Aligments for a candidate for ilvD in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Aligments 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for Amino acid biosynthesis