GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Desulfovibrio vulgaris Hildenborough

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  221 bits (562), Expect = 1e-61
 Identities = 147/468 (31%), Positives = 223/468 (47%), Gaps = 15/468 (3%)

Query: 14  YINGEWLDADNGQTIKVTNPAT-GEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKER 72
           YI G   D      I  TNPA   EV+ ++ + G  E   AI AA KA   WR  +  +R
Sbjct: 515 YIGGR--DVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADR 572

Query: 73  SAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIP 132
           +A LRR  ++  +   +L+     E GK   +A  ++     F+E++A E  R+      
Sbjct: 573 AAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRM 632

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192
           G  P +   +  QP G+ A I PWNFP A+    A  A+  G  ++ KP+S +      L
Sbjct: 633 GRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNL 692

Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK----- 247
            E+   AG+P GV +   G +  +G  L  +  +  + FTGS E+G ++ E+ AK     
Sbjct: 693 AEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQ 752

Query: 248 -DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306
              K+V  E+GG    I+ DDADLD+AV   + S +   GQ C   +R+ V D +YD F 
Sbjct: 753 RQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFI 812

Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL-IEGNF 365
           E+L  A + + IG   +     GP+ D      V ++I  A  +G  +L    L  EG +
Sbjct: 813 ERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCY 872

Query: 366 FEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVF 425
              TI+ D+     +A+EE FGP+  + R     E ++++N T F L    ++R    + 
Sbjct: 873 VPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLD 932

Query: 426 RVAEALEYGMVGINTGLISN--EVAPFGGIKASGLGREGSKYGIEDYL 471
           +       G + +N G      E  PFGG   SG+   GSK G  DYL
Sbjct: 933 KARREFRVGNLYLNKGSTGALVERQPFGGFAMSGV---GSKTGGPDYL 977


Lambda     K      H
   0.317    0.134    0.384 

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: 1041
Number of extensions: 63
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: 480
Length of database: 1006
Length adjustment: 39
Effective length of query: 441
Effective length of database: 967
Effective search space:   426447
Effective search space used:   426447
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 (21.6 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