GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein

Query= SwissProt::Q9SAK4
         (528 letters)



>NCBI__GCF_000828635.1:WP_041097806.1
          Length = 479

 Score =  315 bits (808), Expect = 2e-90
 Identities = 181/473 (38%), Positives = 274/473 (57%), Gaps = 13/473 (2%)

Query: 52  RTQGLIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFTSWSRLTA 111
           RTQ  I G+W+      TI+V +P  G ++A V      + + A+ ++  AF +WS   A
Sbjct: 4   RTQFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPA 63

Query: 112 GERSKVLRRWYDLLIAHKEELGQLITLEQGKPLK--EAIGEVAYGASFIEYYAEEAKRVY 169
            ER+  L++  + L A  +E+ + ITLE G P K  + I   +  ASF  Y    A   +
Sbjct: 64  AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPF 123

Query: 170 GDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPSELTPL 229
            + +  +       V+++ VGVV AITPWN+PL  I  KV  ALA+GCTVV+KPSE+ PL
Sbjct: 124 EEKVGNSK------VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPL 177

Query: 230 TALAAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLMAAAAP 289
            A   AE+   AGVP G  N++ G  P +G+A++T  +V  ++FTGST  G ++   A+ 
Sbjct: 178 NAFLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASA 237

Query: 290 TVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIYDKFAE 349
           TVK+V+LELGG + +I+ DDAD +VAVKG +   + NSGQTC    R+LV    Y + A+
Sbjct: 238 TVKRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAK 297

Query: 350 AFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHSLGMT- 408
              EA Q   VGD   +G T GPL +     +V  ++   +++G +++ GG     G+  
Sbjct: 298 LAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNP 357

Query: 409 ---FYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFTNSV 465
              + +PT+   V  +  +++EEIFGPV  +I +  EEDA+ IAN T+ GLA  +++ + 
Sbjct: 358 DGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATD 417

Query: 466 QRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIK 518
           + + +V   +  G V +N G  +   APFGG KQSG GRE  KYG++++LE K
Sbjct: 418 EHAEQVARRMRTGQVEINGGTFNM-YAPFGGYKQSGNGRELGKYGLEDFLEFK 469


Lambda     K      H
   0.317    0.134    0.383 

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: 547
Number of extensions: 15
Number of successful extensions: 4
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: 528
Length of database: 479
Length adjustment: 34
Effective length of query: 494
Effective length of database: 445
Effective search space:   219830
Effective search space used:   219830
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 Apr 09 2024. 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:

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