Aligments for a candidate for ilvD in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvD in Escherichia coli BW25113

Align Dihydroxy-acid dehydratase 1; DAD 1; EC 4.2.1.9 (uncharacterized)
to candidate 18321 b4297 KpLE2 phage-like element; predicted dehydratase (NCBI)

Query= curated2:Q8TPV2
         (553 letters)



>FitnessBrowser__Keio:18321
          Length = 655

 Score =  249 bits (637), Expect = 2e-70
 Identities = 181/521 (34%), Positives = 272/521 (52%), Gaps = 37/521 (7%)

Query: 46  GHIHLDKLAEAVKAGIRNAGGVPFEFHTIGVCDGLAMGHEGMKYSLPSREVIEDTIELMV 105
           GH  LD   +A    I+    +P+  +    CDG   G  GM  SLP R      +  ++
Sbjct: 88  GHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMVMRRLI 147

Query: 106 RA-HQFDGMVLIPTCDKIVPGHLMA-AGRLDIPAIVVTGGPMLPGYVDDKYTDLISVFEG 163
           R+      ++ + +CDK +P  +MA A + +I  ++V GG  LP     K  +     + 
Sbjct: 148 RSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPA----KDGEDNGKVQT 203

Query: 164 VGA-YSAGKLSEAELKRLENLSCAGAGS-CAGMFTANTMACMTEALGLSLPGCATAHAVD 221
           +GA ++ G+LS  + +R    +CA +G  C  + TA T   + E LGL++P  A A + +
Sbjct: 204 IGARFANGELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPSGE 263

Query: 222 AKKVRIAKESGERIVALVKENLTPRKIVTQKSFENAIMVDMAVGGSTNTTLHLPALAHEF 281
                IA+ S    + L ++ +T R+I+T K+ ENA+ V  A GGSTN  LH+PA+AH+ 
Sbjct: 264 PVWREIARASARAALNLSQKGITTREILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQA 323

Query: 282 GLELP-LKTFDELSRTTPHLISLRPGGPNF--MLHFDRAGGVEAVVQRLAS--KLHLDQL 336
           G  +P +  +  +++  P L+S+ P GP +   ++   AGGV  V+  L S   LH D +
Sbjct: 324 GCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVM 383

Query: 337 TVNGKTIGENLD------------ELEIVNPKLNAEIITTLENPIHAEGGIAVLK---GS 381
           TV G T+ ENLD            +L +   ++NA+ +        A G  + +    G+
Sbjct: 384 TVTGSTLKENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQAKARGLTSTITFPVGN 443

Query: 382 LAPDGSVVKQAAVDPKM------RVHTGPAKVYDCEEDAMKSILAGDVKPGDIVVIRYEG 435
           +AP+GSV+K  A+DP M        H G AKVY  E+ A+  I    +K GDI+VI   G
Sbjct: 444 IAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIGVG 503

Query: 436 PKGGPGMREMLAATAAIGGMGLLESVALITDGRFSGGTRGPCIGHVSPEASEGGPIGLVK 495
           P  G GM E    T+A+  +   + V+LITD RFSG + G CIGHV PEA  GGPIG ++
Sbjct: 504 P-SGTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIGKLR 562

Query: 496 DGDLIEINIPERILNLKVTEEELEKRKAAFVPPKKEVTGYL 536
            GDLIEI I  R L+ +V    L  R    +P ++E T  L
Sbjct: 563 TGDLIEIKIDCRELHGEV--NFLGTRSDEQLPSQEEATAIL 601


Lambda     K      H
   0.317    0.136    0.393 

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: 1000
Number of extensions: 48
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: 553
Length of database: 655
Length adjustment: 37
Effective length of query: 516
Effective length of database: 618
Effective search space:   318888
Effective search space used:   318888
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 (21.6 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