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 GFF2285 PGA1_c23170 succinate-semialdehyde dehdyrogenase GabD

Query= BRENDA::P51650
         (523 letters)



>lcl|FitnessBrowser__Phaeo:GFF2285 PGA1_c23170
           succinate-semialdehyde dehdyrogenase GabD
          Length = 474

 Score =  391 bits (1005), Expect = e-113
 Identities = 204/469 (43%), Positives = 291/469 (62%), Gaps = 3/469 (0%)

Query: 50  DSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERS 109
           D ++ G W  T   F V +PA+   L +VA   + +A AA+ AA  A   W   + ++RS
Sbjct: 5   DLYINGAWHKTSERFDVINPATEEVLASVASADIADADAALDAAEAAMKDWAARTPRQRS 64

Query: 110 SLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYT 169
            +LRK ++LM +  D  A +IT E+GK   +A+GE  Y+A F  WF+EEA R  G I + 
Sbjct: 65  EVLRKAWELMTKRLDYFANLITLENGKAGTDAKGEATYAAEFFRWFAEEAVRADGMITHA 124

Query: 170 SAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALA 229
            A   R +V  +P G+A ++TPWN+P+AM TRK+  ALAAGC V++KPA +TP + LAL 
Sbjct: 125 PASGARIVVQHKPAGLAVLVTPWNYPAAMGTRKIAPALAAGCGVIIKPASETPLTMLALM 184

Query: 230 QLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVK 289
            L  +AG+P G+ NV+P  +T +  + + +  DP +  +SFTGST  G+ LL  AA+ V 
Sbjct: 185 PLLEEAGVPAGLVNVLPSRKTGS--LVDHMLHDPRIRVVSFTGSTGVGRKLLKGAADQVL 242

Query: 290 RVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFA 349
           + +MELGG AP +VF+ A++D A+ G M +K RN G+ C  +NR  V   I D F  + +
Sbjct: 243 KPAMELGGNAPVVVFEDADMDVAIEGTMLAKMRNLGEACTAANRIYVHEDIADEFTKRLS 302

Query: 350 EAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFE 409
            AM  +L+VG+G +     GPL+N    +KV   V DAVAKGA V  GG      G ++ 
Sbjct: 303 AAM-SALKVGDGTDPSVDVGPLVNADTRDKVAAFVADAVAKGAKVECGGTTPNGKGFYYP 361

Query: 410 PTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRV 469
           PT+LSNV+ D  C+ +E FGPVA +  F  ++E +A AN  + GL  Y +S+D  +  +V
Sbjct: 362 PTVLSNVSEDAECVRDEIFGPVAAIQTFTNQDEVIARANDTEYGLVAYVFSEDFKRALQV 421

Query: 470 AEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518
            EQLE GMVG+N GL+S    PFGGVKQSGLGREG   G+ E++E +Y+
Sbjct: 422 CEQLEYGMVGLNRGLVSDPAAPFGGVKQSGLGREGGHEGMLEFMETQYI 470


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: 589
Number of extensions: 28
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: 474
Length adjustment: 34
Effective length of query: 489
Effective length of database: 440
Effective search space:   215160
Effective search space used:   215160
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