GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Dyella japonica UNC79MFTsu3.2

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate N515DRAFT_3177 N515DRAFT_3177 6-phosphogluconate dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3177
          Length = 606

 Score =  240 bits (612), Expect = 1e-67
 Identities = 178/514 (34%), Positives = 263/514 (51%), Gaps = 40/514 (7%)

Query: 32  PLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYS 90
           P +G+  S+N+++  H   ++  E ++   R +G T    G + A+CDG+  G EGM  S
Sbjct: 70  PNLGIVTSYNDMLSAHQPYERYPELIRRIARESGITAQVAGGVPAMCDGVTQGREGMELS 129

Query: 91  LPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGV 149
           L SR++IA    + +     D  + +  CDKI PG L+ A     +P I + GGPM  G+
Sbjct: 130 LFSRDLIAMATAVSLSHDMFDGTLYLGICDKIVPGLLIGALSFGHLPGIFVPGGPMPSGI 189

Query: 150 YGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSCAGLFTANTMNMLSEAMG 207
             +++        ++     EG+    EL + E +A   PG+C    TAN+  ML E MG
Sbjct: 190 TNEQK-------SKVRQAYAEGKANRAELLEAEAAAYHAPGTCTFYGTANSNQMLMEIMG 242

Query: 208 LMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALG 264
           L LPGAS V      R         R+  +   G   L    I+  +A+ N +    A G
Sbjct: 243 LHLPGASFVAPDTPLRDALTAEAVHRVAALSAHGDNHLPIGHIVDERAIINGVIGLHATG 302

Query: 265 GSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLK 324
           GSTN +LHL A+A   GI L  + FD +S  VP +A + P+G   V     AGG+  ++ 
Sbjct: 303 GSTNHLLHLVAMARAAGIQLRWDDFDALSSVVPLLARVYPNGYADVNQFHDAGGMAFLID 362

Query: 325 ELGEAGLIHKDALTV----------------TGKTVWENV-KDAAVLDREVIRPLDNPYS 367
           +L  AGL+H D  TV                +G   W  V K++   +R V+R +  P+ 
Sbjct: 363 QLLGAGLLHGDVRTVFGTGLDGYAQVPSLDASGALQWTPVAKESG--NRGVLRGMAEPFR 420

Query: 368 PFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIV 427
             GGL +L G+L    AV+K S+V  +    +  A VF  +++  KA   GE+    + V
Sbjct: 421 ADGGLRMLAGNL--GRAVIKVSSVPDDRQVIEAPAVVFHDQDEVRKAFERGELNRDFIAV 478

Query: 428 IRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAA 484
           +R++GPR   GM E+  LT T AV+    G ++AL+TDGR SGA+ R PA  HV+PEA A
Sbjct: 479 VRFQGPR-AIGMPELHKLTPTLAVLQ-DRGYRIALLTDGRMSGASGRVPAAIHVTPEAQA 536

Query: 485 GGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518
            G IA ++DGD I +D  +  LD+LVD  E   R
Sbjct: 537 QGAIARIRDGDLIRLDATRGTLDVLVDASEFASR 570


Lambda     K      H
   0.319    0.138    0.401 

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: 848
Number of extensions: 42
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: 552
Length of database: 606
Length adjustment: 36
Effective length of query: 516
Effective length of database: 570
Effective search space:   294120
Effective search space used:   294120
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