GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Desulfovibrio vulgaris Hildenborough

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>lcl|MicrobesOnline__882:208845 DVU3319 proline
           dehydrogenase/delta-1-pyrroline-5-carboxylate
           dehydrogenase
          Length = 1006

 Score =  232 bits (591), Expect = 6e-65
 Identities = 154/478 (32%), Positives = 235/478 (49%), Gaps = 25/478 (5%)

Query: 47  DAVSRKTFPTVNPST-GEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLL 105
           D  +    PT NP+   EV+  + +  + ++D A+ AA+ A      WR    + R   L
Sbjct: 520 DVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKA---ALTWRDTSPADRAAYL 576

Query: 106 NRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAG-----WADKYHGKT 160
            R AD+  +    L+A + ++ GK +  +Y  D+   +  L YYA       A +  G+ 
Sbjct: 577 RRAADICRKRIWELSAWQVVEVGKQWDQAYH-DVTEGIDFLEYYAREMLRLGAPRRMGRA 635

Query: 161 IPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALY 220
                  F    ++P G+   I PWNFP  +       A+ TGN V+ K +  +      
Sbjct: 636 PGEHNHLF----YQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYN 691

Query: 221 VANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQ-----VAAG 275
           +A + +EAG P GV N  PG     G  +  H D+  + FTGS E+G  IQ     V  G
Sbjct: 692 LAEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPG 751

Query: 276 SSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEF 335
               KRV  E+GGK+  II  DAD+D AV Q  ++ F  QGQ C A SR  V + IYD F
Sbjct: 752 QRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRF 811

Query: 336 VERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRG 395
           +ER V  A S  +G   D     GP  D T  K +  YI   ++EG  LL    + A+ G
Sbjct: 812 IERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLLKRTDLPAE-G 870

Query: 396 YFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDK 455
            ++  T+ GD++    IA+EEIFGPV+ +++  T +E +  AN + + L  AVF++  + 
Sbjct: 871 CYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSPEH 930

Query: 456 ANYLSQALQAGTVWVN--CYDVFGAQSPFGGYKMSGSGRELG--EYGLQAYTEVKTVT 509
            +   +  + G +++N         + PFGG+ MSG G + G  +Y LQ + + + VT
Sbjct: 931 LDKARREFRVGNLYLNKGSTGALVERQPFGGFAMSGVGSKTGGPDYLLQ-FMDPRVVT 987


Lambda     K      H
   0.319    0.136    0.409 

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: 1181
Number of extensions: 63
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: 517
Length of database: 1006
Length adjustment: 40
Effective length of query: 477
Effective length of database: 966
Effective search space:   460782
Effective search space used:   460782
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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