GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Verminephrobacter eiseniae EF01-2

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011811026.1 VEIS_RS16060 gamma-aminobutyraldehyde dehydrogenase

Query= metacyc::MONOMER-16246
         (477 letters)



>NCBI__GCF_000015565.1:WP_011811026.1
          Length = 477

 Score =  311 bits (798), Expect = 2e-89
 Identities = 186/463 (40%), Positives = 258/463 (55%), Gaps = 8/463 (1%)

Query: 11  YIDGAFVESAAHLE-VFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAG 69
           +IDG F++     E + NP+ G L+  V  AS  ++ RA+ AA  A   WA   A +RA 
Sbjct: 6   FIDGQFLQGEESAERILNPSTGELICEVREASPTQISRAVDAAHRAWPAWASTSAKDRAA 65

Query: 70  HLRRIAAKIRADAGRIARTITLEQGKI--ASLAEVEVNFTADYLDYMAEWARRLEGEIIA 127
            L ++A  I  +A  +A+   L  GK   A+LA+ E+   AD   + A   R +   +  
Sbjct: 66  MLLKVADHIEQNAAGLAQLEALNCGKPYQAALAD-EMPAIADVFRFFAGAVRCMTAPVAT 124

Query: 128 SDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEF 187
              PG    + R  LGVVA I PWN+P  + A K+ PA+ TGNTIV+KPSE+TP    + 
Sbjct: 125 EYLPGHTSMIRRDSLGVVASISPWNYPLMMAAWKICPAVATGNTIVLKPSEQTPLTTLKL 184

Query: 188 ARLVAETDLPRGVFNVVCGAGQVGGA-LSSHPGVDLISFTGSVETGARIMAAAAPNLTKL 246
           A  +A    P GV N+VCG G+  GA L + P V +IS TG V TG ++M AA   + + 
Sbjct: 185 AEFIASI-FPPGVINIVCGRGESAGATLIAQPQVRMISVTGDVSTGQKVMEAAVRGIKRT 243

Query: 247 NLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAA 306
           +LELGGKAP IV  DAD+   V  IR     N+GQ C  A RVY Q+ + +  +  +AAA
Sbjct: 244 HLELGGKAPVIVFDDADIGEVVAGIRTFGYYNAGQDCTAACRVYAQKGIYDKLVADLAAA 303

Query: 307 MAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQ-GATLVTGGAIAERPGHHYQP 365
           ++  R G+P  +  VEMGP I+     ++ A V  A  +    +V GG IA+R G  YQP
Sbjct: 304 VSTIRIGEP-GDVGVEMGPCISERQRSRVAAFVERAREEKHIKVVAGGKIADRRGFFYQP 362

Query: 366 TVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHAL 425
           T+L  C+    I+R+E+FGPV+ +    DLDE I LAND +YGL SSV++ D+ KAM   
Sbjct: 363 TLLANCKQSDEIVRKEVFGPVVSVTPFSDLDEVIGLANDSDYGLASSVWSSDVGKAMRVA 422

Query: 426 RELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYT 468
             L +G T+IN       +  H G++KSG G       L EYT
Sbjct: 423 AALHYGTTWINTHFMLVAEMPHGGMKKSGYGKDQSMFALEEYT 465


Lambda     K      H
   0.320    0.136    0.395 

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: 536
Number of extensions: 24
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: 477
Length of database: 477
Length adjustment: 33
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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