GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas litoralis 2SM5

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_090272720.1 BLU11_RS07260 aldehyde dehydrogenase family protein

Query= BRENDA::Q97UA1
         (478 letters)



>NCBI__GCF_900105005.1:WP_090272720.1
          Length = 483

 Score =  335 bits (859), Expect = 2e-96
 Identities = 183/457 (40%), Positives = 266/457 (58%), Gaps = 6/457 (1%)

Query: 23  NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEF 82
           NP++ + ++ +         ++AI  A      W RT    R  IL + G  + +  QE 
Sbjct: 28  NPSNAEEIVDRFARADAALTEKAIAAARDAAGSWGRTNPQVRADILDRIGSEILERRQEL 87

Query: 83  ALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVV 142
           A L++ EEGK +++++ EV R+    KFY     + +G+   S      +    +P+GVV
Sbjct: 88  AELLSREEGKVVREALGEVERAGRSFKFYAQEVLRANGEKYESVREGVSVDVFTQPIGVV 147

Query: 143 ALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVV 202
            +I+PWNFP++IP WK APALA GNT V+KPA   P     L E++S++G+P GV NLV+
Sbjct: 148 GIISPWNFPIAIPAWKAAPALAFGNTVVMKPAELVPSSAWALAEIISRSGMPAGVFNLVI 207

Query: 203 GKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSA 262
           G G  VGDTI+    + A++FTGS   G+++ ++     R+ R+QLE+GGKN L V   A
Sbjct: 208 GPGRTVGDTIIRSPKVDAITFTGSEGTGRQVAEIAA--QRLIRVQLEMGGKNPLVVLDDA 265

Query: 263 DLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDVDM 321
           DL +A E+A+ G F  TGQ CTA+SRLI+   ++ +F  RL ER +  RVG P   D D+
Sbjct: 266 DLDVAIEVALNGSFYSTGQRCTASSRLIVTTGIHDEFVARLAERTRALRVGDPLCADTDI 325

Query: 322 GPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG-KG-YFLEPTIFEGVTSDMRLFKEE 379
           GPVVD  Q K++L YIE G   GA LI GG  +   KG Y   P +F  V   MR+++EE
Sbjct: 326 GPVVDPSQLKQNLAYIESGLQEGATLICGGEYLENDKGAYHFSPALFVDVQPHMRIYREE 385

Query: 380 IFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVG 439
           IFGPVLSV +  + +EA++      Y  +AGIV + +K    F     AG++ VN PT G
Sbjct: 386 IFGPVLSVLKVANYEEALQAAEDTQYSLSAGIVTTSLKYAEHFKKHSSAGMVMVNLPTAG 445

Query: 440 LELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYE 476
           ++  APFGG + S     +E G  A +F+ + KT Y+
Sbjct: 446 VDYHAPFGGNRGSSLGP-REQGTYARQFFTRVKTAYQ 481


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: 529
Number of extensions: 21
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: 483
Length adjustment: 34
Effective length of query: 444
Effective length of database: 449
Effective search space:   199356
Effective search space used:   199356
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.

Links

Downloads

Related tools

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