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 GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd

Query= curated2:Q3Z888
         (555 letters)



>FitnessBrowser__Phaeo:GFF2757
          Length = 607

 Score =  251 bits (642), Expect = 4e-71
 Identities = 178/543 (32%), Positives = 280/543 (51%), Gaps = 38/543 (6%)

Query: 34  IGIVNSFTEVVPGHIHLRRISEAVKEGINAAGGVGFEFNTI-AVCDGIAMNHAGMKYSLP 92
           +GIV ++ +++  H       + +++ +   GG       + A+CDG+    AGM+ SL 
Sbjct: 69  LGIVTAYNDMLSAHQPFETYPQRIRDAVRRVGGTAQVAGGVPAMCDGVTQGEAGMELSLF 128

Query: 93  SREIIANTVEIMAMAHAFDGLVFIPNCDKVVPGMLMAACRL-NIPSIFVSGGPMLAGRLR 151
           SR+ IA    I    + FD  V++  CDK+VPG+++ A    ++P++F+  GPM +G   
Sbjct: 129 SRDTIAMATGIALSHNVFDATVYLGVCDKIVPGLVIGAQVFGHLPAVFLPAGPMTSG--- 185

Query: 152 KNDQVSCVDLNSVFEAVGQVAKGQMTEEELLELEKVACPGCGSCAGMFTANTMNCLTEAL 211
               +S  D   V +   + A G++  +ELL+ E  A  G G+C    TANT   L E +
Sbjct: 186 ----ISNDDKAKVRQ---KFAAGEIGRDELLKSEMAAYHGPGTCTFYGTANTNQMLMEFM 238

Query: 212 GMALPGNGTIPAVDSRRTQLAKDTGRQILKLI---KDNTCPKDIITPDAIYNAFSLDVAL 268
           G+ LPG+  +      R  L ++  R+ L L     D T   DI+   A  N     +  
Sbjct: 239 GLHLPGSSFVNPGTDMRAALTEEGARRALALSALGNDYTPVCDILDERAYVNGIVGLMTT 298

Query: 269 GGSTNSVLHVMAVAHEAGADFSLEEINRVSDTTPNLCKLRPSGPYHIENLDQAGGIGSVL 328
           GGSTN ++H++A+A   G     ++ + +SD  P L ++ P+G   + +   AGG+G V+
Sbjct: 299 GGSTNLLIHLIAMARAGGIILDWQDFSELSDVVPLLARVYPNGLADVNHFHAAGGLGYVI 358

Query: 329 KEL--KPWLKNDARTVSGKTIGQMA--------------DAAPKADNKVIRFASNPYSPK 372
            +L     L +D RTV+G  +                   AA   ++K+IR AS P+ P 
Sbjct: 359 GQLLNSGHLHSDTRTVAGSGLESYTAEPFLSDDGLVWKPGAAESLNDKIIRPASAPFQPT 418

Query: 373 GGLAILFGNLAPSGSVVKRSAVAPEMMVHRGPARIFDSEELATKAIMGGKIIPGD-VLVI 431
           GGLA L GNL     V+K SAVAPE  +   PAR+F  +E    A   G++  GD ++V+
Sbjct: 419 GGLARLSGNLGT--GVMKISAVAPEHRMVEAPARVFHDQEEVKAAFKAGELDKGDMIIVV 476

Query: 432 RYEGPKGGPGMREMLTPTSLLAGM-GLDKEVALITDGRFSGAT-RGAAMGHVSPEAAARG 489
           R++GPK   GM E+ + T  L  M G  ++VAL+TDGR SGA+ +  +  HV PEA   G
Sbjct: 477 RFQGPKAN-GMPELHSMTPFLGIMQGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGG 535

Query: 490 PIAALQDGDMINIDIHNYKLSVELSD-EEIQKRLANVPAFKPKITSGYLKYYTENVTSAS 548
           PI+ L+DGDM+ +D     L V+    ++    +A++ A++          +   VTSA 
Sbjct: 536 PISKLRDGDMVRVDALTGTLEVKAEGFDDRDPVVADLSAYQHGTGREMFALFRNAVTSAD 595

Query: 549 TGA 551
           TGA
Sbjct: 596 TGA 598


Lambda     K      H
   0.318    0.135    0.391 

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: 923
Number of extensions: 49
Number of successful extensions: 10
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: 555
Length of database: 607
Length adjustment: 36
Effective length of query: 519
Effective length of database: 571
Effective search space:   296349
Effective search space used:   296349
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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:

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