GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Verminephrobacter eiseniae EF01-2

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011812184.1 VEIS_RS21780 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000015565.1:WP_011812184.1
          Length = 496

 Score =  335 bits (859), Expect = 2e-96
 Identities = 192/473 (40%), Positives = 282/473 (59%), Gaps = 12/473 (2%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI+G Y A A +   E+ DP +    A+ A G  V++D A+ AA+       WS ++PA+
Sbjct: 26  FIDGAYQAGATSAALESFDPGSGRVFAQFAAGGEVEVDAAVHAAKRALPA--WSETAPAE 83

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  VL  +A  +  HA+ LAL+E LD+GK +  + + D+ G  RA  +YA A+DK+ G+ 
Sbjct: 84  RSRVLWAIAQQVRQHADRLALIECLDSGKRLGEA-QGDVRGVIRAFEYYAGAVDKMQGDS 142

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
                  +   V EP+GV A I+PWN+P+      + PALAAG +V+ KP+E++PLSA+ 
Sbjct: 143 FPLGKDYIGFTVEEPIGVAAQIIPWNYPVGTAARGIAPALAAGCTVVAKPAEQTPLSALL 202

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           LA LA  AGLP GVLNVVTG G  AG AL  H  I  I FTGS  TG+++++ A D N+ 
Sbjct: 203 LAELASAAGLPAGVLNVVTGTGAAAGAALVAHPGIGHITFTGSVATGQRVMRAAAD-NVT 261

Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322
           RV LE GGKS  +V ADC D++QA       I+ N GQ+C AG+RL++E  +   F+A L
Sbjct: 262 RVLLELGGKSPLVVLADC-DVEQALDGVLGAIYENAGQICSAGSRLIIERKLHGSFMARL 320

Query: 323 KQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN-AGLAAAIG- 380
            ++      GH LD    +G +    H + +H  +    ++G  +L G + A  A A G 
Sbjct: 321 LERVGKLGLGHGLD-QPDVGPVNSLLHLNRIHEHVATAAARGNAVLAGGSIAQPANAPGG 379

Query: 381 ----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSR 436
               PT+         + +EEIFGPVLVV +    EQA+ LAN + Y L A ++TRD+++
Sbjct: 380 WFYRPTVIEARSAQDPVVQEEIFGPVLVVQQADDLEQAIALANGTDYALVAGIYTRDITQ 439

Query: 437 AHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489
           A+R +RR+ AG V++N Y  G + VPFGG ++SG GR+K L  ++ + +LK++
Sbjct: 440 AYRFARRVDAGQVYINEYFAGGIEVPFGGNRKSGFGREKGLEGIKSYCKLKSV 492


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: 600
Number of extensions: 25
Number of successful extensions: 6
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: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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