GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Phaeobacter inhibens BS107

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate GFF769 PGA1_c07830 acetylornithine deacetylase ArgE

Query= curated2:Q2P492
         (376 letters)



>FitnessBrowser__Phaeo:GFF769
          Length = 384

 Score =  101 bits (252), Expect = 3e-26
 Identities = 113/398 (28%), Positives = 178/398 (44%), Gaps = 42/398 (10%)

Query: 1   MNDVLDLTCDLIARASVTPE-DAGCQALLAGRLTAAGFACEHL--RLGEVDNLWATHGSG 57
           M     +  DLIA  +V+ + +    A LA RL   G   + +    G+  NL+AT G  
Sbjct: 2   MEQTTRILSDLIAYPTVSADSNLEMIAYLANRLEDCGARVDVMFDAGGQKANLFATLGPD 61

Query: 58  APV-LVLLGHTDVVPPGPREAWTSDPFDPQIRDGVLYGRGVADMKGSVAAFVVAAEQFVA 116
               +VL GH+DVVP   ++ WTSDPF  +  DG LYGRG  DMKG +AA +  A +F  
Sbjct: 62  TDGGIVLSGHSDVVPVTDQD-WTSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKF-- 118

Query: 117 AHRAHAGTLAVLLTSDEEGDAIDGVRRVANLFLERGQAIDWCITGEPSSTERLGDLLRV- 175
           A +     +    T DEE   I G   +     ERG      + GEP+S       +RV 
Sbjct: 119 AEQISRRPIHFAFTYDEEVGCI-GAGHLVQALRERGLKPRLALIGEPTS-------MRVV 170

Query: 176 -GRRGSLSGTLTVKGVQGHVAYPHKARNPIHLAAPALAELVARQWD-------DGFESFP 227
            G +G    +   +G++GH + P +  N +  AA  ++ L+  + D       D     P
Sbjct: 171 EGHKGCHEYSTRFQGLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQRTPPDSRFDPP 230

Query: 228 PTSLQVSNIHAGTGANNVIPGELQVAFNLRYTPHWDAPRLEAEITALLDRHALDYALRWH 287
            T+L +  ++ G+ A+NVI  + QV + +R     DA  ++  +     R+  D  L   
Sbjct: 231 WTTLNIGALNGGS-AHNVIASKAQVDWEMRPVQPSDADHVKDTMA----RYCRDTLLPAM 285

Query: 288 RSGEPFYTPEGRL-----------RSVAREVLGAFAGAPPEESTGGGTSDARFIAPLGAQ 336
           ++  P  + E  +           ++ ARE++    G+   E    GT +A     LG  
Sbjct: 286 QAIYPEASIETEVVGEVAGLTPTTQNEARELMADLLGSNAAELVPFGT-EAGLFQELGMD 344

Query: 337 CIEVGPVN-ASIHQVDEHVRVADLQALPALYRTLIERL 373
            +  GP + A  H+ DE++ +  L     +   L  RL
Sbjct: 345 VVVCGPGSIAQAHKADEYLSLDQLSQCLTVLNRLAGRL 382


Lambda     K      H
   0.319    0.137    0.417 

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: 370
Number of extensions: 19
Number of successful extensions: 2
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: 376
Length of database: 384
Length adjustment: 30
Effective length of query: 346
Effective length of database: 354
Effective search space:   122484
Effective search space used:   122484
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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