GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Phaeobacter inhibens BS107

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate GFF3161 PGA1_c32120 aldehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>FitnessBrowser__Phaeo:GFF3161
          Length = 485

 Score =  204 bits (519), Expect = 6e-57
 Identities = 153/459 (33%), Positives = 216/459 (47%), Gaps = 9/459 (1%)

Query: 6   IAGQWLA-GQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPA-WARRPLEQRI 63
           I G W A   G TL   +P     +      DA  +DAAV AAR A    W      +R 
Sbjct: 16  IDGSWQAPAGGGTLPLTNPSDGSPLCQIARGDARDIDAAVAAARAALDGPWGGMTATERG 75

Query: 64  ELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEKSGP 123
            LL R    +  R D LA++   + GKPL ++  +  ++   +     A  +  GE    
Sbjct: 76  RLLTRMGQMVLERVDTLAQLEAMDVGKPLTQARADAVALARYLEFYGGAADKLHGETIPY 135

Query: 124 LADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLK 183
            A  T     +PHGV     P+N+P  +    +  AL  GN  V KP+E     A     
Sbjct: 136 QAGYTVYTLREPHGVTGHIVPWNYPMQIIGRSVGAALAMGNACVLKPAEEACLTALAFAH 195

Query: 184 AWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILA 242
             ++AGLPAG LN+V G G E G ALA H G+D + FTGS RTG L+    G     +  
Sbjct: 196 IAVEAGLPAGALNVVPGIGAEAGAALAGHPGVDHISFTGSVRTGALVQQAAGANVVPV-T 254

Query: 243 LEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAV 302
           LE+GG +P +V + ADL+AA+  ++ +   +AGQ C+ A R+LV +G + D + A + A 
Sbjct: 255 LELGGKSPQLVFDDADLEAALPFLVNAGIQNAGQTCSAASRILVQRGVY-DQVRAAMAAA 313

Query: 303 SATLRVGRF--DEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLT 360
            + L VG    D +  P +          +L K  +  I   AQ +L+      GA +  
Sbjct: 314 YSQLTVGPALSDLRLGPLISTRQKEIVEGYLAKGADLAIA--AQGVLSEEASDKGAYVRP 371

Query: 361 PGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFL 420
               DV A      EE FGP+  +I + D A A+R AN+T YGL AG+ +    R  +  
Sbjct: 372 TLFADVGADHPLAQEEIFGPVQVLIPFEDEAEAVRIANSTDYGLVAGIWTRDGARQMRLA 431

Query: 421 VESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459
              RAG V  N    G     PFGG+G SG+ R   + A
Sbjct: 432 KRLRAGQVFLNNYGAGGGVELPFGGVGKSGHGREKGFEA 470


Lambda     K      H
   0.318    0.134    0.396 

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: 588
Number of extensions: 35
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: 487
Length of database: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
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 (21.7 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