GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Sinorhizobium meliloti 1021

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate SMc02780 SMc02780 succinate-semialdehyde dehydrogenase [NADP+] protein

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__Smeli:SMc02780 SMc02780 succinate-semialdehyde
           dehydrogenase [NADP+] protein
          Length = 484

 Score =  337 bits (864), Expect = 5e-97
 Identities = 186/465 (40%), Positives = 261/465 (56%)

Query: 12  LIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71
           L+   W++A     I+V NPATG+ IGRV   G AD   A+ AA    + W    A ER+
Sbjct: 14  LVGETWIEADPKNAIEVNNPATGEIIGRVPKLGAADTRTAIEAAARVQKEWAARTAKERS 73

Query: 72  ATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPP 131
           A +R+   L+ E  D + +++T EQGKPL EA  E++  A  IEWFA+E RRVYG +VP 
Sbjct: 74  AVLRRWFELMIENKDDLGRILTMEQGKPLAEATGEIVYGASFIEWFAEEARRVYGDLVPG 133

Query: 132 RNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191
                +  V+K+P+G VAA TPWNFP   + RK   ALA GC+ ++K   +TP S  A+ 
Sbjct: 134 HQKDKRILVMKQPIGVVAAITPWNFPNAMITRKAGPALAAGCAMVLKPAAQTPFSAIAIA 193

Query: 192 RAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRAT 251
                AG+P G+  ++ G   EI + +  +P +RK+TFTGST VG +L   +   +K+  
Sbjct: 194 VLAERAGMPKGLFSVITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKKLG 253

Query: 252 MELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHA 311
           +ELGG+AP IV +DAD+  AV+ A  AKFRN GQ C+   R  V + + + F+  L +  
Sbjct: 254 LELGGNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRIYVQDGVYEAFSDKLAQAV 313

Query: 312 EGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVI 371
             LK GNG+E+G  LG L +   L  +   + +A   GA +  GG R    G F+  TV+
Sbjct: 314 AKLKTGNGMEDGVILGPLIDQPALKKVEEHVADALAKGARVVQGGRRHSLGGTFYEATVL 373

Query: 372 ANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRL 431
           A+V     V   E FGPVA +  F    + IA+AN   FGLA Y + +  A V  + + L
Sbjct: 374 ADVTQAMAVAREETFGPVAPLFRFKDESDVIAQANDTEFGLASYFYAKDLARVFRVAEAL 433

Query: 432 EVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           E GM+ +N       E PFGGVK SG G EG    +E ++  K V
Sbjct: 434 EYGMVGVNTGLISTAEAPFGGVKLSGLGREGSKYGIEEFMEIKYV 478


Lambda     K      H
   0.318    0.134    0.393 

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: 616
Number of extensions: 29
Number of successful extensions: 1
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: 481
Length of database: 484
Length adjustment: 34
Effective length of query: 447
Effective length of database: 450
Effective search space:   201150
Effective search space used:   201150
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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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