GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Escherichia coli BW25113

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)

Query= curated2:Q12QD2
         (498 letters)



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

 Score =  196 bits (498), Expect = 2e-54
 Identities = 146/456 (32%), Positives = 221/456 (48%), Gaps = 22/456 (4%)

Query: 18  GQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTERLVIVE 77
           G   A  G +F ++NPANG V+     A    VD A+ SA+     W++M+  ER  I+ 
Sbjct: 14  GYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIWASMTAMERSRILR 73

Query: 78  AFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANA--ERTGTVENPMP 135
              + L+E  +  A+   L+TGKA  E+ T V  +TG   +   A       G+      
Sbjct: 74  RAVDILRERNDELAKLETLDTGKAYSETST-VDIVTGADVLEYYAGLIPALEGSQIPLRE 132

Query: 136 GAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELTMQLW 195
            +  + R +P GVVA  G +N+P  +      PAL AGN ++FKPSE+TP  A    +++
Sbjct: 133 TSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTALKLAEIY 192

Query: 196 QQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 254
            +AGLP+GV N+L G  A TG+ L  H GI  + FTG   +G  +    A    K + +E
Sbjct: 193 SEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMANSAASSLKEVTME 252

Query: 255 MGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKLLTSTA 314
           +GG +PLI+ + A++D A    + + F SSGQ CT   R+F+P      A   K+L    
Sbjct: 253 LGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKA-AFEQKILARVE 311

Query: 315 KIALGDPFAETQPFFGAMIS----DKAAAGMVKAQADIQAAGGVSLIELTQVTPGLGF-- 368
           +I  GD F + Q  FG ++S    D     + K + +     G  ++    V  G GF  
Sbjct: 312 RIRAGDVF-DPQTNFGPLVSFPHRDNVLRYIAKGKEE-----GARVLCGGDVLKGDGFDN 365

Query: 369 ---VTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSET 424
              V P +  D +D   +  EE FGP++ +  Y   D  I  AN+T +GL+AG++     
Sbjct: 366 GAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIVTADLN 425

Query: 425 DYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASG 460
                  ++ AGI  W      + +  P GG   SG
Sbjct: 426 RAHRVIHQLEAGIC-WINTWGESPAEMPVGGYKHSG 460


Lambda     K      H
   0.317    0.133    0.390 

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: 601
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: 498
Length of database: 490
Length adjustment: 34
Effective length of query: 464
Effective length of database: 456
Effective search space:   211584
Effective search space used:   211584
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