sbjct: 252 QSVAPNVTGLTLELGGKSPLVAFGDANVDAVVEGALWAIFSNAGQICSAGSRLVIHRSLH 311

Query: 310 KKFNERMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGGVRPA 369
            +  +++VA A+ ++V   L  G  +G V S     +I   +S A+++G  I+TGG    
Sbjct: 312 AEVRDKLVARAQRLRVGHGL-RGPDIGAVNSARHLAQIDDHVSRARTRGVEIVTGGEILT 370

Query: 370 HLE--KGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAV 427
            +E  KG+F  PTI+ D+  + +   +E+FGPVL ++ F  E EA+ LAN T++ LA  +
Sbjct: 371 DVESGKGWFYAPTILDDLAANDDAVLQEIFGPVLAIQVFEDEAEALALANGTEFALAAGI 430

Query: 428 ISGDRERCQRLSEEIDAGCIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVKQV 487
            + D     R++  +DAG + VN       + P+GGN++SGFGRE G  G+D Y   K V
Sbjct: 431 YTRDIATALRMARRVDAGQVTVNDYWAGGIELPFGGNRKSGFGREKGLEGLDAYTRSKAV 490

Query: 488 T 488
           T
Sbjct: 491 T 491


Lambda     K      H
   0.318    0.135    0.422 

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: 611
Number of extensions: 22
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: 505
Length of database: 494
Length adjustment: 34
Effective length of query: 471
Effective length of database: 460
Effective search space:   216660
Effective search space used:   216660
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