GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Desulfovibrio vulgaris Hildenborough

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= BRENDA::Q9CZS1
         (519 letters)



>lcl|MicrobesOnline__882:208821 DVU3294 aldehyde dehydrogenase
           (NADP) family protein
          Length = 464

 Score =  189 bits (481), Expect = 1e-52
 Identities = 146/463 (31%), Positives = 213/463 (46%), Gaps = 16/463 (3%)

Query: 60  NPTTGEVIGHVAEGDRADVDLAVKAAREAFRLGSPWRRMDASERGRLLNRLADLVERDRV 119
           NP     +G V     A+   A++ A      G P  R+ A ER  +L RLA L+     
Sbjct: 8   NPFDLSTVGEVPLMSEAEAFAALERAHALH--GDPAHRIPAHERLAILERLATLMRTHAE 65

Query: 120 YLASLETLDNGKPFQESYVLDLDEVIKVYRYFAGWADKWHGKTIPM-----DGEHFCFTR 174
            L      + GKP+ +S V++++  I   R+ A    +  G+ +PM           FT 
Sbjct: 66  ALVRDAVREGGKPWADS-VVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLAFTV 124

Query: 175 HEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAGFPP 234
            EP GV   I  +N P+ +   +  PA A G  V++K A  TPLS   +  L+ EAG P 
Sbjct: 125 REPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEAGVPE 184

Query: 235 GVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVG-HLIQKAAGESNLKRVTLELGGKSP 293
               ++     TA   +A    V  ++F GS+ VG HL  K A  +      LE GG +P
Sbjct: 185 AWATMLPCAAATAEKLVADPR-VAFLSFIGSSRVGWHLRSKLAPGATC---ALEHGGAAP 240

Query: 294 SIVLADADMEHAVDQCHEALFFNMGQCCCAGSRTFVEESIYREFLERTVEKAKQRKVGNP 353
            ++ A AD++ A+    +  F++ GQ C +  R F      R F ER    A Q   G+P
Sbjct: 241 VVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPTGDP 300

Query: 354 FELDTQQGPQVDKEQFERILGYIRLGQKEGAKLLCGGERLGERGFFIKPTVFGDVQDGMR 413
              DT  GP +D  +  R+  ++   +  G  +LCGG  L E      PTV  D   G R
Sbjct: 301 MRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSET--LYSPTVVYDPPQGCR 358

Query: 414 IAKEEIFGPVQPLFKFKKIEEVIQRANNTRYGLAAAVFTRDLDKAIYFTQALQAGTVWVN 473
           +A+ E+FGPV  +F  +  +E I RAN+  +   AAVF RD+D A+   + L A  V VN
Sbjct: 359 LARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVMVN 418

Query: 474 TYNIVTCH-TPFGGFKESGNGRELGEDGLRAYTEVKTVTIKVP 515
            +        PFGG  ESG G       +   T  K + ++ P
Sbjct: 419 DHTAFRVDWMPFGGRGESGMGTGGIGPAMHEMTTEKLIVLRSP 461


Lambda     K      H
   0.320    0.137    0.416 

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: 522
Number of extensions: 28
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: 519
Length of database: 464
Length adjustment: 34
Effective length of query: 485
Effective length of database: 430
Effective search space:   208550
Effective search space used:   208550
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: 52 (24.6 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