Alignments for a candidate for adh in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Sphingomonas koreensis DSMZ 15582

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Ga0059261_4132 Ga0059261_4132 succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__Korea:Ga0059261_4132
          Length = 471

 Score =  456 bits (1173), Expect = e-133
 Identities = 234/455 (51%), Positives = 309/455 (67%), Gaps = 4/455 (0%)

Query: 21  NPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLESNKAELT 80
           NP +GE LW+G  A A    +A   AR AFP WA  S   R A++ R+AA+L   K  L 
Sbjct: 9   NPATGETLWEGPVASAEDCARAVERARTAFPAWAAQSPDARAAILTRYAAVLGERKDALA 68

Query: 81  AIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHRPHGVLAV 140
             IARETGKP WE ATEV +MI K+AISI+A   R G + S MP G A L HRPHGV+AV
Sbjct: 69  EAIARETGKPLWETATEVASMIGKVAISIEAMAARAGTRESAMPFGRAVLAHRPHGVMAV 128

Query: 141 FGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQAGLPPGVLNLVQGG 200
            GPYNFPGHLPNGHIVPALLAGNT++FKPSE TP  G+ ++     AG+P  V  L+QGG
Sbjct: 129 LGPYNFPGHLPNGHIVPALLAGNTLVFKPSEETPLVGQLMVEALHAAGIPEDVAILLQGG 188

Query: 201 RETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLIIDEVADIDA 260
           RETG AL + +D+DGLLFTGSA  G    R  + +P  ILALE+GGNNPL+  +  + +A
Sbjct: 189 RETGAALVS-QDIDGLLFTGSAGAGMHFRRSFAERPAVILALELGGNNPLVAWD-GEPEA 246

Query: 261 AVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDEPQPFIGG 320
              + + S F+T GQRC+CARRL++  GA GDA +  + A+S RL  G WD+ P+PF+G 
Sbjct: 247 VASIVVASTFITTGQRCSCARRLIVPEGAAGDAIVDAVAALSDRLRIGRWDETPEPFMGP 306

Query: 321 LISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGT-SLLTPGIIEMTGVAGVPDEEVFGP 379
           L+S  AA++       L  +G R +     ++  + + + P I+++TG+  VPDEE+F P
Sbjct: 307 LVSTGAAERAAAQVAALVGLGAREIRPFGGVEGRSGAFVRPAILDVTGLE-VPDEEIFAP 365

Query: 380 LLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPLTGAAST 439
           +L+V R   FD A+  AN TRFGL+ GL+S +   + +   +ARAG+VN N+P TGAAS+
Sbjct: 366 VLQVRRVADFDAALAAANQTRFGLAAGLISDDDALWARFQAQARAGVVNRNRPTTGAASS 425

Query: 440 APFGGIGASGNHRPSAWYAADYCAWPMASLESDSL 474
            PFGG+G SGNHRPSA+YAADYCA+P+ASLE++ +
Sbjct: 426 MPFGGLGDSGNHRPSAYYAADYCAYPVASLEAERI 460


Lambda     K      H
   0.318    0.134    0.412 

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: 735
Number of extensions: 36
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: 492
Length of database: 471
Length adjustment: 34
Effective length of query: 458
Effective length of database: 437
Effective search space:   200146
Effective search space used:   200146
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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources