GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Trichormus variabilis ATCC 29413

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::Q97UA1
         (478 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  355 bits (910), Expect = e-102
 Identities = 187/472 (39%), Positives = 278/472 (58%), Gaps = 9/472 (1%)

Query: 10  KWIKGSGEEYLDI-NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSIL 68
           +W+  + E  L+  NPA+K  ++A       DD   A+  A   +  W + PAP R   +
Sbjct: 14  QWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAPARAEYI 73

Query: 69  LKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADP 128
            + GEL+ Q  +E A L++ E GK + ++  +V    +   +      ++ G+T PS  P
Sbjct: 74  FRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRRLFGQTTPSEMP 133

Query: 129 NTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVL 188
           N    TV+ P+GV ALITPWNFP++IP WK  PAL  GNT ++KPA  TP    KL+E+ 
Sbjct: 134 NKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACATKLIEIF 193

Query: 189 SKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQL 248
           + AGLP GV+NLV G G E G  +V   NI  VSFTGS+  G  + +  G  ++  R+ L
Sbjct: 194 AAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHK--RVCL 251

Query: 249 ELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVK 308
           E+GGKNA  V + ADL LA + A+ G FG TGQ CTATSRLI+++D+  +F   L ER  
Sbjct: 252 EMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLRERTS 311

Query: 309 KWRVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIP----GKGYFLEP 363
           + R+G GTE + D+GP+++  Q ++  EY+   +  GAK++ GG I+      +GYF +P
Sbjct: 312 QLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQGYFFQP 371

Query: 364 TIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFV 423
           TI + VT  MR+ +EEIFGPV+++ E    +EAI ++N   YG ++ +   DI      +
Sbjct: 372 TILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRAFVAM 431

Query: 424 SRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
             +E G+  +N PT+G E+  PFGG K +G    +E G  AL+ + + K+VY
Sbjct: 432 RDIEVGITYINGPTIGAEVHLPFGGVKQTG-NGHREAGTTALDVFTEWKSVY 482


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: 625
Number of extensions: 27
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 Apr 09 2024. 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