GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609634
          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.

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 (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