GapMind for Amino acid biosynthesis

 

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

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)

Query= curated2:B1I250
         (569 letters)



>lcl|FitnessBrowser__ANA3:7024978 Shewana3_2149 phosphogluconate
           dehydratase (RefSeq)
          Length = 608

 Score =  237 bits (605), Expect = 9e-67
 Identities = 181/522 (34%), Positives = 258/522 (49%), Gaps = 46/522 (8%)

Query: 33  KPFVAIANSFAEIVPGHAHLNEFVKEIKEAVRE-------AGGVPFEFNTLALCDGIAMN 85
           K  + I  +F +++  H     + + +K+A +E       AGGVP      A+CDG+   
Sbjct: 65  KANIGIITAFNDMLSAHQPYETYPELLKKACQEVGSVAQVAGGVP------AMCDGVTQG 118

Query: 86  HPGMRYSLPSRELVADSVETMVQGHRFDGLICIPNCDKIVPGMLMAAVRL-NIPTIFVSG 144
            PGM  SL SRE++A +    +  + FDG + +  CDKIVPG+L+ A+   ++P +FV  
Sbjct: 119 QPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPA 178

Query: 145 GPMKAGRAKDGRPIDLISVFEGIGAFRAGKIDAGDLLELEQAACPGYGSCAGMFTANSMN 204
           GPMK+G     +             F  GK+D   LLE E  +    G+C    TANS  
Sbjct: 179 GPMKSGIPNKEKA-------RIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQ 231

Query: 205 CLCEALGLALPGNGTILAVDPRRSELKKWAGRQIVELIKRDLRPR---DIVTPEAIDNAF 261
            + E +GL LPG+  +   DP R  L K A +Q+  L +   +     ++V  +++ N  
Sbjct: 232 LMLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGI 291

Query: 262 ALDVAMGGSTNTILHLLAVAQEAGINYPLKRVNLISARTPTLCKISPASSLHIEDVDRAG 321
              +A GGSTN  +H++A A+ AGI       + +S   P L ++ P     I     AG
Sbjct: 292 VALLATGGSTNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAG 351

Query: 322 GVSAVLGELSRKPGLLNLDCLTVTGETL-----------GE---TVGQVQSLDPRVIRGV 367
           G++ ++ EL    GLL+ D  TV G  L           GE     G   SLD  V+  V
Sbjct: 352 GMAFLIKEL-LDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSV 410

Query: 368 EEPLSPVGGLKVLFGSLAPEGAVVKTAAVVPQMMRHQGPAVVFNSEAEASAAILGGRIKH 427
             P    GGLK+L G+L    AV+K +AV  +    + PAVV + + +  A    G +  
Sbjct: 411 ATPFQNNGGLKLLKGNLG--RAVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKSGALDR 468

Query: 428 GDVVVIRFEGPKGGPGFMEMLGPTAALVGM-GLGESVALVTDGRFSG--GTRGACIGHVC 484
             VVV++ +GPK   G  E+   T  L  +   G  VAL+TDGR SG  G   A I H+ 
Sbjct: 469 DCVVVVKGQGPKAN-GMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAI-HLT 526

Query: 485 PEAASGGPIALIKDGDLISYDLEAGTLELLVPQEELAARKAA 526
           PEA  GG IA ++DGDLI  D   G L LLV   ELAAR AA
Sbjct: 527 PEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDAELAARTAA 568


Lambda     K      H
   0.319    0.138    0.409 

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: 856
Number of extensions: 52
Number of successful extensions: 8
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: 569
Length of database: 608
Length adjustment: 37
Effective length of query: 532
Effective length of database: 571
Effective search space:   303772
Effective search space used:   303772
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 (21.7 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 preprint 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