GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Desulfovibrio vulgaris Miyazaki F

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  229 bits (585), Expect = 3e-64
 Identities = 151/468 (32%), Positives = 230/468 (49%), Gaps = 15/468 (3%)

Query: 14  FIDGAWVDADNGQTIKVNNPAT-GEILGTVPKMGAAETRRAIEAADKALPAWRALTAKER 72
           FI G  V  D+  TI   NPA   E++  V + G  E   AIEAA KA PAWR  +  +R
Sbjct: 522 FIGGKDVTTDD--TIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADR 579

Query: 73  ATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIP 132
           A  L R  ++      +L+    LE GK   +A  ++     F++++A E  R+      
Sbjct: 580 AMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRM 639

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFAL 192
           G  P +   +  QP G+ A I PWNFP A+    A  A+  G  ++ KP+S      + L
Sbjct: 640 GRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNL 699

Query: 193 AELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK----- 247
            E+ + AG+P GVF+ V G +  +G  L  +P V  + FTGS E+G ++  + AK     
Sbjct: 700 TEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQ 759

Query: 248 -DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFA 306
              K+V  E+GG    I+ DDADLD+AV   + S +   GQ C   +R+ + D +YD F 
Sbjct: 760 MQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFV 819

Query: 307 EKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGK-PMEGNF 365
           E+L  A   +KIG   +     GP+ D      + E++  A  +G  ++     P EG +
Sbjct: 820 ERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCY 879

Query: 366 FEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVF 425
              TI+  +  +  +A+EE FGP+  + R  +  + +A++N T F L    ++R    + 
Sbjct: 880 VPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLT 939

Query: 426 RVAEALEYGMVGVNTGLISN--EVAPFGGIKASGLGREGSKYGIEDYL 471
           +       G + +N G      E  PFGG K SG+   GSK G  DYL
Sbjct: 940 KARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGV---GSKTGGPDYL 984


Lambda     K      H
   0.317    0.135    0.390 

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: 54
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: 480
Length of database: 1013
Length adjustment: 39
Effective length of query: 441
Effective length of database: 974
Effective search space:   429534
Effective search space used:   429534
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