GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__ANA3:7023422
          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:

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