GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Gracilibacillus halophilus YIM-C55.5

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_003466863.1 J416_RS06115 aldehyde dehydrogenase family protein

Query= BRENDA::Q9RW56
         (523 letters)



>NCBI__GCF_000359605.1:WP_003466863.1
          Length = 486

 Score =  202 bits (515), Expect = 2e-56
 Identities = 142/461 (30%), Positives = 235/461 (50%), Gaps = 22/461 (4%)

Query: 44  IDGQ--EVDTEGKIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARA 101
           IDGQ  E +++  +++ NP +  E + T   A+  D ++A Q A KA + W++ +   + 
Sbjct: 12  IDGQWKEGNSQLSMKNQNPYN-QETLTTYQAASKTDIDHAYQVAQKAQKKWQQQNPTFQR 70

Query: 102 RILLKAAAILKRRRLEACALMSIEVGKNYAEADVEVAEAIDFLEYYARSAMKYAGFGSSE 161
            I  +A  +++        +++ E+G    +A+ E++   + L+    S   +   G   
Sbjct: 71  GIFEQAVHVIEDHHEAIVEVINKEIGGTRLKAEFEISLVKNMLK--EASTFPFRMDGKIL 128

Query: 162 TTWFEGEENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGF 221
            +  +G+EN +  IP+GV   ISP+NFP  + +   A  +  GN VVVKP E   +  G 
Sbjct: 129 PSMTDGKENQVYRIPIGVVGVISPFNFPFFLSMKSIAPALATGNGVVVKPHEHTVITGGT 188

Query: 222 MV-DILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQP 280
           M+  I  EAGLP G+L  +     E+G+    H   + I+FTGS A+G HI  +A +   
Sbjct: 189 MIAKIFEEAGLPQGLLNIVTTEISEIGDAFVEHPIPQSISFTGSTAIGRHIGSIAGRE-- 246

Query: 281 GQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDE 340
               +K V +ELGG  GLIV + ADI+ A++AA    F   GQ C + +R+I+ + VYD 
Sbjct: 247 ----LKDVHLELGGNSGLIVLDDADIDLAVSAAIFSRFTHQGQICMSANRIIIHEDVYDT 302

Query: 341 VVNGFVERAKALKMGTGEENANVTA-VVNQMSFNKIKGYLELAPSEGK-VLLGGEATGEA 398
            V  +V +   L  G   ++  +   ++N+      K  +E   +EG   L+ G+  G  
Sbjct: 303 FVEKYVAKVNELSCGDPCDDTTIIGPLINEKQVENTKQIIEAGINEGADPLVHGQVRGNV 362

Query: 399 NGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCS 458
                  ++P + G+V +N  +A+EE+F PVV++ +A   ++ LDI N T YGL+G V +
Sbjct: 363 -------VEPVVFGNVTKNMTVAKEEMFAPVVSLFKASSEEEILDIVNDTSYGLSGAVHT 415

Query: 459 NSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSG 499
            + ER  Q   + E G ++ N         V  FGG   SG
Sbjct: 416 QNIERGAQLAKQMETGMIHINDGTINDEPNV-AFGGMKNSG 455


Lambda     K      H
   0.317    0.134    0.391 

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: 589
Number of extensions: 23
Number of successful extensions: 5
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: 523
Length of database: 486
Length adjustment: 34
Effective length of query: 489
Effective length of database: 452
Effective search space:   221028
Effective search space used:   221028
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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