GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Streptomyces kebangsaanensis SUK12

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

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



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  322 bits (826), Expect = 1e-92
 Identities = 183/474 (38%), Positives = 274/474 (57%), Gaps = 14/474 (2%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           +I     +  S +T   V P+T EE+     A  +D+D AV AA  AF   W+ + P  R
Sbjct: 24  YIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAF-PGWAGATPGDR 82

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALT---AAYFRSCAGWTDKIKG 139
              L++ A+++ + A+  A  E+L  GK L  ++  DV  T   AA+F   AG    ++G
Sbjct: 83  SDALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFF---AGAARHLQG 139

Query: 140 -SVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198
            S  E    H +Y RREPIGV G I PWN+PL MA+WK+ P +  G T VLK AE TPL+
Sbjct: 140 QSAGEYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLT 199

Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAES 258
           +L  A    EAG P GV+N+V+G G  AG  +  HP +  V+FTGSTA G+ + + A  S
Sbjct: 200 SLLFAQAATEAGIPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATAS 259

Query: 259 NLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVS 318
            +K++ LELGGK+P +VFDDAD+++ +   V G   NTG+ C A +R YVQ  +Y++ V+
Sbjct: 260 -VKRLHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVA 318

Query: 319 EFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK--- 375
                 E++++GDPF   T +G   S +  D++  ++D  +   A V+TGGE    +   
Sbjct: 319 RTAALMETVRLGDPFAPGTDLGPLISHVHRDRVAGFVDRARAY-ARVVTGGEAPQGELKN 377

Query: 376 GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLS 435
           G + +PT+     +D +IV+ EIFGPV+ +  F + +E I LAND+ YGLAA   + ++ 
Sbjct: 378 GAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVY 437

Query: 436 TAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
            A   + +I +G +WVN +      +P GG  QSG G++M   + + YTQ+K V
Sbjct: 438 RANRATREIKAGCVWVNDHIPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHV 491


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: 636
Number of extensions: 34
Number of successful extensions: 5
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: 511
Length adjustment: 34
Effective length of query: 461
Effective length of database: 477
Effective search space:   219897
Effective search space used:   219897
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