GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:14450
          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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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