GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Dyella japonica UNC79MFTsu3.2

Align fused aspartate kinase/homoserine dehydrogenase 1 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate N515DRAFT_4002 N515DRAFT_4002 aspartate kinase

Query= ecocyc::ASPKINIHOMOSERDEHYDROGI-MONOMER
         (820 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4002
          Length = 853

 Score =  174 bits (442), Expect = 1e-47
 Identities = 147/470 (31%), Positives = 226/470 (48%), Gaps = 37/470 (7%)

Query: 4   LKFGGTSVANAERFLRVADILESNARQG-QVATVLSAPAKITNHLVAMIEKTISGQDALP 62
           +KFGGTSVA   R+  + +++ S   +G +V  V+SA   IT+ L  M  +   G+    
Sbjct: 1   MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60

Query: 63  NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAAL 122
             + A+R + +LL  +  A P     +L      E A +     G   +G+   +  A +
Sbjct: 61  ARAIAQRHY-DLLDHMQLAVPATLAERLS-----ELAMLAE--DGPGAMGELAWA--ALV 110

Query: 123 ICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVG-------HYLESTVDIAESTRRIA 175
              GE MS A+ A  L   G     +D  + L AV          L S +  A     + 
Sbjct: 111 QAHGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALN 170

Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235
           A       + +  GF A   +G  V+LGR GSD SA+   A L+A   EIWTDV G++T 
Sbjct: 171 ARLAELGEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTA 230

Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295
           +PRQVP ARLL+ + Y+EA E++  GAKVLHPR ++P+ + ++P LIK+T  P+  GT+I
Sbjct: 231 NPRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVI 290

Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355
           G    E    VK IS    + + S+   GM   VG  A VFA   +  +SV LI  + + 
Sbjct: 291 GPEVREHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETN 350

Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLE--PLAVTERLAIISVVGDGMR----TL 409
            ++S           E  +  +    L   L +   + V    A I++VG GMR    TL
Sbjct: 351 VTVSL-------DPTENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTL 403

Query: 410 RGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQML 459
            G+ A+F        I +  I+Q S+  +++ VV+ +     +   H++L
Sbjct: 404 SGVLAEF------GQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447


Lambda     K      H
   0.319    0.135    0.384 

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: 1365
Number of extensions: 60
Number of successful extensions: 3
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: 820
Length of database: 853
Length adjustment: 42
Effective length of query: 778
Effective length of database: 811
Effective search space:   630958
Effective search space used:   630958
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: 56 (26.2 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