Alignments for a candidate for ilvD in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Alicycliphilus denitrificans K601

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_013722484.1 ALIDE2_RS14965 phosphogluconate dehydratase

Query= curated2:A8AB39
         (552 letters)



>NCBI__GCF_000204645.1:WP_013722484.1
          Length = 605

 Score =  266 bits (680), Expect = 2e-75
 Identities = 191/544 (35%), Positives = 283/544 (52%), Gaps = 35/544 (6%)

Query: 30  RRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMR 88
           + P IG+  S+N+++  H  L      +K   R  G T    G + A+CDG+  G  GM 
Sbjct: 66  KAPNIGIVTSYNDMLSAHAPLASYPGLIKDEARRCGATAQVAGGVPAMCDGVTQGTPGME 125

Query: 89  YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLE-VPVILINGGPMMP 147
            SL SR+VIA    + +     DA +M+  CDKI PG L+ A +   +P + +  GPM  
Sbjct: 126 LSLFSRDVIAMATAVALSHDVFDAALMLGVCDKIVPGLLVGALQFGYLPTVFVPAGPMTS 185

Query: 148 GVYGKERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMG 207
           G+    +   ++  +    L+  G   EL + E +A   PG+C    TAN+  ML EAMG
Sbjct: 186 GLSNSAKAKVRE--QAAQGLVGRG---ELLQAEMAAYHSPGTCTFYGTANSNQMLLEAMG 240

Query: 208 LMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTP-DKILTRKALENAIAVDMALGGS 266
           L +PG + V    A R    +     ++        P  +++  +A+ NA+   +A GGS
Sbjct: 241 LHVPGTAFVNPGHALREELTREAARTVLGSAGAPCPPIGRVVDERAIVNAMVALLATGGS 300

Query: 267 TNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKEL 326
           TN ++H  A+A   GI +  + F  +S  VP +A + P+G   V     AGG   V++EL
Sbjct: 301 TNHLIHWVAVARAAGIVIDWDDFSALSAAVPLLARVYPNGSADVNRFQAAGGPGYVIREL 360

Query: 327 GEAGLIHKDALTVTGKTVWENVK----DA----------AVLDREVIRPLDNPYSPFGGL 372
            +AGL+H+D LTV    + E  +    DA          A  D  V+RP  +P+S  GGL
Sbjct: 361 LDAGLMHEDVLTVRPGGIREYTRVPEGDAGQRLRWADVGASRDDSVLRPAADPFSATGGL 420

Query: 373 AILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEG 432
            +L G+L    +V+K SAV R+    +  ARVF  + + ++A + GE+E   V V+R++G
Sbjct: 421 KLLSGNL--GRSVIKVSAVPRDHHVVEAPARVFASQGELLQAFQAGELERDVVCVVRWQG 478

Query: 433 PRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIA 489
           PR   GM E+  LT   AV+  G G KVALVTDGR SGA+ + PA  H SPEA AGGP+A
Sbjct: 479 PRAN-GMPELHKLTPPLAVLQ-GKGHKVALVTDGRMSGASGKVPAAIHASPEAHAGGPLA 536

Query: 490 LVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKP------KVKPLRRGILRRYAKMALS 543
            V+DGD I +D     LD+L+D  E + R+    P            R +   + + ALS
Sbjct: 537 RVRDGDPIRLDAVAGTLDVLIDAAEWQARQPAAMPPGLHEDNAHGWGRELFAGFRRNALS 596

Query: 544 ADKG 547
           A++G
Sbjct: 597 AEEG 600


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: 898
Number of extensions: 55
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: 605
Length adjustment: 36
Effective length of query: 516
Effective length of database: 569
Effective search space:   293604
Effective search space used:   293604
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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
the source code
instructions for running GapMind on your computer
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