GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Desulfovibrio vulgaris Miyazaki F

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  239 bits (610), Expect = 3e-67
 Identities = 162/465 (34%), Positives = 240/465 (51%), Gaps = 15/465 (3%)

Query: 8   PMYIDGQFVTWRGDAWIDVVNPATEA-VISRIPDGQAEDARKAIDAAERAQPEWEALPAI 66
           P++I G+ VT   D  I   NPA  A VI+R+  G   +   AI+AA++A P W      
Sbjct: 520 PLFIGGKDVTT--DDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPA 577

Query: 67  ERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEI 126
           +RA +L + +   R R  E+SA  V E GK    A  +V    D++DY A    R     
Sbjct: 578 DRAMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPR 637

Query: 127 IQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186
                PGE   LF +  G+   I PWNFPF +     A A++TGN ++ KPS        
Sbjct: 638 RMGRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGY 697

Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK--- 243
              +I  E GLP GVFN V GR   +G  L  +P+V+M+  TGS+  G +I   AAK   
Sbjct: 698 NLTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQP 757

Query: 244 ---NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300
                 +V  E+GGK   I+ DDADL+ AV  ++ S     GQ C+   RV V   IYD+
Sbjct: 758 GQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDR 817

Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG 360
           FV RL +A QA++ G P+E     MGP+ +A+  + + + V  A +EG +V      +  
Sbjct: 818 FVERLVKAAQAIKIG-PSEDPANYMGPVADASLQKNILEYVKVAEQEG-KVLVKRTDIPA 875

Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420
           +G Y P T++  ++    I  EE FGPVL V+     ++A+++AN + + LT  +++++ 
Sbjct: 876 EGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSP 935

Query: 421 NVAMKAIKGLKFGETYINRENFEAM---QGFHAGWRKSGIGGADG 462
               KA +  + G  Y+NR +  AM   Q F  G++ SG+G   G
Sbjct: 936 ENLTKARREFRVGNLYLNRGSTGAMVERQPF-GGFKMSGVGSKTG 979


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: 1113
Number of extensions: 56
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: 1013
Length adjustment: 39
Effective length of query: 440
Effective length of database: 974
Effective search space:   428560
Effective search space used:   428560
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