GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens FW300-N2E3

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate AO353_24475 AO353_24475 aldehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24475
          Length = 477

 Score =  341 bits (874), Expect = 4e-98
 Identities = 175/470 (37%), Positives = 267/470 (56%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           ++ G W +    ++I V NPAT E IG + K   A+   A  AA+K    W+ ++A ERA
Sbjct: 7   FIGGVWRNTHPDESIPVINPATEEQIGLIAKASLADIEDAAIAAEKGFATWKQVSALERA 66

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133
             + +   L+ E  +++A ++T E GKPL EA GE+A  A  ++W  EE +R YG  IP 
Sbjct: 67  TIMHKAASLIRERAENIALILTTEHGKPLGEAMGEVAATADTIDWHAEEGRRAYGRVIPS 126

Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193
                    + +PIG      PWNFP     +K   ALAAGC+++LK A++ P  A+ L 
Sbjct: 127 RALGVHQFTVMEPIGPVVGFAPWNFPLIQAVKKVAGALAAGCSIILKGATEAPTCAVELV 186

Query: 194 ELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKVS 253
           +    AG+  G  +++ G +G++   L ++P +RK+TFTGST +G++L +     +K+ +
Sbjct: 187 KAFADAGVSPGAVNLLFGDSGQISEHLIAHPSIRKVTFTGSTPVGKKLASLAGLHMKRST 246

Query: 254 LELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAAV 313
           +ELGG+AP IV DDAD+  AV+ ++ +KYRN GQ CV   R  V   V+D FV +     
Sbjct: 247 MELGGHAPVIVMDDADIATAVKISVAAKYRNAGQVCVSPTRFLVHSKVFDEFVSRFVEGA 306

Query: 314 AKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTIL 373
             + +G+GL+  VT GP+  A  +   EE +ADAVS GAK+ +GG      G FFEPT+L
Sbjct: 307 RAVMVGDGLDPNVTMGPMAHAGRLKATEELVADAVSHGAKLETGGNRIGHKGYFFEPTVL 366

Query: 374 VDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQL 433
            +VP  A    DE FGP+A +  F D  E I  +N   +GL++Y Y R L+   ++   +
Sbjct: 367 TNVPVTARAMIDEPFGPIALINSFDDIDEAIKEANRLPYGLSAYAYTRSLSSANKLFNGI 426

Query: 434 EYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483
           E G + IN   ++    PFGG+K SG G EG    ++ ++  K++ L  +
Sbjct: 427 ESGAISINHHSVALPEHPFGGVKDSGYGTEGGPGALDAFMTTKFVSLASV 476


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: 560
Number of extensions: 24
Number of successful extensions: 1
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: 477
Length adjustment: 34
Effective length of query: 449
Effective length of database: 443
Effective search space:   198907
Effective search space used:   198907
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: 51 (24.3 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