GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocA in Magnetospirillum magneticum AMB-1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383730.1 AMB_RS06710 NAD-dependent
           succinate-semialdehyde dehydrogenase
          Length = 485

 Score =  232 bits (592), Expect = 2e-65
 Identities = 163/475 (34%), Positives = 232/475 (48%), Gaps = 16/475 (3%)

Query: 41  YIGGEWVDTK--ERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98
           YI G WV  +  ER+   NP+  S ++   A  G AE   A+EAA +A+  WK    ++R
Sbjct: 15  YINGSWVAAQSGERLAVTNPADGSLIIRVPAM-GAAETRQAIEAADRAWGPWKAKTAKER 73

Query: 99  SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158
           S +L +   L+   + +L   +  E GK   EA  +VA    F+E++A  A R  Y    
Sbjct: 74  SAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRV-YGDTI 132

Query: 159 VVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAK 218
               PG        P+G    I PWNFP+A+ T      +A G  V+ KPAED  +    
Sbjct: 133 PEHMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALA 192

Query: 219 VFEIFHEAGFPPGVVNFLP-GVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAP 277
           + E+   AGFPPGV N +  G  + VG  L  +P+ R ++FTGS EVG  +      +A 
Sbjct: 193 LAELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLL------MAQ 246

Query: 278 GQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEP 337
                K+  +E GG    +V + AD D A  G + S Y   GQ C  A+RL++  G Y+ 
Sbjct: 247 CAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDA 306

Query: 338 VLERVLKRAERLSVGPAEENP-DLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEGE 395
              R+ +    L VGP  E     GP+++ E  RKV  +I     +G ++V+GGKR    
Sbjct: 307 FTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRHARG 366

Query: 396 GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE 455
           G F  PT+  +V P    A+EE FGPV  + R K   EA+ +ANDT +GL    YSR   
Sbjct: 367 GTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVG 426

Query: 456 HLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMK 510
            +    R    G +  N  +      V PFGG K SG   + G+   +  FLE+K
Sbjct: 427 RVWRVSRALEYGIVGINEGLIS--TEVAPFGGVKESGL-GREGSKYGIEDFLEVK 478


Lambda     K      H
   0.319    0.137    0.403 

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: 625
Number of extensions: 40
Number of successful extensions: 6
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: 516
Length of database: 485
Length adjustment: 34
Effective length of query: 482
Effective length of database: 451
Effective search space:   217382
Effective search space used:   217382
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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