GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Amycolatopsis halophila YIM 93223

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  287 bits (734), Expect = 7e-82
 Identities = 170/475 (35%), Positives = 258/475 (54%), Gaps = 8/475 (1%)

Query: 9   MYIDGQFVTWRGDAWIDVV-NPATEAVISRIPDGQAEDARKAIDAAERAQPE--WEALPA 65
           ++IDG++V   G A   VV NPA  A ++ + +   +D   A+ AA RA  +  W A  A
Sbjct: 4   LFIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTA 63

Query: 66  IERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGE 125
            ER   LR+I+  ++     ++     + GK      V+V        Y A  A    G 
Sbjct: 64  RERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAGR 123

Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185
           ++ +        +    +GV + I PWN+P   ++ K+APAL  GNT+V+KPSE TP   
Sbjct: 124 VVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLTT 183

Query: 186 IAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNI 245
           I   ++V+E G+P GV NLVLG G  VG  +  +P V +VS TG +  G+KIMA AA+ +
Sbjct: 184 IELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEGV 243

Query: 246 TKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRL 305
            +V LELGGK P +V  DAD + AV   + +   +SGQVC+   R+ V+  I+D+FV  L
Sbjct: 244 KRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAEL 303

Query: 306 GEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG----KAVEGK 361
                A++ G+  +      GPL +A   ++VE+ +  A  EGAR+  GG    +     
Sbjct: 304 ARRADAIRLGDGLD-PATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELAD 362

Query: 362 GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLN 421
           GY+  PT+  D  +EM I+ +E FGPV+ V  FDT ++AI +AND++YGL  +++T + +
Sbjct: 363 GYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDAS 422

Query: 422 VAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVY 476
            A +    L+ G  +IN  +    Q    G+ KSGIG   G  GL EY +T+ +Y
Sbjct: 423 RAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHIY 477


Lambda     K      H
   0.318    0.135    0.392 

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: 551
Number of extensions: 22
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: 479
Length of database: 496
Length adjustment: 34
Effective length of query: 445
Effective length of database: 462
Effective search space:   205590
Effective search space used:   205590
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 (21.7 bits)
S2: 52 (24.6 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