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_043769867.1 U743_RS16355 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000733765.1:WP_043769867.1
          Length = 494

 Score =  390 bits (1001), Expect = e-113
 Identities = 199/477 (41%), Positives = 297/477 (62%), Gaps = 7/477 (1%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQV 82
           FI  E+      +      P++E  +  +  + +  +D AV AA  AF+  +WS   P  
Sbjct: 19  FIAGEWRDESGAERITVTDPASETVLGDIPCSSAATVDKAVRAARKAFNDPAWSNLAPME 78

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS- 140
           R  +L++LA L+++HAD LA IE+LDNGK +  S   DV L+A +    AGW  K+ G  
Sbjct: 79  REALLHRLAALVEQHADDLATIESLDNGKPIAFSSTLDVPLSAQWLHYFAGWPSKLSGRS 138

Query: 141 ---VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197
               ++   +H  YT R+P+GV G I+PWNFPL++A WKL P L  G T V+K AE TP 
Sbjct: 139 MHPAVQPTGSHHAYTLRQPVGVVGAIVPWNFPLVLAIWKLAPALAAGNTVVIKPAEQTPY 198

Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257
           S L LA LI+ AG PPGVVNVV G G T G  I  HP + K++FTGSTA G+H++ +AA 
Sbjct: 199 SLLKLAELIEAAGFPPGVVNVVLGDGRTTGQAIVDHPGVDKISFTGSTAVGKHLLTSAA- 257

Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317
           ++LK+VTLELGGKSP ++  DAD+++ I      +F N+G++C AG+R++     +D+I+
Sbjct: 258 NDLKRVTLELGGKSPTVILPDADLETAIPGAAQAVFVNSGQICFAGTRLFAPRKHFDRIL 317

Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGY 377
                AA+S  +G     ++ +G   SQ Q+D IL  ++ G K GA+   GG R   +GY
Sbjct: 318 EGVAEAAKSFPVGAGLDPNSMLGPVVSQQQMDSILGKVEAGVKAGASTFCGGGRLDREGY 377

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           F++PTI       +   R+EIFGPV+T T++  ++++IA+ANDSEYGL+A ++T++   A
Sbjct: 378 FLEPTILVTDDAQNPAYREEIFGPVLTATRYDELDDIIAMANDSEYGLSANLYTSHFGLA 437

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494
             ++ ++ +GT+W+NT     P +PFGG+ QSG GRE GE+   +YT+ K+V   L+
Sbjct: 438 HRLAAQLQAGTVWINTQLSPDPHIPFGGFKQSGWGRENGEDVFAHYTETKSVIASLA 494


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: 620
Number of extensions: 19
Number of successful extensions: 3
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: 494
Length adjustment: 34
Effective length of query: 461
Effective length of database: 460
Effective search space:   212060
Effective search space used:   212060
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