GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__ANA3:7024978
          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:

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