GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Azospirillum brasilense Sp245

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS26825 AZOBR_RS26825 aldehyde
           dehydrogenase
          Length = 494

 Score =  273 bits (698), Expect = 1e-77
 Identities = 154/470 (32%), Positives = 258/470 (54%), Gaps = 11/470 (2%)

Query: 15  VDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERAN 74
           + G    A  G+T  V NPATG++I +    G  +   A+ AA  A  AW  L+A+ER  
Sbjct: 20  IGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAAQGAWARLSARERGR 79

Query: 75  KLRRWFDLMIENQDDLARLMTIEQGKPL-AEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133
            L      ++ + +++ RL+ +E GK +  E++ E +  A  L ++G  A  + G+T+P 
Sbjct: 80  LLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASELKGETVPF 139

Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193
           H P       ++PIGV  AI PWN P  ++  K  PAL AG  +++K A + P +AL + 
Sbjct: 140 H-PKMLTFTQREPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAEEAPLAALRVI 198

Query: 194 ELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKVS 253
           ++  +  +P GV ++++G     G  L ++P V K+TFTGS E G+ +    A  +  V+
Sbjct: 199 QVMNQL-LPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVETGKIISHLAADKLIPVT 257

Query: 254 LELGGNAPFIVFDDADLDAAVEGALIS-KYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312
           LELGG +P IV  DADLD A++GA+   ++   GQ+C  ++R++V + ++DAF+DKLKA 
Sbjct: 258 LELGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLHDAFIDKLKAK 317

Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIA------DAVSKGAKVVSGGKPHALGGT 366
           V  + +G+ L+     G +I  +   +V+ +IA       A++     +   +  A G  
Sbjct: 318 VDAMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALPTDERLARG-L 376

Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426
           F +P +   +  +  ++++E FGP+  V  F+D  + +AM+ND++FGLA+  + RDL   
Sbjct: 377 FVQPVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAATIWTRDLRTA 436

Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476
                +L+ G V +N  L+      +GG K SGLG+E S   + D+   K
Sbjct: 437 LDATRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHK 486


Lambda     K      H
   0.317    0.135    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: 531
Number of extensions: 30
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
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 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