GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapC in Cupriavidus basilensis 4G11

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate RR42_RS05770 RR42_RS05770 aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS05770 RR42_RS05770
           aminotransferase
          Length = 395

 Score =  270 bits (690), Expect = 5e-77
 Identities = 157/388 (40%), Positives = 221/388 (56%), Gaps = 12/388 (3%)

Query: 4   SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63
           SRL    TT+F  MSALA    AVNLGQGFPD D  PK++ A   A+  G+NQYPP  G 
Sbjct: 20  SRLPKVGTTIFTVMSALAAERNAVNLGQGFPDFDCDPKIVDAVAHAMRSGLNQYPPMAGV 79

Query: 64  APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123
             LR+AIA +  + +G  YD ++E+ VT GAT+ I   +L  V PG EV+++EP YDSY 
Sbjct: 80  PKLRQAIAGKIGKLYGHAYDWDSEITVTAGATQGILTTILCAVHPGDEVIVLEPCYDSYI 139

Query: 124 PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAA 183
           P + MAG   V+V L  D   F +  D L  A+TPRTR L+IN+PHNPTG +  A ++  
Sbjct: 140 PAIEMAGGKVVSVAL--DAPHFHIPFDRLAAAITPRTRMLLINTPHNPTGTIWRAGDMDR 197

Query: 184 IAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGW 243
           +A +    ++++++DEVYEH+VFD   H  ++    +A R+  +SS  K ++ TGWK+G+
Sbjct: 198 LAGLLAGTDILLLSDEVYEHMVFDGQPHQSVSRHPELARRSFVVSSFGKTYHVTGWKVGY 257

Query: 244 ACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLT 303
              PA L A  R   Q+  +    P Q  +A  +  + A    L    +A+RD   AGL 
Sbjct: 258 VAAPAALSAEFRKVHQFNVFTVNTPVQHGLADYM-ADPAPYLDLAAFYQAKRDFFRAGLA 316

Query: 304 EIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQA 363
              F +  S GTYF C D   +      +F   L  ++GVAAIP+SAF        SQ  
Sbjct: 317 ATRFKLLPSDGTYFQCVDYSAISDMSEADFSMWLTREIGVAAIPVSAF-------YSQPR 369

Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRLSVL 391
           +  + +VRF F K+++TL  A+ RL  L
Sbjct: 370 E--SGVVRFCFAKKEETLALALARLKAL 395


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: 425
Number of extensions: 21
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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