GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Erythrobacter marinus HWDM-33

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_047092763.1 AAV99_RS05185 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_001013305.1:WP_047092763.1
          Length = 459

 Score =  228 bits (580), Expect = 4e-64
 Identities = 147/458 (32%), Positives = 235/458 (51%), Gaps = 7/458 (1%)

Query: 24  IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83
           I   NPAT   ++       ++A   I+ A+ A  +W      ERA +LR+I+  +R  +
Sbjct: 4   IQTCNPATGETLATYDLMSEQEAFGKIEHAQSAFLDWREKSHEERAEYLRQIAKVLRGNS 63

Query: 84  SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEW--ARRYEGEIIQSDRPGENILLFKR 141
             IS L+  E GK+ +    EV   A   +Y AE   A   + E   S      I+ F  
Sbjct: 64  DRISQLMTREMGKLLRDGATEVELCAGIFEYTAENGPAELADQEREYSGGEKRGIVSFA- 122

Query: 142 ALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGV 201
            +G+   + PWNFP +  AR +A  L+ GN +++K +     + +    +  E GLP G+
Sbjct: 123 PIGIIYSVQPWNFPLYQPARVLAANLMAGNAVILKHASICTGSGLLLRDLCLEAGLPAGL 182

Query: 202 FNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVM 261
           F++VL  G  +  ++  +  +  V+MTGS  AG  I   AAKN+ K  LELG     +V+
Sbjct: 183 FDVVLV-GHDLSDKIIEHKLIRAVTMTGSDGAGSHIGELAAKNLKKTVLELGSNDAYLVL 241

Query: 262 DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERN 321
            DAD+ELAVK  V  R+ N+G+ C  A+R  V   +YD FV+   + M+A + G+P +  
Sbjct: 242 ADADIELAVKTCVQGRLYNNGETCVSAKRFVVVDAVYDAFVSAFVDQMKATKMGDPND-E 300

Query: 322 DIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGK-GYYYPPTLLLDVRQEMSIM 380
           D  +GP+ +    + + ++V ++V+ GA +  GG   EG+ G+YYP T+L D +      
Sbjct: 301 DTQLGPVSSKEQFDTLVEQVGKSVDGGATLLCGGDPEEGREGFYYPATVLADCKPGTPAY 360

Query: 381 HEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG-LKFGETYINR 439
            +E FGPV  V+     EDA+ +ANDS YGL   I++++ + A+K  +     G   IN 
Sbjct: 361 DDELFGPVASVIRAKDDEDAMRIANDSRYGLGGGIFSKDEDKAIKLARDHFDTGMVRINS 420

Query: 440 ENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
                      G + SG G   G  G+ E++ T+ ++L
Sbjct: 421 FGAADPNMPFGGVKDSGYGREHGGFGMKEFVNTKAIFL 458


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: 521
Number of extensions: 35
Number of successful extensions: 5
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: 459
Length adjustment: 33
Effective length of query: 446
Effective length of database: 426
Effective search space:   189996
Effective search space used:   189996
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: 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