GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Phaeobacter inhibens BS107

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__Phaeo:GFF2918 PGA1_c29650
           succinate-semialdehyde dehdyrogenase GabD
          Length = 491

 Score =  627 bits (1617), Expect = 0.0
 Identities = 311/479 (64%), Positives = 377/479 (78%), Gaps = 2/479 (0%)

Query: 3   LKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP 62
           L D  L   +AY+ GA+VD  +G T  V NPA G++I +V  +  ++   AI  A+ A  
Sbjct: 12  LTDPSLLEPRAYIGGAFVDGADG-TFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQK 70

Query: 63  AWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEE 122
            W   T KERAN LR+WFDLM+ENQ+DLA ++T E GKPLAE++GEI Y ASF+E+F EE
Sbjct: 71  DWAKWTGKERANVLRKWFDLMMENQEDLAVILTAEMGKPLAESRGEIGYGASFIEFFAEE 130

Query: 123 AKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPA 182
           AKRIYG+TIPGHQ DKRI V+KQPIGV A+ITPWNFP+AMITRKAGPALAAGC  V +PA
Sbjct: 131 AKRIYGETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARPA 190

Query: 183 SQTPYSALALAELAERAGIPKGVFSVVTGS-AGEVGGELTSNPIVRKLTFTGSTEIGRQL 241
             TP SA ALA LA+RAGIP GVF+VVT S A E G E   N  VRKLTFTGSTE+GR L
Sbjct: 191 ELTPLSATALAVLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRIL 250

Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301
           M + A  + K S+ELGGNAPFIVFDDADLDAAVEGA++ K+RNNGQTCVCANR+YVQ GV
Sbjct: 251 MRQAADTVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAGV 310

Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361
           YDAF  KLK AVAK+ +G+GL  G   GPLI+ KAV KV+ HIADA  KGA+V+ GG P 
Sbjct: 311 YDAFAAKLKEAVAKMTVGDGLAEGTQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNPS 370

Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421
            LGGTFFEPTI+    ++ + S+DETFGP+AP+F+F+ E +VI M+NDT FGLASYFYA+
Sbjct: 371 ELGGTFFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYAK 430

Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           DL+RV++VAE LEYG+VG+NTG+IS E+APFGG+K SGLGREGS +GIEDYLE+KY+C+
Sbjct: 431 DLSRVYKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYICM 489


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: 694
Number of extensions: 21
Number of successful extensions: 3
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: 491
Length adjustment: 34
Effective length of query: 449
Effective length of database: 457
Effective search space:   205193
Effective search space used:   205193
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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