GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Desulfobacter vibrioformis DSM 8776

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  317 bits (813), Expect = 4e-91
 Identities = 166/462 (35%), Positives = 270/462 (58%), Gaps = 1/462 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +I  ++V       +DV NPAT  ++  +P   A++ ++AI+AA  +   W +  A ER+
Sbjct: 15  FIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERS 74

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + LRK    + E   +++ ++  E GK    +  E+A+ A + ++ AE A+R  G++I  
Sbjct: 75  AILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVYGDVIPQ 134

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
               + +++ K+ +GV   I PWNFP  +I RK   AL  G T+V+KP+  TP +A+A A
Sbjct: 135 TVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIA 194

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
           K+  + G+P+GVFN+V G    +G EL  NP V  ++ TGS   G+K+M   A  + ++ 
Sbjct: 195 KLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMKRLS 254

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           +ELGG AP IV DDAD++ AV+  +  +  NSGQ C CA R+YVQ G+YD+F  +L  A+
Sbjct: 255 MELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLTAAV 314

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
           Q ++ GN  + + +  GPLI+ AA+E VE  +  AV++G +V  GG        ++ PT+
Sbjct: 315 QELKVGNGFD-DGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHALGRTFFAPTI 373

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           + DV  +M +  EETFGP+ PV  FDT E+ +  AND+++GL +  YT+++  + +  + 
Sbjct: 374 IADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDMARSWRIGEK 433

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471
           L++G   IN            G ++SG G    K+GL +YL+
Sbjct: 434 LEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLE 475


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: 540
Number of extensions: 24
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: 484
Length adjustment: 34
Effective length of query: 445
Effective length of database: 450
Effective search space:   200250
Effective search space used:   200250
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 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