GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Desulfovibrio vulgaris Hildenborough

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= BRENDA::P23883
         (495 letters)



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

 Score =  171 bits (432), Expect = 7e-47
 Identities = 135/424 (31%), Positives = 197/424 (46%), Gaps = 12/424 (2%)

Query: 73  GDWSLSSPA-KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWY 131
           GD +   PA +R A+L +LA LM  HAE L      + GKP   S+ + +  A   +RW 
Sbjct: 38  GDPAHRIPAHERLAILERLATLMRTHAEALVRDAVREGGKPWADSVVE-VERAIDGVRWA 96

Query: 132 AEAIDKVYGE-----VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186
           A  + ++ G      +   S+  LA  VREP GV+ AI  +N P+ L   +  PA AAG 
Sbjct: 97  ARELAQLGGREVPMGLTPASAGRLAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGC 156

Query: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246
            V++KP+  +PLS   +  L  EAG+P+    ++      A + L     +  ++F GS+
Sbjct: 157 PVLVKPASATPLSCRNVLRLMHEAGVPEAWATMLPCAAATA-EKLVADPRVAFLSFIGSS 215

Query: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306
           R G  L             LE GG +A +V     DL  A      G FY+ GQVC++  
Sbjct: 216 RVGWHLRSKLAPG--ATCALEHGG-AAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQ 272

Query: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366
           R+      A  F   L   A     G P+   T +G LID      VH ++ E  + G  
Sbjct: 273 RVFAPHETARTFAERLAAAAAQLPTGDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGT 332

Query: 367 LLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLG 426
           +L G          PT+  D      L+R E+FGPV+ V      ++A+  AND  +   
Sbjct: 333 VLCGGAPLSETLYSPTVVYDPPQGCRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQ 392

Query: 427 AAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMT-VPFGGYKQSGNGRDKSLHALEKFTE 485
           AAV+ RD+  A   +RRL A  V VN++    +  +PFGG  +SG G      A+ + T 
Sbjct: 393 AAVFARDVDVALDTARRLNATGVMVNDHTAFRVDWMPFGGRGESGMGTGGIGPAMHEMTT 452

Query: 486 LKTI 489
            K I
Sbjct: 453 EKLI 456


Lambda     K      H
   0.317    0.133    0.389 

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: 545
Number of extensions: 28
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: 495
Length of database: 464
Length adjustment: 34
Effective length of query: 461
Effective length of database: 430
Effective search space:   198230
Effective search space used:   198230
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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