GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Dinoroseobacter shibae DFL-12

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)

Query= curated2:Q12QD2
         (498 letters)



>lcl|FitnessBrowser__Dino:3609634 Dshi_3017 aldehyde dehydrogenase
           (RefSeq)
          Length = 780

 Score =  201 bits (512), Expect = 6e-56
 Identities = 152/486 (31%), Positives = 237/486 (48%), Gaps = 25/486 (5%)

Query: 15  FIAGQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTERLV 74
           FI G + A  G +F++ NPA G  + Q        ++AA+T+AR A   W+ +       
Sbjct: 36  FIGGTFQA-PGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWAR 94

Query: 75  IVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAERTGTVENPM 134
           ++ A A  L++H+ LFA    L+ GK + ESR     +  +       +A     +E+ +
Sbjct: 95  VLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQR---HFYYHAGMAALMEDEL 151

Query: 135 PGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELTMQL 194
           P         P GV     P+NFP  +    I PAL  GNTV+ KP+E TP  A L  ++
Sbjct: 152 PD------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLFAEI 205

Query: 195 WQQAGLPNGVLNLLQGEIATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 254
             +AG+P GV+N++ G+ ATG AL SH G+D + FTGS++ G  + +  AG  GK L LE
Sbjct: 206 CGEAGVPPGVVNIVTGDGATGAALVSHPGVDKIAFTGSTDVGREIRRATAG-TGKALTLE 264

Query: 255 MGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKLLTSTA 314
           +GG +P ++ E A++D+AV  ++ + + + GQ C    RL + +    +A  AKL    A
Sbjct: 265 LGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLV-QEGIAEAFYAKLRARMA 323

Query: 315 KIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLG-FVTPGI 373
            + +GDP  +     GAM+     A + +       AG    +      P  G F  P +
Sbjct: 324 TLRIGDPLDKCID-VGAMVDPAHCAKVAE-----MVAGSNGEVHQPGTVPAEGAFYPPTL 377

Query: 374 I-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSETDYQHFYRR 432
           I  +  A PL  +E FGP+L    +     A++ AN T +GL+A L +++         +
Sbjct: 378 ITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDIAPK 437

Query: 433 IRAGIVNWNKPITGASSAAPFGGIGASGNHRASAYYA----ADYCAYPVSSVEAQAVSLP 488
           + AG+V W        +AA FGG+  SG  R   +          A P + V   A+  P
Sbjct: 438 LAAGVV-WVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTKQAAPPKALVPVAAIPAP 496

Query: 489 ASLSPG 494
           A+  PG
Sbjct: 497 AAPKPG 502



 Score = 61.6 bits (148), Expect = 1e-13
 Identities = 52/185 (28%), Positives = 82/185 (44%), Gaps = 3/185 (1%)

Query: 63  TWSAMSLTERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKA 122
           +W   +   R  I+   AE L    E FA  IA  TG  +  +  EV A   ++  +  A
Sbjct: 558 SWGRTTGHLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRAEAEVSAAIDRL-FTYAA 616

Query: 123 NAERTGTVENPMP-GAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPS 181
            A++      P+P    A    +P GV+  F P + P       +  AL  GN ++  PS
Sbjct: 617 WADKYDGAVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPS 676

Query: 182 ELTPKVAELTMQLWQQAGLPNGVLNLLQG-EIATGKALASHKGIDGLFFTGSSNTGHLLH 240
           E  P  A    Q+   + +P GV+N++ G   A  K LASH G+D ++    ++    + 
Sbjct: 677 EPFPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIE 736

Query: 241 QQYAG 245
            + AG
Sbjct: 737 AEAAG 741


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: 966
Number of extensions: 50
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 498
Length of database: 780
Length adjustment: 37
Effective length of query: 461
Effective length of database: 743
Effective search space:   342523
Effective search space used:   342523
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: 54 (25.4 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