GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Sphingomonas koreensis DSMZ 15582

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Ga0059261_1006 Ga0059261_1006 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q72IB9
         (516 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1006 Ga0059261_1006
           NAD-dependent aldehyde dehydrogenases
          Length = 453

 Score =  198 bits (504), Expect = 3e-55
 Identities = 146/459 (31%), Positives = 210/459 (45%), Gaps = 14/459 (3%)

Query: 55  SLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKR 114
           S+NP A  E   T A       EAAL  A  AF++W+      R+ LL   A      KR
Sbjct: 4   SINP-ATGEAGATFAALDDDAIEAALTRAEAAFRSWRASDIAQRTALLTAIADRFEANKR 62

Query: 115 ELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPL 174
            L  T   E+GK    A A+V + I    +YA     Y  P +E     G      ++PL
Sbjct: 63  HLAETATKEMGKTLASAIAEVEKCIAGFRHYADKGPGYLAP-IETKTASGRA-VGHWLPL 120

Query: 175 GAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVN 234
           G  + + PWNFP       +   +  GN  + K A       A + ++   AG P G+  
Sbjct: 121 GPILAVMPWNFPYWQVVRWLAPTILAGNVGLLKHASLTQGCAALIQQMVSAAGAPDGLFQ 180

Query: 235 FLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDA 294
            LP   ++V   + +  R   +  TGS   G K+ EAAGR        K+  +E GG D 
Sbjct: 181 NLPIKSDKVSRIIAD-TRVAAVTLTGSEGAGAKVAEAAGRA------LKKVVLELGGSDP 233

Query: 295 IIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG-P 353
            IV  +AD D A    V +     GQ C  A R+I+    Y+  L++       + +G P
Sbjct: 234 FIVMPSADLDKAVATAVKARVQNAGQSCICAKRMIVHADVYDAFLDKFTAAMLAVKIGDP 293

Query: 354 AEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARI 413
            E+  ++GP+ S EQ   VL  +E    +G  + GG ++E +G ++   V T V P A  
Sbjct: 294 MEDGVEMGPLSSVEQRDTVLEQVERAVADGATLAGGAKIERDGAWMEAGVLTHVHPDADF 353

Query: 414 AQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNR 473
           AQEEIFGPV  V R  D   A+ +AND P+GL   V++  +  ++   R+   G    N+
Sbjct: 354 AQEEIFGPVAMVFRADDIDAAIALANDVPFGLGSSVWTSDQAEIDRFVRDIESGMTAVNQ 413

Query: 474 KITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAV 512
            +  A     PFGG KLSG   + G    L  F+ +KAV
Sbjct: 414 LL--ASTPEAPFGGVKLSGHGRELGPWG-LHEFMNLKAV 449


Lambda     K      H
   0.319    0.137    0.403 

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: 480
Number of extensions: 28
Number of successful extensions: 6
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: 516
Length of database: 453
Length adjustment: 34
Effective length of query: 482
Effective length of database: 419
Effective search space:   201958
Effective search space used:   201958
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 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