GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Pseudomonas simiae WCS417

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3406 PS417_17430 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__WCS417:GFF3406 PS417_17430 aldehyde
           dehydrogenase
          Length = 506

 Score =  363 bits (933), Expect = e-105
 Identities = 213/484 (44%), Positives = 289/484 (59%), Gaps = 17/484 (3%)

Query: 16  TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75
           +++Q  G +I  EFV   S + F   SP T E I +   + + DID A++AA AA   +W
Sbjct: 14  SFKQRYGNYIGGEFVAPLSGEYFTNTSPVTGEVIAEFPRSNAADIDKALDAAHAAA-DAW 72

Query: 76  STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWT 134
             + PQ R  VL K+AD I++H + LA  E+ DNGK++  +   DV L A +FR  AG  
Sbjct: 73  GKTSPQDRSLVLLKIADRIEQHLEVLAVTESWDNGKAVRETLNADVPLAADHFRYFAGCI 132

Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194
              +G   E  +    Y   EP+GV GQIIPWNFPLLMA+WKL P L  G   VLK AE 
Sbjct: 133 RAQEGGAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQ 192

Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254
           TPLS +  A LI +   PPGV+N+V GFG  AG  +++  +I K+AFTGST  G HIM A
Sbjct: 193 TPLSIMVFAELINDL-LPPGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPIGAHIMHA 251

Query: 255 AAESNLKKVTLELGGKSPNIVFDDAD------VKSTIQHLVTGIFYNTGEVCCAGSRIYV 308
           AAE NL   T+ELGGKSPNI F+D        ++   + LV   F+N GEVC   SR  V
Sbjct: 252 AAE-NLIPSTVELGGKSPNIFFEDIMQAEPQFIEKAAEGLVLA-FFNQGEVCTCPSRALV 309

Query: 309 QEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITG 368
           QE IYD  +         +K G+P   +T +GAQ S+ Q DKIL Y+ I ++EGA ++TG
Sbjct: 310 QESIYDDFMKVVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEGAELLTG 369

Query: 369 G--ERFG---NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEY 423
           G  ER     + GY+I+PT+     +  ++ ++EIFGPVV IT FK   E +A+ANDSE+
Sbjct: 370 GAAERLEGDLSSGYYIQPTLLKGHNK-MRVFQEEIFGPVVGITTFKDEAEALAIANDSEF 428

Query: 424 GLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNY 483
           GL AG+ T +++ A  +   I +G +W N Y+ +     FGGY +SG+GRE  +  LD+Y
Sbjct: 429 GLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHY 488

Query: 484 TQVK 487
            Q K
Sbjct: 489 QQTK 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: 621
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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