GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2918
          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 (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