Alignments for a candidate for ilvD in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudomonas stutzeri RCH2

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF1853 Psest_1892 6-phosphogluconate dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__psRCH2:GFF1853
          Length = 609

 Score =  263 bits (671), Expect = 2e-74
 Identities = 175/521 (33%), Positives = 271/521 (52%), Gaps = 33/521 (6%)

Query: 34  IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92
           + + +++N+++  H   +   E ++  +R  G      G + A+CDG+  G  GM  SL 
Sbjct: 69  VAIVSAYNDMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGEAGMEMSLA 128

Query: 93  SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151
           SREVIA +  + +  +  DA +M+  CDKI PG ++ A R   +P I + GGPM  G+  
Sbjct: 129 SREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMIGALRFGHLPTIFVPGGPMPSGIPN 188

Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211
           K + +      R      +   EEL + E  +   PG+C    TANT  ++ E MGL LP
Sbjct: 189 KAKAEV-----RQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQVVMEIMGLHLP 243

Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG--LTP-DKILTRKALENAIAVDMALGGSTN 268
           G+S V      R    +    ++ ++  +    TP  +++  K++ N++    A GGSTN
Sbjct: 244 GSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGGSTN 303

Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328
             LH+ A A   GI L  +   ++S  VP +A + P+G+  V      GG+P +++ L +
Sbjct: 304 HTLHIPAFARAAGIQLTWKDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRTLLD 363

Query: 329 AGLIHKDALTVTGKTVWENVKDAAV--------------LDREVIRPLDNPYSPFGGLAI 374
           AGL+H+D  TV GK +   +++  +              LD  ++RP + P+SP GGL +
Sbjct: 364 AGLLHEDVHTVVGKGLRRYIQEPFLDGDRLVWRDGPTQSLDESILRPAERPFSPEGGLRV 423

Query: 375 LKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGPR 434
           L+G+L     V K SAV  E    +  ARVF  + +   A + GE+E   + V+R++GP+
Sbjct: 424 LEGNL--GRGVTKISAVAPEHRVVEAPARVFIDQSELAAAFKAGELERDFIAVVRFQGPK 481

Query: 435 GGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALVQ 492
              GM E+   T  +  L   G KVALVTDGR SGA+ + PA  HV PEA  GGP+A V+
Sbjct: 482 AN-GMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVCPEALDGGPLARVR 540

Query: 493 DGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGI 533
           DGD + +D E   L  LVD  E   R    +P ++P   GI
Sbjct: 541 DGDILRVDGESGELLALVDPVEWGAR----EPAIRPEDVGI 577


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: 845
Number of extensions: 48
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: 609
Length adjustment: 36
Effective length of query: 516
Effective length of database: 573
Effective search space:   295668
Effective search space used:   295668
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 09 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