GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Desulfovibrio vulgaris Hildenborough

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= BRENDA::Q97XA5
         (470 letters)



>MicrobesOnline__882:208821
          Length = 464

 Score =  245 bits (626), Expect = 2e-69
 Identities = 151/462 (32%), Positives = 250/462 (54%), Gaps = 8/462 (1%)

Query: 7   IEVRSPSNLKVIGTVKRMSKDEVRGEIEEAYKGF-EIISRMPLYKRTAILRKISEILERE 65
           I VR+P +L  +G V  MS+ E    +E A+    +   R+P ++R AIL +++ ++   
Sbjct: 4   ITVRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHRIPAHERLAILERLATLMRTH 63

Query: 66  QERLARLLAMEAGKPISDSRVEVLRASRLFRQAAEEVGIVLEGKNYRVDAYEYPPGNENR 125
            E L R    E GKP +DS VEV RA    R AA E+   L G+   +      P +  R
Sbjct: 64  AEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELA-QLGGREVPMGL---TPASAGR 119

Query: 126 IVLSTREPIGVVTAILPFNFPINSFAHKVAPALAVGNSVVVKPSINTPLAAVEMKKILVE 185
           +  + REP GVV AI  FN P+N   H+  PA A G  V+VKP+  TPL+   + +++ E
Sbjct: 120 LAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHE 179

Query: 186 AGLPDSAVRVVTGYSSEIGDEIITHPLVGLITLTGSTQTGLKIASKAISLGKRIIMELGG 245
           AG+P++   ++   ++   ++++  P V  ++  GS++ G  + SK ++ G    +E GG
Sbjct: 180 AGVPEAWATMLP-CAAATAEKLVADPRVAFLSFIGSSRVGWHLRSK-LAPGATCALEHGG 237

Query: 246 SDPIIILEDANIERASSIAVRARFEYAGQNCNAGKRIIVRQEVYDKFVKAFNEKAKALKV 305
           + P+++   A+++ A  + ++  F +AGQ C + +R+    E    F +     A  L  
Sbjct: 238 AAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPT 297

Query: 306 GEPLDETTDVGPVINKESVENLNSVLEDAKVKGGRVEILNRGPESGSFFPLTMVTNPSLD 365
           G+P+   T VGP+I+   V  ++  +E+A+  GG V +    P S + +  T+V +P   
Sbjct: 298 GDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTV-LCGGAPLSETLYSPTVVYDPPQG 356

Query: 366 MLVLKSEVFGPIVPIVSVKSDEEAIRIANSTEYGLQSAIFTNDVNRALKLSRELKFGAVI 425
             + ++EVFGP+V + S +  +EAI  AN   +  Q+A+F  DV+ AL  +R L    V+
Sbjct: 357 CRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVM 416

Query: 426 INDSTRLRWDSLPFGGFKKTGIGREGVRETMLEMTENKLIAI 467
           +ND T  R D +PFGG  ++G+G  G+   M EMT  KLI +
Sbjct: 417 VNDHTAFRVDWMPFGGRGESGMGTGGIGPAMHEMTTEKLIVL 458


Lambda     K      H
   0.316    0.135    0.366 

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: 403
Number of extensions: 14
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: 470
Length of database: 464
Length adjustment: 33
Effective length of query: 437
Effective length of database: 431
Effective search space:   188347
Effective search space used:   188347
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