GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Phaeobacter inhibens BS107

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD

Query= BRENDA::P51650
         (523 letters)



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

 Score =  511 bits (1316), Expect = e-149
 Identities = 262/497 (52%), Positives = 352/497 (70%), Gaps = 19/497 (3%)

Query: 23  LLREPAGAQRRSYVGGPADLHADLLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCG 82
           LL +P+  + R+Y+GG            +FV G       TF V +PA G  +  VAD  
Sbjct: 11  LLTDPSLLEPRAYIGG------------AFVDG----ADGTFAVKNPARGDVIANVADVS 54

Query: 83  VPEARAAVRAAYDAFSSWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQ 142
             +   A+  A  A   W + + KER+++LRKW+DLM++N+++LA I+TAE GKPL E++
Sbjct: 55  RSQVAGAIAQAEVAQKDWAKWTGKERANVLRKWFDLMMENQEDLAVILTAEMGKPLAESR 114

Query: 143 GEILYSAFFLEWFSEEARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRK 202
           GEI Y A F+E+F+EEA+R+YG+ I    +DKR  VLKQP+GVA+ ITPWNFP+AMITRK
Sbjct: 115 GEIGYGASFIEFFAEEAKRIYGETIPGHQRDKRITVLKQPIGVAASITPWNFPNAMITRK 174

Query: 203 VGAALAAGCTVVVKPAEDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTD 262
            G ALAAGC  V +PAE TP SA ALA LA++AGIP GV+NV+  S   A E G+  C +
Sbjct: 175 AGPALAAGCAFVARPAELTPLSATALAVLADRAGIPAGVFNVVTSS--NASETGKEFCEN 232

Query: 263 PLVSKISFTGSTATGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFR 322
             V K++FTGST  G+IL+  AA++V + SMELGG APFIVFD A++D AV GA+  KFR
Sbjct: 233 NAVRKLTFTGSTEVGRILMRQAADTVMKCSMELGGNAPFIVFDDADLDAAVEGAIMCKFR 292

Query: 323 NAGQTCVCSNRFLVQRGIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEK 382
           N GQTCVC+NR  VQ G++D+F  K  EA+ K + VG+G  EGT  GPLINEKAVEKV+ 
Sbjct: 293 NNGQTCVCANRIYVQAGVYDAFAAKLKEAVAK-MTVGDGLAEGTQFGPLINEKAVEKVQA 351

Query: 383 HVNDAVAKGATVVTGGKRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEE 442
           H+ DA  KGA V+ GG   + GG FFEPT+++  T+DM+   +ETFGP+AP+ KF+ E++
Sbjct: 352 HIADAKEKGAEVILGGNPSELGGTFFEPTIITGATQDMVFSQDETFGPMAPLFKFETEDD 411

Query: 443 AVAIANAADVGLAGYFYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGR 502
            + +AN    GLA YFY++D +++++VAE LE G+VGVN G+IS+   PFGGVKQSGLGR
Sbjct: 412 VIEMANDTIFGLASYFYAKDLSRVYKVAEALEYGIVGVNTGIISTELAPFGGVKQSGLGR 471

Query: 503 EGSKYGIDEYLEVKYVC 519
           EGS +GI++YLE+KY+C
Sbjct: 472 EGSHHGIEDYLEMKYIC 488


Lambda     K      H
   0.318    0.135    0.400 

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: 626
Number of extensions: 24
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: 523
Length of database: 491
Length adjustment: 34
Effective length of query: 489
Effective length of database: 457
Effective search space:   223473
Effective search space used:   223473
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