GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Dechlorosoma suillum PS

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::P80668
         (499 letters)



>lcl|FitnessBrowser__PS:Dsui_0105 Dsui_0105 NAD-dependent aldehyde
           dehydrogenase
          Length = 476

 Score =  290 bits (743), Expect = 6e-83
 Identities = 186/484 (38%), Positives = 267/484 (55%), Gaps = 21/484 (4%)

Query: 18  RQHG-LYIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWA 76
           +QH   YI G+         + + +PAT   IA   +    D D A  +A  AF +  WA
Sbjct: 2   QQHSRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPA--WA 59

Query: 77  GRLPAERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTT 136
               AER   L + AD ++   +EL +L   E G  + ++   + G  +    +T     
Sbjct: 60  ALSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPI----FTFAACA 115

Query: 137 KIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVI 196
           +IA +         +    Q+   K P G VA I PWNFPL     KV  ALAAGC++V+
Sbjct: 116 RIAAEGF------AEERIGQSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVL 169

Query: 197 KPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTATGK 256
           KPSE  PL    +AE+   AG+P GVFN+VTG G V G AL +HP +A +SFTGSTA GK
Sbjct: 170 KPSEVAPLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGK 229

Query: 257 GIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEA 316
            +A  AA  + RV+LELGGK+ ++VL DAD    ++G + G FLN GQ C+A +R+ +  
Sbjct: 230 RVAAVAAATVKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQ 289

Query: 317 PLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELI-RGS 375
             +    +   QA  +  +G  ++  +++ PLVS     +V + ++ A A  AEL+  GS
Sbjct: 290 ERYAEAAALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGS 349

Query: 376 NGPAG--EGYYVAPTLV--VNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGL 431
             P G   GYYV PT+   V PDA   L REEVFGPV+ ++   D  EA  +AN T+YGL
Sbjct: 350 AAPEGLPTGYYVRPTVFGRVRPDA--ALAREEVFGPVLAILTYRDEAEAEAIANGTDYGL 407

Query: 432 TASVWTQNLSQALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDGWCE 491
            A+VW+   ++AL ++ RL+AG V +N     +   PFGG KQSG GR+ G   ++ + E
Sbjct: 408 AAAVWSAEEARALAFARRLRAGQVDING-AFFNLLAPFGGFKQSGYGRELGRHGVEDFLE 466

Query: 492 TKSV 495
           T+S+
Sbjct: 467 TQSI 470


Lambda     K      H
   0.318    0.133    0.402 

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: 599
Number of extensions: 29
Number of successful extensions: 5
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: 499
Length of database: 476
Length adjustment: 34
Effective length of query: 465
Effective length of database: 442
Effective search space:   205530
Effective search space used:   205530
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, the preprint on GapMind for carbon sources, 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