GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N2C3

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-15732
         (497 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28685 AO356_28685
           betaine-aldehyde dehydrogenase
          Length = 496

 Score =  485 bits (1249), Expect = e-141
 Identities = 246/498 (49%), Positives = 334/498 (67%), Gaps = 11/498 (2%)

Query: 5   LPILPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRA 64
           + +LPA   FL +  ++ IG  WQDAA+GR  +  NPAT   L EV      DVD AV A
Sbjct: 4   IQLLPAVEKFLSQPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAA 63

Query: 65  ARQAFDDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAI 124
           AR AF  + W++  P +R  LL+RLA+L+++   +LA+L  L NGK    A+  +   A 
Sbjct: 64  ARAAFTGT-WAQQSPAQRGLLLFRLAELLDQHREELAQLITLENGKPIGAARG-EAASAA 121

Query: 125 DFLRYMAGWATKIEGSTVEASMPLMPND--QFHGFVRREAIGVVGAIVAWNFPLLLACWK 182
           + +RY AGW TKIEGST    +P+ P+       +  RE +GV   IV WNFPL +  WK
Sbjct: 122 NIIRYFAGWPTKIEGST----LPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWK 177

Query: 183 LGPALATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGV 242
           LGP LATGC  VLKPA++TPL  ++L +L++ AG+PAGV N++TG G   GA L++HP V
Sbjct: 178 LGPVLATGCVAVLKPAEQTPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDV 237

Query: 243 DKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQG 302
           DK+ FTGST+VG+LI +AA  NM +V+LELGGKSP I++PDA++  AA GAA  IF+NQG
Sbjct: 238 DKIAFTGSTQVGRLIAQAATGNMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQG 297

Query: 303 QVCCAGSRLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIEL 362
           QVC AGSRLYVH    D V+ ++   A    LG GLDPA  MGPL+SA+Q   V GY++ 
Sbjct: 298 QVCTAGSRLYVHASVLDQVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQR 357

Query: 363 GRELGATVACGGE---GFGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVI 419
           G+E GA + CGG+       G+F++P+V +D  +R  + +EEIFGPVL  M + ++DE++
Sbjct: 358 GQEEGAELICGGDRPAHLERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELV 417

Query: 420 GMANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREV 479
             AND+PYGL A +W+ DL + HR+  ++K+GSVW+NC + +DPA PFGGYK SG GRE+
Sbjct: 418 LRANDSPYGLAAGLWTRDLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREM 477

Query: 480 GAAAIEHYTELKSVLIKL 497
           G   I+ YTE KSV + L
Sbjct: 478 GKNVIDAYTETKSVYVDL 495


Lambda     K      H
   0.320    0.137    0.413 

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: 730
Number of extensions: 31
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: 497
Length of database: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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