GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Leeuwenhoekiella blandensis MED217

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_009780586.1 MED217_RS10945 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q97UA1
         (478 letters)



>NCBI__GCF_000152985.1:WP_009780586.1
          Length = 452

 Score =  227 bits (578), Expect = 7e-64
 Identities = 149/456 (32%), Positives = 245/456 (53%), Gaps = 14/456 (3%)

Query: 22  INPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQE 81
           INP  K+HV    +L TK +  EAI  A  +F  W +T   +R S++  A + ++   ++
Sbjct: 5   INPYTKEHVFQNKQL-TKAEAVEAIEVAYERFLSWRKTTFAERASLMRAAADELKTNKED 63

Query: 82  FALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALA-FKISGKTLPSADPNTRIFTVKEPLG 140
           +A  +TLE GK +K ++ EV +   + ++Y   A  +++ KT+ +    T  +   EPLG
Sbjct: 64  YATTITLEMGKPIKQAVAEVEKCAWVCEYYAQNAQTQLAPKTITT--DATESYVSYEPLG 121

Query: 141 VVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNL 200
           VV  + PWN+P        APAL AGN A++K A+        +  V  +AG P+     
Sbjct: 122 VVLAVMPWNYPFWQVFRFAAPALMAGNVALLKHASNVMESAMNIQRVFERAGFPKSCFTN 181

Query: 201 VVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDK 260
           +  +  ++ + I+ +  + AV+ TGS   G  +    G++  + +  LELGG NAL V +
Sbjct: 182 LPLRSDKI-EGIIKNPRVKAVTLTGSKPAGSAVAATAGSE--IKKSVLELGGSNALVVFE 238

Query: 261 SADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDV 319
             ++    + AV+  F  TGQSC A  RL+++KD+  +F Q+ + +VK+ + G P  E+ 
Sbjct: 239 DCNMDETIKTAVQARFQNTGQSCIAGKRLLLHKDIAEEFTQKFVAKVKELQSGDPMDENT 298

Query: 320 DMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTIFEGVTSDMRLFKEE 379
            +G +  E   ++  E ++     GAK++ GG     K YF EPT+   VT+ M LFKEE
Sbjct: 299 FIGVMAREDLAEELEEQLKSSVRQGAKILTGGT--RKKAYF-EPTVVTNVTTKMALFKEE 355

Query: 380 IFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVG 439
            FGPV+ +T  K+ DEAI L N  D+G    +   D +   + V   + G + +N+  V 
Sbjct: 356 TFGPVIGITTFKNEDEAIHLANYTDFGLGVSVFTEDKERARKLVPLFDDGAVFINE-LVK 414

Query: 440 LELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
            + + PFGG K SG    +E+ ED ++ ++ +KTVY
Sbjct: 415 SDPRLPFGGTKISG--YGRELSEDGIKEFVNKKTVY 448


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: 508
Number of extensions: 30
Number of successful extensions: 6
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: 452
Length adjustment: 33
Effective length of query: 445
Effective length of database: 419
Effective search space:   186455
Effective search space used:   186455
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: 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