GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA 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)



>NCBI__GCF_000009985.1:WP_011383730.1
          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.

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