GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas fluorescens GW456-L13

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PfGW456L13_1342 Aldehyde dehydrogenase (EC 1.2.1.3)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1342
          Length = 506

 Score =  362 bits (929), Expect = e-104
 Identities = 208/483 (43%), Positives = 287/483 (59%), Gaps = 15/483 (3%)

Query: 16  TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75
           +++   G +I  EFV     + F   SP   + I +   + +EDID A++AA AA   +W
Sbjct: 14  SFKAKYGNYIGGEFVAPVKGQYFTNTSPVNGQPIAEFPRSTAEDIDKALDAAHAAA-DAW 72

Query: 76  STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWT 134
             +  Q R  VL K+AD I+++ + LA  E+ DNGK++  +   D+ L A +FR  AG  
Sbjct: 73  GATSAQARSLVLLKIADRIEQNLELLAITESWDNGKAVRETLNADIPLAADHFRYFAGCI 132

Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194
              +GS  E       Y   EP+GV GQIIPWNFP+LMA+WKL P L  G   VLK AE 
Sbjct: 133 RAQEGSAAEIDGNTVAYHIHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQ 192

Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254
           TPL    L  LI +   PPGV+N+V GFG  AG  +++  +I K+AFTGST  G HIMK 
Sbjct: 193 TPLGITVLVELIGDL-LPPGVLNIVQGFGKEAGEALATSKRIAKIAFTGSTPVGSHIMKC 251

Query: 255 AAESNLKKVTLELGGKSPNIVFDDA--DVKSTIQHLVTGI---FYNTGEVCCAGSRIYVQ 309
           AAE N+   T+ELGGKSPNI F+D      S I+    G+   F+N GEVC   SR  VQ
Sbjct: 252 AAE-NIIPSTVELGGKSPNIFFEDIMKAEPSFIEKAAEGLVLAFFNQGEVCTCPSRALVQ 310

Query: 310 EGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG 369
           E IYD+ ++        +K GDP   DT +GAQ S+ Q DKIL Y++I K EGA ++TGG
Sbjct: 311 ESIYDEFMAVVMKKVLQIKRGDPLDTDTMVGAQASEQQFDKILSYLEIAKGEGAELLTGG 370

Query: 370 E---RFGN--KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYG 424
           +     GN   GY+I+PT+     +  ++ ++EIFGPVV+IT FK   E +A+AND+E+G
Sbjct: 371 KVEKLEGNLASGYYIQPTLLKGTNK-MRVFQEEIFGPVVSITTFKDEAEALAIANDTEFG 429

Query: 425 LAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYT 484
           L AG+ T +++ A  +   I +G +W N Y+ +     FGGY +SG+GRE  +  LD+Y 
Sbjct: 430 LGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQ 489

Query: 485 QVK 487
           Q K
Sbjct: 490 QTK 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: 633
Number of extensions: 28
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:

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