GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Marinobacter adhaerens HP15

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 GFF3462 HP15_3404 succinic semialdehyde dehydrogenase

Query= SwissProt::Q9SAK4
         (528 letters)



>lcl|FitnessBrowser__Marino:GFF3462 HP15_3404 succinic semialdehyde
           dehydrogenase
          Length = 483

 Score =  412 bits (1059), Expect = e-119
 Identities = 223/481 (46%), Positives = 291/481 (60%), Gaps = 2/481 (0%)

Query: 45  LRSSGLLRTQGLIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFT 104
           + S  L +  G IGG+W D+    T  V NPATG++IA VA M   E N A+AS   A  
Sbjct: 2   IESPLLEKLTGYIGGRWTDNEHGNTFDVYNPATGKVIAQVASMSEDEVNAAVASGKSALR 61

Query: 105 SWSRLTAGERSKVLRRWYDLLIAHKEELGQLITLEQGKPLKEAIGEVAYGASFIEYYAEE 164
             S  +   R K L    D L A+KEE+G+++ +E GKPL+EA GEV Y A F +Y ++ 
Sbjct: 62  LTSPYSIETRRKWLEDIRDALKANKEEVGRILCMEHGKPLQEAQGEVDYAAGFFDYCSKH 121

Query: 165 AKRVYGDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPS 224
            + +    IP    D    V  +P+GV G ITPWNFP+ MI +K+  ALA+GC  V+KP+
Sbjct: 122 IQALDAHTIPEKPKDCTWTVHYRPIGVTGLITPWNFPIGMIAKKLSAALAAGCPSVIKPA 181

Query: 225 ELTPLTALAAAELA-LQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKL 283
             TPLT +A   L      +P G +N+VMG A  IG  L  SP V  ++FTGST VG+KL
Sbjct: 182 SETPLTMIALFSLMDKHTDIPDGMVNLVMGKASVIGKVLCESPDVPMLSFTGSTEVGRKL 241

Query: 284 MAAAAPTVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGI 343
           +   A  VKK++LELGGNAP IVFDDADLD A    +A KFR  GQTCVCANR+ V + +
Sbjct: 242 IVDTADQVKKLALELGGNAPFIVFDDADLDAAADNLIANKFRGGGQTCVCANRIFVHEKV 301

Query: 344 YDKFAEAFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRH 403
            D F E  +E V K+ VGDG       GPLIN A   KV+  VQDA+ KGA ++ G K  
Sbjct: 302 ADAFGEKLAERVNKMTVGDGINGDVDLGPLINQAGYDKVKRHVQDALEKGATLVAGKKPE 361

Query: 404 SLGM-TFYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFT 462
            LG   F+ PTV+  V+ +M   +EE FGP+ P+  F+TEE+ I   NDT  GLA+Y+FT
Sbjct: 362 DLGNDLFFPPTVVHGVNRDMCCYQEETFGPLVPMALFRTEEEVIEAGNDTEFGLASYVFT 421

Query: 463 NSVQRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIKYVCL 522
           N  +R+ RV   L +G  G N G   T  APFGG+K SG+GREG   G+ E++E + V  
Sbjct: 422 NDAERAQRVAAGLRFGHCGWNTGTGPTPEAPFGGMKASGIGREGGLEGLFEFVEAQTVPR 481

Query: 523 G 523
           G
Sbjct: 482 G 482


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: 637
Number of extensions: 23
Number of successful extensions: 3
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: 483
Length adjustment: 34
Effective length of query: 494
Effective length of database: 449
Effective search space:   221806
Effective search space used:   221806
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.

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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 preprint 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