GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Synechococcus elongatus PCC 7942

Align anthranilate synthase (EC 4.1.3.27) (characterized)
to candidate Synpcc7942_1003 Synpcc7942_1003 anthranilate synthase, component I

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__SynE:Synpcc7942_1003
          Length = 517

 Score =  383 bits (983), Expect = e-111
 Identities = 230/500 (46%), Positives = 308/500 (61%), Gaps = 25/500 (5%)

Query: 6   FLRLAADGYNRIPLSFETLADFDTPLSIYLKLA-DAPNSYLLESVQGGEKWGRYSIIGLP 64
           F  LA  G N IP+  E +AD DTP+S + ++  D P S+LLESV+GGE  GRYS +G  
Sbjct: 9   FASLAEQG-NFIPVYQEWVADLDTPVSAWYRICRDRPYSFLLESVEGGEHLGRYSFLGCD 67

Query: 65  CRTVLRVY-DHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYF 123
              VL    D   R   DG  +E     DP A +++  A YQ   +P LP   GGL G++
Sbjct: 68  PLWVLEARGDRTTRRFRDG--SEEVFSGDPFAALKQCLAPYQPVHLPQLPSGVGGLFGFW 125

Query: 124 GYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLAD----PSEEN 179
           GY+ +R++E R+      +    PD   M  D++++FD +  +++AI  AD    P    
Sbjct: 126 GYELMRWIEPRVPVHSGGEN-DLPDGCWMQVDSLMIFDQVKRRLYAIAYADLQAEPDLHR 184

Query: 180 AYERGQARLEELLERLRQPITPRRG----LDLEAAQGREPAFRASFTREDYENAVGRIKD 235
           AY     R++EL+ R +  ++        L  ++A  R   ++++ T+E +   V   +D
Sbjct: 185 AYALACNRVQELVNRFQGSLSASDRQLPWLPPQSAPSRPVDYQSNTTQEQFCANVLTAQD 244

Query: 236 YILAGDCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVR 295
           YI AGD  QVV SQR++  +   P DLYR+LR  NP+PYM FF FGD+ ++GSSPEV+V+
Sbjct: 245 YIRAGDIFQVVLSQRLTTHYSGDPFDLYRSLRLINPSPYMAFFRFGDWQLIGSSPEVMVK 304

Query: 296 VEDG-------LVTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVG 348
            E         + TVRPIAGTRPRG     D AL  DLL+D KE+AEH+ML+DLGRND+G
Sbjct: 305 AEQDPHQSDRQVATVRPIAGTRPRGRTAPEDAALATDLLADPKEVAEHVMLVDLGRNDLG 364

Query: 349 RVSDIGAVKVTEKMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRA 408
           RV + G+V+V E MVIERYS+VMHIVSNV G L     A D LRA  PAGT+SGAPKIRA
Sbjct: 365 RVCEKGSVRVDELMVIERYSHVMHIVSNVVGLLDRDRDAWDLLRATFPAGTVSGAPKIRA 424

Query: 409 MEIIDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIK-NGELH---VQAGGGIVADS 464
           MEII ELE  +RG Y GA GY  + G ++TAI IRT +++  G  H   VQAG G+VADS
Sbjct: 425 MEIIHELEGCRRGPYSGAYGYYDFEGQLNTAITIRTMIVQAEGSGHRVSVQAGAGVVADS 484

Query: 465 VPALEWEETINKRRAMFRAV 484
           VP  E+EET+NK R +  A+
Sbjct: 485 VPIKEYEETLNKARGLLEAI 504


Lambda     K      H
   0.321    0.139    0.408 

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: 649
Number of extensions: 41
Number of successful extensions: 6
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: 492
Length of database: 517
Length adjustment: 34
Effective length of query: 458
Effective length of database: 483
Effective search space:   221214
Effective search space used:   221214
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: 52 (24.6 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