GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Algiphilus aromaticivorans DG1253

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_043765072.1 U743_RS01785 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000733765.1:WP_043765072.1
          Length = 506

 Score =  361 bits (927), Expect = e-104
 Identities = 209/500 (41%), Positives = 291/500 (58%), Gaps = 21/500 (4%)

Query: 8   PIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAA 67
           P K P  + Y+     FI  ++V  +S K F  VSP T  +I ++  + + D++ A++AA
Sbjct: 10  PAKTPFKSRYDN----FIGGDWVAPESGKYFDNVSPVTGGKICEIARSEAADVEKALDAA 65

Query: 68  TAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSK-GDVALTAAY 126
            AA  + W+ +    R  +L  +A  ++++ + LA  E  DNGK++  S   DV L   +
Sbjct: 66  HAA-RARWANTSTTERSNILNAIAQRMEDNLEALAQAETWDNGKAVRESTVADVPLAIDH 124

Query: 127 FRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCT 186
           FR  AG     +GS+    +    Y   EP+GV GQIIPWNFPLLMA WKL P L  G  
Sbjct: 125 FRYFAGAIRAQEGSISMIDEQTVAYHFHEPLGVVGQIIPWNFPLLMAVWKLAPALAAGNC 184

Query: 187 TVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTA 246
            V+K AE TP S L+   +I +   PPGV+N+V+GFG  AG P++S P+I K AFTG T 
Sbjct: 185 VVIKPAEQTPASILHWMEMIADL-LPPGVINIVNGFGLEAGKPLASSPRIAKAAFTGETT 243

Query: 247 TGRHIMKAAAESNLKKVTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVC 300
           TGR IM+ AA+ NL  VTLELGGKSPN+ F      DDA     I+  V     N GEVC
Sbjct: 244 TGRMIMQYAAQ-NLIPVTLELGGKSPNVFFEDVMREDDAYFDKAIEGFVL-FALNQGEVC 301

Query: 301 CAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKK 360
              SR  +QE I+D+ +       E++++GDP   DT MGAQ S  Q++KIL Y DIGK+
Sbjct: 302 TCPSRALIQESIFDRFMERALKRVEAIQMGDPLSMDTMMGAQASSEQMEKILSYFDIGKQ 361

Query: 361 EGATVITGGERFG-----NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVI 415
           EGA V+TGG R         GY+IKPT+F    +  ++ ++EIFGPVV++T FK   E +
Sbjct: 362 EGAEVLTGGGRAQLDGELANGYYIKPTVFRGHNK-MRVFQEEIFGPVVSVTTFKDEAEAL 420

Query: 416 ALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREM 475
            +AND+ YGL AGV + + +    +   I +G +W N Y+ +     FGGY QSGIGRE 
Sbjct: 421 EIANDTLYGLGAGVWSRDANICYRMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGREN 480

Query: 476 GEEALDNYTQVKAVRIGLSQ 495
            +  LD+Y Q K + +   +
Sbjct: 481 HKMMLDHYQQTKNMLVSYDE 500


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: 614
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 24 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