GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Desulfovibrio vulgaris Hildenborough

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  234 bits (597), Expect = 1e-65
 Identities = 157/465 (33%), Positives = 238/465 (51%), Gaps = 15/465 (3%)

Query: 8   PMYIDGQFVTWRGDAWIDVVNPATEA-VISRIPDGQAEDARKAIDAAERAQPEWEALPAI 66
           P+YI G+ VT      I   NPA  A V++ I      +   AI AA++A   W      
Sbjct: 513 PLYIGGRDVTTAD--LIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPA 570

Query: 67  ERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEI 126
           +RA++LR+ +   R+R  E+SA  V E GK    A  +V    D+++Y A    R     
Sbjct: 571 DRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPR 630

Query: 127 IQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186
                PGE+  LF +  G+   I PWNFPF +     + A++TGN ++ KPS  +     
Sbjct: 631 RMGRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGY 690

Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK--- 243
             A++  E GLP GVFN   GR   +G  L  +P ++++  TGS+  G +I   AAK   
Sbjct: 691 NLAEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQP 750

Query: 244 ---NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300
                 +V  E+GGK   I+ DDADL+ AV  ++ S     GQ C+   RV V   IYD+
Sbjct: 751 GQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDR 810

Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG 360
           F+ RL +A  ++  G P+E     MGP+ +A   + V   +  A EEG RV      +  
Sbjct: 811 FIERLVKAASSIHIG-PSEDPSNYMGPVADATLQKNVSDYIRIAEEEG-RVLLKRTDLPA 868

Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420
           +G Y P T++ D+R E  I  EE FGPVL V+   T ++A+S+AN + + LT ++++++ 
Sbjct: 869 EGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSP 928

Query: 421 NVAMKAIKGLKFGETYINRENFEAM---QGFHAGWRKSGIGGADG 462
               KA +  + G  Y+N+ +  A+   Q F  G+  SG+G   G
Sbjct: 929 EHLDKARREFRVGNLYLNKGSTGALVERQPF-GGFAMSGVGSKTG 972



 Score = 29.3 bits (64), Expect = 7e-04
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 19  RGDAWIDVVNPATEAVISRIP-DGQAEDARKAIDAAERAQPEWEALPA---IERASW--L 72
           R D +   V+   EA +S    +  A+   + +DA  R Q +W+ALP    +E   W   
Sbjct: 137 RKDGFTFTVDLLGEATVSEEESEAYAQGYHEVVDAIAREQEKWKALPGNGPVEGFDWGAT 196

Query: 73  RKISAGIRERASEISALIVEEGGKIQ 98
            K++  I+  A    A  V+  G ++
Sbjct: 197 PKVNVSIKPSALYSQAKPVDVEGSVR 222


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: 1042
Number of extensions: 49
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 479
Length of database: 1006
Length adjustment: 39
Effective length of query: 440
Effective length of database: 967
Effective search space:   425480
Effective search space used:   425480
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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