GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Sphingomonas koreensis DSMZ 15582

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)

Query= metacyc::MONOMER-15736
         (480 letters)



>FitnessBrowser__Korea:Ga0059261_0516
          Length = 478

 Score =  293 bits (751), Expect = 7e-84
 Identities = 168/461 (36%), Positives = 250/461 (54%), Gaps = 8/461 (1%)

Query: 25  GQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERATKLRRWYELLI 84
           G+T    NP TGE+          +   A+EAA  A PAW  L    R   L +  E L 
Sbjct: 10  GKTFARLNPVTGEVATEAQAFTVDQANEAVEAAAAAFPAWSTLGPNARRAALNKAAEALA 69

Query: 85  ENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDVIPGHQPDKRLIVIK 144
              +D    M  E G     A+  +  A S +   A    +I G+VIP  +P    + I+
Sbjct: 70  AKAEDFVEAMNGEIGATEGWARFNLMLAVSMVREAAALTTQIGGEVIPSDKPGCIAMAIR 129

Query: 145 QPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALALVELAHRAGIPKG 204
           +P+GV   I PWN P  +  R     LA G T+V+K + Q P +   + E    A +PKG
Sbjct: 130 EPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSLIAEAFDEA-LPKG 188

Query: 205 VLSVVTGS---AGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKDIKKVSLELGGNAP 261
            +S+VT +   A +I G L  NP +R+++FTGST +GR +    A+ +K V LELGG AP
Sbjct: 189 AVSIVTNAPEDAPEIVGALIDNPHIRRINFTGSTAVGRIIAKRAAEHLKPVLLELGGKAP 248

Query: 262 FIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEKLKAAVAKLKIGNG 321
            +V +DADLD+AV+ A    + N GQ C+   R+ + D+V DAF EK  A V  + +G+ 
Sbjct: 249 MLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEKFAAKVGTMPVGDP 308

Query: 322 LEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKSMEGN---FFEPTILVNVPKDA 378
            E  T  G ++D+K VA V+  I DAL  GA  + GG  +EG         ++ +V  D 
Sbjct: 309 REGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVLEGTGGVLMPAHVIDHVTPDM 368

Query: 379 AVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGV 438
            + ++E+FGP+  + R +DEA  I ++NDTE+GL++  + RD  R  RVA  ++ G+  V
Sbjct: 369 KLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTARGLRVARQIKSGICHV 428

Query: 439 NTGLISNEV-APFGGIKASGLGREGSKYGIEDYLEIKYLCL 478
           N   + +E   PFGG+KASG GR G K GI+ + E++++ +
Sbjct: 429 NGPTVHDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWITI 469


Lambda     K      H
   0.317    0.135    0.390 

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: 600
Number of extensions: 25
Number of successful extensions: 5
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: 480
Length of database: 478
Length adjustment: 34
Effective length of query: 446
Effective length of database: 444
Effective search space:   198024
Effective search space used:   198024
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: 51 (24.3 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:

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