GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Lentibacillus jeotgali Grbi

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_010529654.1 ON01_RS03650 aldehyde dehydrogenase family protein

Query= BRENDA::Q97UA1
         (478 letters)



>NCBI__GCF_000224785.1:WP_010529654.1
          Length = 498

 Score =  338 bits (868), Expect = 2e-97
 Identities = 178/471 (37%), Positives = 287/471 (60%), Gaps = 10/471 (2%)

Query: 10  KWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILL 69
           +W++ S E    INPA+ D ++  + L     V  A+  A     EW+  PAP+R  +L 
Sbjct: 18  EWVETS-ESTRVINPANGDTIV-NVPLSDSGAVNNAVEGAKKAQKEWALVPAPQRAEVLF 75

Query: 70  KAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPN 129
           K G++M++  +  + L+T+E GK L+++  EV    ++  +      ++ G T P+  PN
Sbjct: 76  KVGQMMKERKERLSQLLTMENGKVLEEARGEVQEGIDMAFYMAGEGRRLFGHTTPAELPN 135

Query: 130 TRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLS 189
               + + P+GVV +ITPWNFP++I  WK  PA+ AGN  + KPAT+TP+M  +L ++L 
Sbjct: 136 KFSMSQRAPVGVVGIITPWNFPIAIATWKSFPAIVAGNAVIWKPATETPIMAYELAKILE 195

Query: 190 KAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLE 249
           +AGLP+G++N+V GKGS+VGD +V   +I  +SFTGS + G+ I    G   ++ ++ LE
Sbjct: 196 EAGLPKGIMNVVYGKGSQVGDAMVHHADIKVISFTGSNDTGRHIASECG--RQLKKVSLE 253

Query: 250 LGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKK 309
           +GGKNA+ V   ADL LA E  +   +G +GQ CTA SR+I+++DV  Q ++RLL  ++K
Sbjct: 254 MGGKNAITVMDDADLDLAVEGILWSAYGTSGQRCTAASRVIVHEDVKEQLEERLLVEIEK 313

Query: 310 WRVGPGTEDVD-MGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII-PGK---GYFLEPT 364
             +G G ++ + +GP++++   +K  +YI+ GK  GA LI GG ++  GK   G++  PT
Sbjct: 314 LTIGDGLDESNTVGPIINKAGLEKIEKYIQIGKEEGANLIAGGYVLDDGKYTNGHYFAPT 373

Query: 365 IFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVS 424
           +F   T+DMR+ +EEIFGPV+S+   K  +EAI + N V YG ++ I  +D   + +   
Sbjct: 374 LFTDCTADMRISQEEIFGPVISLIPVKSFEEAIEVNNGVSYGLSSSIFTTDANRVFKAQR 433

Query: 425 RVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
            ++ G++ VN  T G E+  PFGG K +G    ++ G  AL+ + + K VY
Sbjct: 434 DLDTGIVYVNAGTTGAEIHLPFGGTKGTG-NGHRDSGVQALDVFTEWKAVY 483


Lambda     K      H
   0.316    0.135    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: 687
Number of extensions: 33
Number of successful extensions: 4
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: 478
Length of database: 498
Length adjustment: 34
Effective length of query: 444
Effective length of database: 464
Effective search space:   206016
Effective search space used:   206016
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