GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:208821
          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.

Links

Downloads

Related tools

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