GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hom in Shewanella sp. ANA-3

Align fused aspartate kinase/homoserine dehydrogenase 1 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 7023422 Shewana3_0652 aspartate kinase III (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7023422 Shewana3_0652 aspartate kinase III
           (RefSeq)
          Length = 451

 Score =  191 bits (484), Expect = 1e-52
 Identities = 140/460 (30%), Positives = 226/460 (49%), Gaps = 18/460 (3%)

Query: 3   VLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALP 62
           V KFGGTSVA+     R ADI+  N     V  V+SA + +TN LV + +++++    L 
Sbjct: 5   VAKFGGTSVADYGAMNRCADIVLGNPDCRLV--VVSASSGVTNLLVELTQESMNDDGRLQ 62

Query: 63  NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAAL 122
            +    +I   +L  L   +P    A L   +       +  +   +L  Q   +    L
Sbjct: 63  RLKQIAQIQYAILDKLG--RPNDVAAALDKLLS------RMAVLSEALASQRSKATMDEL 114

Query: 123 ICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP-- 180
           +  GE+ S A+ A VL  +G N +  D    L    H+  +   + +         +P  
Sbjct: 115 LSLGEQCSSALFAAVLREKGANSSAFDVRRVLRTDSHFGRAEPQVEQIAILSREHLLPLL 174

Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240
           ++ +++  GF   +E G+   LGR GSDYSAA+LA  L+A   EIWTDV G+YT DPR  
Sbjct: 175 SEQVIVTQGFIGSDEAGQTTTLGRGGSDYSAALLAEALKASAVEIWTDVAGIYTTDPRLA 234

Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300
           P+A  +  +S+ EA E++ FGAKVLHP TI P  + QI   + ++  P+  GT I   + 
Sbjct: 235 PNAHPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSKEPEKGGTWI-RHQV 293

Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360
           ED    + ++   +  + ++    M    G  A  FA ++R +ISV LIT S    S++ 
Sbjct: 294 EDAPVFRAVALRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSEVNVSLTL 353

Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420
               SD    +  + E    EL +     + V + LA+++++G+ + T  GI  + F  L
Sbjct: 354 DKTGSDS-SGQGLLSEALLQELSQHC--RVRVEDGLALVAIIGNRIATTAGICRRVFEVL 410

Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLF 460
              N+ +  I QG+S  ++ V+V   +A   V+  H+ LF
Sbjct: 411 EPHNVRM--ICQGASPHNLCVLVAESEAAQVVKALHENLF 448


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: 661
Number of extensions: 23
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: 820
Length of database: 451
Length adjustment: 37
Effective length of query: 783
Effective length of database: 414
Effective search space:   324162
Effective search space used:   324162
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: 53 (25.0 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