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 GFF2285 PGA1_c23170 succinate-semialdehyde dehdyrogenase GabD

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__Phaeo:GFF2285
          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 (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