GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Pseudomonas fluorescens FW300-N1B4

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Pf1N1B4_4502 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= metacyc::MONOMER-16244
         (495 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4502 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 506

 Score =  349 bits (896), Expect = e-100
 Identities = 206/478 (43%), Positives = 283/478 (59%), Gaps = 17/478 (3%)

Query: 22  GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81
           G FI  EFV   + + F   SP T E I +   + + DI+ A++AA AA   +W  +  Q
Sbjct: 20  GNFIGGEFVAPINGEYFTNTSPVTGEVIAEFPRSSAADIEKALDAAHAAA-DAWGKTSAQ 78

Query: 82  VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWTDKIKGS 140
            R  VL K+AD I+++ + LA  E  DNGK++  +   DV L A +FR  AG     +G 
Sbjct: 79  DRSLVLLKIADRIEQNLEILAVTETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGG 138

Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200
             E  +    Y   EP+GV GQIIPWNFPLLMA+WKL P L  G   VLK AE TPLS +
Sbjct: 139 AAEINELTTAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIM 198

Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260
             A LI +   P GV+N+V GFG  AG  +++  +I K+AFTGST  G HIM  AAE N+
Sbjct: 199 VFAELIADL-LPAGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPIGAHIMHCAAE-NI 256

Query: 261 KKVTLELGGKSPNIVFDDAD------VKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314
              T+ELGGKSPNI F+D        ++   + LV   F+N GEVC   SR  VQE IY+
Sbjct: 257 IPSTVELGGKSPNIFFEDIMNAEPQFIEKAAEGLVLA-FFNQGEVCTCPSRALVQESIYE 315

Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG--ERF 372
             ++E       +K G+P   +T +GAQ S+ Q DKIL Y+ I ++EGA ++TGG  ER 
Sbjct: 316 PFMAEVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEGAELLTGGAAERL 375

Query: 373 G---NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGV 429
               + GY+I+PT+     +  ++ ++EIFGPVV IT FK   E +A+ANDSE+GL AG+
Sbjct: 376 EGDLSSGYYIQPTLLKGHNK-MRVFQEEIFGPVVGITTFKDEAEALAIANDSEFGLGAGL 434

Query: 430 HTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487
            T +++ A  +   I +G +W N Y+ +     FGGY +SG+GRE  +  LD+Y Q K
Sbjct: 435 WTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHYQQTK 492


Lambda     K      H
   0.316    0.133    0.389 

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: 609
Number of extensions: 25
Number of successful extensions: 7
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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 (21.6 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