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 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= BRENDA::Q88RC0
         (480 letters)



>MicrobesOnline__882:208821
          Length = 464

 Score =  226 bits (576), Expect = 1e-63
 Identities = 152/443 (34%), Positives = 224/443 (50%), Gaps = 10/443 (2%)

Query: 27  TIKVTNPATGEVIGTVPKMGTAETRRAIEAADKAL--PAWRALTAKERSAKLRRWFELMI 84
           +I V NP     +G VP M  AE   A+E A      PA R + A ER A L R   LM 
Sbjct: 3   SITVRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHR-IPAHERLAILERLATLMR 61

Query: 85  ENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIP-GHQP---DKRL 140
            + + L R    E GKP A++  E+  A   + W A E  ++ G  +P G  P    +  
Sbjct: 62  THAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLA 121

Query: 141 IVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAG 200
             +++P GV  AI+ +N P  +I  +A PA AAGC +++KPAS TP S   ++ L H AG
Sbjct: 122 FTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEAG 181

Query: 201 IPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNA 260
           +P    +++  +A     +L  +  V  LSF GS+ +G  L  + A      +LE GG A
Sbjct: 182 VPEAWATMLPCAAA-TAEKLVADPRVAFLSFIGSSRVGWHLRSKLAPGAT-CALEHGGAA 239

Query: 261 PFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGN 320
           P ++   ADLD A+   +   + + GQ CV   R++        FAE+LAAA A+L  G+
Sbjct: 240 PVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPTGD 299

Query: 321 GLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGNFFEPTILVDVPKTAAV 380
            +   T  GPLID + V++V E +E+A + G  VL GG  +    + PT++ D P+   +
Sbjct: 300 PMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSETLYSPTVVYDPPQGCRL 359

Query: 381 AKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGINT 440
           A+ E FGP+  +F  +D  E IA +ND  F   +  +ARD+      A  L    V +N 
Sbjct: 360 ARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVMVND 419

Query: 441 GLISN-EVAPFGGIKASGLGREG 462
                 +  PFGG   SG+G  G
Sbjct: 420 HTAFRVDWMPFGGRGESGMGTGG 442


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: 484
Number of extensions: 25
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: 464
Length adjustment: 33
Effective length of query: 447
Effective length of database: 431
Effective search space:   192657
Effective search space used:   192657
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: 51 (24.3 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