GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Dinoroseobacter shibae DFL-12

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 3608023 Dshi_1430 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__Dino:3608023
          Length = 487

 Score =  237 bits (604), Expect = 8e-67
 Identities = 170/492 (34%), Positives = 245/492 (49%), Gaps = 23/492 (4%)

Query: 33  EFGRHYPLYIG--GEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKT- 89
           E  R +P  IG   E+ D + R+   NP A  E +      G  E + A+ AA +AF+  
Sbjct: 6   EVKRSFPCIIGCAAEFADHRPRIDVTNP-ATGEKIAQIPACGPDEVDRAVTAARRAFEDG 64

Query: 90  -WKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARA 148
            W      DR RLL K    +    +EL      + GK   +A AD+  A  + EYY  A
Sbjct: 65  EWSRLTAVDRGRLLHKLGEAITAHGQELAEWEAKDTGKPLAQARADMVAAARYFEYYGAA 124

Query: 149 ALRYRYPAVEVVPY-PGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAK 207
           A +      E +P+  G   ++ + P G    I PWN+P  +F       +A+GN V+ K
Sbjct: 125 ADKVHG---ETIPFLSGYQVQTIFEPYGVTGHIIPWNYPAQMFGRSCAPALAMGNAVVLK 181

Query: 208 PAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLK 267
           PAEDA +   ++ E+  E GFP G +N + G G+E GA L  H    F++FTGS EVG+ 
Sbjct: 182 PAEDACLTPLRIAELALEVGFPGGAINVVTGYGQEAGAALTTHRDVDFLSFTGSPEVGVM 241

Query: 268 IYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASR 327
           I  AA R   G T      +E GGK   IV   AD D A   ++       GQ CSA SR
Sbjct: 242 IQTAAARNHIGCT------LELGGKSPQIVFADADLDAAIPVLLNGIVQNGGQTCSAGSR 295

Query: 328 LILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYI-EIGKNEGQLV 386
            ++ +  ++ VL R+    E L+  P +EN +LGP++S +Q+R+V  +I E G  +  LV
Sbjct: 296 ALIQRDIFDAVLARLKAGFEALTAAPWQENGNLGPLISHKQKRRVEGFIAEGGGADAPLV 355

Query: 387 LGGK---RLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPY 443
             G+        G F+AP +F  V     +A+EE+FGPVLS I   D A+A+ +AN T Y
Sbjct: 356 ARGRIAASASEAGSFVAPALFGPVIEGHVLAREEVFGPVLSCIPFTDEADAIRIANATDY 415

Query: 444 GLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQ-PFGGFKLSGTNAKTGALDY 502
           GL   V+S          +   VG ++ N    GA  G++ PFGG + SG   + G    
Sbjct: 416 GLVASVWSADGGRQMRLAKRLRVGQVFLN--CYGAGGGIELPFGGMRKSGHGREKG-FAA 472

Query: 503 LRLFLEMKAVAE 514
           L  F ++K V +
Sbjct: 473 LHEFSQIKTVVQ 484


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: 579
Number of extensions: 30
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: 516
Length of database: 487
Length adjustment: 34
Effective length of query: 482
Effective length of database: 453
Effective search space:   218346
Effective search space used:   218346
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