GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Phaeobacter inhibens BS107

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD

Query= curated2:A5UY13
         (559 letters)



>FitnessBrowser__Phaeo:GFF723
          Length = 571

 Score =  351 bits (900), Expect = e-101
 Identities = 214/543 (39%), Positives = 304/543 (55%), Gaps = 17/543 (3%)

Query: 22  RAMLKAIGFTDEDL-AKPIIGIANTWIETMPCNINLRALAARVKEGVRAAGGTPMEFNTV 80
           R+ +K  GF D     +PIIGI NTW E  PCN  LR LA  VK GV  AGG P+EF  +
Sbjct: 22  RSWMKNQGFPDHAFDGRPIIGICNTWSELTPCNSGLRDLAEGVKRGVWEAGGFPVEFPVM 81

Query: 81  AIADGVTMGTEGMKASLISRDLIADSIELMGRGYMFDAIIALVACDKTIPGAAMGLTRLN 140
           ++ +     T+    +++ R+L+A  +E   R Y  D ++ L  CDKT PG  MG   ++
Sbjct: 82  SLGE-----TQMKPTAMLFRNLLAMDVEESIRAYGIDGVVLLGGCDKTTPGQLMGAASVD 136

Query: 141 IPGFLLYGGSIAPGHWRGKEI-TIQHVYEAIGAVAAGKMTDEELKEIEDAACPGPGACGG 199
           +P  ++  G +  G W+GK+I +   V++   AV AG+MT ++    E       G C  
Sbjct: 137 LPAIVVSSGPMLNGKWQGKDIGSGTDVWKFSEAVRAGEMTLQDFMAAESGMSRSKGVCMT 196

Query: 200 QYTANTMATVMEIIGLSPMGTAAVPAADPRKDSVGYRAGQLIMDVLRRDLKPRDILTRAA 259
             TA+TMA+++E +G+S    AA+PA D R+ ++ +  G+ I++++  D+KP D+LTR A
Sbjct: 197 MGTASTMASLVEAMGMSLPTNAALPAVDARRMALAHLTGKRIVEMVEEDIKPSDVLTREA 256

Query: 260 FENAIASVALTGGSTNAVLHLLALAREAGVPLTLDDFDAISRRTPLCCDLMPSGKYSAIH 319
           F NAI + A  GGSTNAV+HLLALA   G  L+LDDFD +    PL  + MPSGKY    
Sbjct: 257 FVNAIMANAAVGGSTNAVVHLLALAGRVGAELSLDDFD-LGSDIPLLVNCMPSGKYLMED 315

Query: 320 VDQAGGIQVIARRLVDGGFAHGDAITVTGRTLAEEAADAVETPGQDVIRPLDNPIKPTGG 379
              AGG+ V+ ++L D G    +   + G  LA   A+  E    DVI+  D P+KP  G
Sbjct: 316 FCYAGGMPVVLKQLADNGHLRSNTTVLGGDILA--YAEGAECFNDDVIKSFDEPVKPAAG 373

Query: 380 LLVLRGNLAPEGSVVKLFGY--ERTYHRGPARVFDGEEAAMAAIVGGE--IRPDDIVIIR 435
           L VLRGNLAP G++VK          H G A VF+  E   A I   +  +  D I++++
Sbjct: 374 LRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDDLPVTKDSILVLK 433

Query: 436 YEGPRGGPGMREM--LGVTSAIVGAGLGQSVSLITDGRFSGATRGVMIGHVAPEAARGGP 493
             GP+G PGM E+  + +   +V  G+   +  I+DGR SG   G +I HV+PE+  GGP
Sbjct: 434 GVGPKGYPGMPEVGNMPIPRKLVREGVRDMIR-ISDGRMSGTAFGTVILHVSPESQAGGP 492

Query: 494 LAIVQEGDEIEINLDERRVDLLLSEEEIADRLLAWQPPAPRYEWGVMARYGALVSSASEG 553
           L +VQ GD I ++     +DLL+SEEE+  R  AWQP    Y  G    Y   V  A +G
Sbjct: 493 LGLVQTGDRIRVSAKNGTLDLLVSEEELTARREAWQPEPLHYTRGYAKLYVDSVLQAEKG 552

Query: 554 AVL 556
           A L
Sbjct: 553 ADL 555


Lambda     K      H
   0.319    0.137    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: 858
Number of extensions: 46
Number of successful extensions: 7
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: 559
Length of database: 571
Length adjustment: 36
Effective length of query: 523
Effective length of database: 535
Effective search space:   279805
Effective search space used:   279805
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