GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Pedobacter sp. GW460-11-11-14-LB5

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate CA265_RS18510 CA265_RS18510 acetylglutamate kinase

Query= curated2:A0RWW1
         (266 letters)



>FitnessBrowser__Pedo557:CA265_RS18510
          Length = 278

 Score =  119 bits (298), Expect = 7e-32
 Identities = 93/261 (35%), Positives = 136/261 (52%), Gaps = 29/261 (11%)

Query: 4   IKIGGSIVDS---LHPSAIPDIKKAAAGGVVLVHGGGKEVTKVCEQLGKEPRFVTSPGNI 60
           IKIGG+++D+   LH   +     A  G  +LVHGGGK  T++ E LG E + +      
Sbjct: 9   IKIGGNVIDNSENLHQFLLDFT--ALPGDKILVHGGGKIATELGESLGIEAKMIDG---- 62

Query: 61  KSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNAVGLSGIDGGLIRAERKSRLVIVNE 120
             R TD ET  I TMV +G INK +V  LQ  G NA+GLSG DG +IRA  K R VI   
Sbjct: 63  -RRITDIETLRIVTMVYAGLINKNMVAQLQAKGSNAIGLSGADGNVIRA--KKRPVITKT 119

Query: 121 RGRKQ------AIEGGYTGRI--TSVNSELLETLLGKGIVPVVSPIAMGNEYELLNVDGD 172
            G +        I+ G+ G +   +V+S  LE+LL  G+VPV+  I    + +LLN + D
Sbjct: 120 YGAESGPMAGAVIDYGFVGDLDENAVSSTTLESLLKAGLVPVLCAITHDGDTQLLNTNAD 179

Query: 173 RAAANIA---GATKSERILFVTDVDGLMM----DEKLVSRLSAAEAEEIRP--KIGPGME 223
             A+++A    A    R+++  +  G++     D  +V  + A E E ++    +  GM 
Sbjct: 180 TIASSVAVAMSALYETRLVYCFEKKGVLKNVNDDGSVVREIKADEFEGLKADGTVQGGMI 239

Query: 224 KKVLAATEALKMGVREAIIAR 244
            K+  A EA+K GV    I +
Sbjct: 240 PKLHNAFEAIKKGVSAVYIGK 260


Lambda     K      H
   0.316    0.135    0.370 

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: 168
Number of extensions: 9
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: 266
Length of database: 278
Length adjustment: 25
Effective length of query: 241
Effective length of database: 253
Effective search space:    60973
Effective search space used:    60973
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 (21.6 bits)
S2: 47 (22.7 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