GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Escherichia coli BW25113

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)

Query= BRENDA::P49189
         (494 letters)



>lcl|FitnessBrowser__Keio:14450 b0312 betaine aldehyde
           dehydrogenase, NAD-dependent (NCBI)
          Length = 490

 Score =  494 bits (1271), Expect = e-144
 Identities = 254/491 (51%), Positives = 339/491 (69%), Gaps = 7/491 (1%)

Query: 7   VVSQPLNYRGGARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWS 66
           +  Q L   GG     A +  T +   PA G V+AT   +G ++V+ AV++A+   KIW+
Sbjct: 4   MAEQQLYIHGG--YTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIWA 61

Query: 67  QKSGMERCRILLEAARIIREREDEIATMECINNGKSIFE-ARLDIDISWQCLEYYAGLAA 125
             + MER RIL  A  I+RER DE+A +E ++ GK+  E + +DI      LEYYAGL  
Sbjct: 62  SMTAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIP 121

Query: 126 SMAGEHIQLPGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFT 185
           ++ G  I L   SF YTRREPLGV  GIGAWNYP QIA WKSAPALA GNAM+FKPS  T
Sbjct: 122 ALEGSQIPLRETSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVT 181

Query: 186 PVSALLLAEIYSEAGVPPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMS 244
           P++AL LAEIYSEAG+P G+FNV+ G GA TGQ+L +HP +AKVSFTG V +G K+M  S
Sbjct: 182 PLTALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMANS 241

Query: 245 A-KGIKPVTLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDK 303
           A   +K VT+ELGGKSPLI+F D D++ A   A+MANF + GQVC NGTRVFV  +    
Sbjct: 242 AASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKAA 301

Query: 304 FTEEVVKQTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPE 363
           F ++++ + +RI+ GD     T  GPL++ PH + VL ++   KE+GA+VLCGGD+   +
Sbjct: 302 FEQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGDVLKGD 361

Query: 364 DPKLKDGYYMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGV 423
                +G ++ P V T+C DDMT V+EEIFGPVMSIL++++E EV+ RANDT +GLAAG+
Sbjct: 362 G--FDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGI 419

Query: 424 FTRDIQRAHRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTV 483
            T D+ RAHRV+ +L+AG C+IN +  SP E+P GGYK SG GRENG +T++ Y+Q+K++
Sbjct: 420 VTADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSYTQVKSI 479

Query: 484 CVEMGDVESAF 494
            VEM   +S F
Sbjct: 480 QVEMAKFQSIF 490


Lambda     K      H
   0.320    0.137    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: 651
Number of extensions: 28
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: 494
Length of database: 490
Length adjustment: 34
Effective length of query: 460
Effective length of database: 456
Effective search space:   209760
Effective search space used:   209760
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