GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_4132 Ga0059261_4132
           succinylglutamic semialdehyde dehydrogenase (EC
           1.2.1.71)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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