GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Paraburkholderia bryophila 376MFSha3.1

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate H281DRAFT_04597 H281DRAFT_04597 2-keto-4-methylthiobutyrate aminotransferase apoenzyme

Query= BRENDA::P9WPZ5
         (397 letters)



>FitnessBrowser__Burk376:H281DRAFT_04597
          Length = 390

 Score =  278 bits (710), Expect = 3e-79
 Identities = 160/388 (41%), Positives = 222/388 (57%), Gaps = 12/388 (3%)

Query: 4   SRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGS 63
           SRL    TT+F  MSALA   GAVNLGQGFPD    P+++ A  +A+  G NQYPP  G+
Sbjct: 15  SRLPNVGTTIFTVMSALAAEKGAVNLGQGFPDFGCDPRIVDAVANAMRDGHNQYPPMAGA 74

Query: 64  APLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYS 123
           APLR AI+ +    +G  YD  TE+ VT GAT+A+  A+L  V PG EV++IEP YDSY 
Sbjct: 75  APLREAISDKIANVYGRRYDATTEITVTAGATQALLTAILCAVHPGDEVVVIEPTYDSYL 134

Query: 124 PVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAA 183
           P + +AG   V V L  D   +A+  D L  A+TP+TR L+IN+PHNPTG V  A ++  
Sbjct: 135 PSIELAGGKPVFVTL--DAPDYAIPFDKLAAAITPKTRLLLINTPHNPTGTVWRAEDMRK 192

Query: 184 IAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGW 243
           + EI    N+++++DEVYEH+V+D A H  +A +  +A+R+  +SS  K ++ TGWK+G+
Sbjct: 193 LEEIVRGTNVLILSDEVYEHMVYDGAPHESVARYPELAQRSFVVSSFGKTYHVTGWKVGY 252

Query: 244 ACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLT 303
              PA L A  R   Q+  +    P Q  +A  +  + A    L    +++RD   AGL 
Sbjct: 253 VAAPAALTAEFRKVHQFNVFTVNTPMQIGLAEYM-KDPAPYLELPAFYQSKRDFFRAGLA 311

Query: 304 EIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQA 363
              F +    GTYF C D   +      EF   L  ++GVAAIP+SAF   A        
Sbjct: 312 NSRFKLLPCTGTYFQCVDYSAISDLPEAEFAQWLTGEIGVAAIPVSAFYHEAHESG---- 367

Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRLSVL 391
                +VRF F K++ TL  A+ RL+ L
Sbjct: 368 -----VVRFCFAKQESTLATALERLARL 390


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: 400
Number of extensions: 19
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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