GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Bacteroides thetaiotaomicron VPI-5482

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)

Query= BRENDA::P9WPZ5
         (397 letters)



>FitnessBrowser__Btheta:351943
          Length = 397

 Score =  162 bits (409), Expect = 2e-44
 Identities = 122/399 (30%), Positives = 197/399 (49%), Gaps = 30/399 (7%)

Query: 3   VSRLRPYATTVFAEMS--ALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60
           ++ L P AT   ++ S    A  I  +NL  G PD + P  + +AA+ AI    ++Y P 
Sbjct: 8   LNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFSRYSPV 67

Query: 61  PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120
           PG   LR AI  + ++  G++Y    ++    GA +++  A+L LV PG EV++  P++ 
Sbjct: 68  PGYPALRNAIVEKLKKENGLEYTA-AQISCANGAKQSVCNAILVLVNPGDEVIVPAPYWV 126

Query: 121 SYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATE 180
           SY  +V MA    V V    + + F +    L  A+TP+T+ALI+ SP NPTG+V S  E
Sbjct: 127 SYPEMVKMAEGTPVIVSAGIE-QDFKITPKQLEAAITPKTKALILCSPSNPTGSVYSKEE 185

Query: 181 LAAIAEI-AVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGW 239
           LA +A + A    +VVI DE+YEH+ +  A H  +A F  M ERT+ ++  +K +  TGW
Sbjct: 186 LAGLAAVLAKYPQVVVIADEIYEHINYIGA-HQSIAQFPEMKERTVIVNGVSKAYAMTGW 244

Query: 240 KIGWACGPAELIAGVRAAK-QYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRL 298
           +IG+  GP  ++      + QY S       + A A  + T++  V  ++ +   RRD +
Sbjct: 245 RIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAAYVGTQEP-VKEMQKAFERRRDLI 303

Query: 299 AAGLTEI-GFAVHDSYG--------TYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMS 349
                E+ GF V+   G        +YF          ++S +    L E   VA +  +
Sbjct: 304 VKLAKEVPGFEVNVPQGAFYLFPKCSYFFGKSNGERKIENSDDLAMYLLEDAHVACVGGT 363

Query: 350 AFCDPAAGQASQQADVWNHLVRFTFCKRDDTLDEAIRRL 388
           +F  P               +R ++   D+ + EAIRR+
Sbjct: 364 SFGAP-------------ECIRMSYATSDENIVEAIRRI 389


Lambda     K      H
   0.321    0.135    0.405 

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: 310
Number of extensions: 16
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: 397
Length of database: 397
Length adjustment: 31
Effective length of query: 366
Effective length of database: 366
Effective search space:   133956
Effective search space used:   133956
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 (21.9 bits)
S2: 50 (23.9 bits)

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