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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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