GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pseudomonas simiae WCS417

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF4432 PS417_22690 phosphogluconate dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__WCS417:GFF4432
          Length = 608

 Score =  271 bits (693), Expect = 5e-77
 Identities = 177/506 (34%), Positives = 271/506 (53%), Gaps = 29/506 (5%)

Query: 34  IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGT-PLEFGTIAVCDGIAMGHEGMRYSLP 92
           + + +S+N+++  H   +   E +K  +R  G       GT A+CDG+  G  GM  SL 
Sbjct: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREVGSVGQFAGGTPAMCDGVTQGEPGMELSLL 127

Query: 93  SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151
           SREVIA +  + +  +  DA +M+  CDKI PG ++ A R   +P+I + GGPM  G+  
Sbjct: 128 SREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRYGHLPMIFVPGGPMPSGISN 187

Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211
           K++ D      R      +   EEL + E  +   PG+C    TANT  +L E MGL LP
Sbjct: 188 KQKADV-----RQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242

Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALGGSTN 268
           GAS V      R    +    ++ ++ +     +   +I+  K++ N+I    A GGSTN
Sbjct: 243 GASFVNPYTPLRDALTREAAHQVTRLTKANGSFMPIGEIVDEKSIVNSIIALNATGGSTN 302

Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328
             LH+ A+A   GI L  +   ++S  VP ++ + P+G+  +     AGG+  +++EL E
Sbjct: 303 HTLHMPAIAMSAGIILTWDDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLE 362

Query: 329 AGLIHKDALTVTGKTVWENVKDAAVLDRE--------------VIRPLDNPYSPFGGLAI 374
           AGL+H+D  TV GK +    ++  ++D E              ++RP+   +SP GGL +
Sbjct: 363 AGLLHEDVNTVAGKGLSRYTQEPFLVDGELIWREGPIESLDETILRPVARAFSPEGGLRV 422

Query: 375 LKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGPR 434
           ++G+L     V+K SAV  E    +  A VF  ++D   A + G++E   V V+R++GPR
Sbjct: 423 MEGNL--GRGVMKVSAVAPEHQIVEAPAVVFQDQQDLADAFKAGQLEKDFVAVMRFQGPR 480

Query: 435 GGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALVQ 492
              GM E+   T  +  L   G KVALVTDGR SGA+ + PA  HV+PEA +GGP+A V+
Sbjct: 481 SN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVNPEAQSGGPLARVR 539

Query: 493 DGDEIVIDIEKRRLDLLVDEKELEER 518
           DGD I +D  K  L+L VD +E   R
Sbjct: 540 DGDIIRVDGVKGTLELKVDAEEFAAR 565


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: 870
Number of extensions: 54
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: 608
Length adjustment: 36
Effective length of query: 516
Effective length of database: 572
Effective search space:   295152
Effective search space used:   295152
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