Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N1B4

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Pf1N1B4_601 Phosphogluconate dehydratase (EC 4.2.1.12)

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601
          Length = 608

 Score =  265 bits (678), Expect = 3e-75
 Identities = 178/507 (35%), Positives = 265/507 (52%), Gaps = 31/507 (6%)

Query: 34  IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGT-PLEFGTIAVCDGIAMGHEGMRYSLP 92
           I + +S+N+++  H   +   E +K  +R  G       GT A+CDG+  G  GM  SLP
Sbjct: 68  IAIVSSYNDMLSAHQPYEVFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEPGMELSLP 127

Query: 93  SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151
           SREVIA +  + +  +  D  +M+  CDKI PG ++ A R   +P I + GGPM+ G+  
Sbjct: 128 SREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISN 187

Query: 152 KERIDFKDLMERMNVLIKEGRTEELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLMLP 211
           K++ D      R      +   EEL + E  +   PG+C    TANT  +L E MGL LP
Sbjct: 188 KQKADV-----RQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242

Query: 212 GASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKALENAIAVDMALGGSTN 268
           GAS V      R    +    ++ ++ ++    +   +I+   +L N+I    A GGSTN
Sbjct: 243 GASFVNPNTPLRDALTREAAHQVTRLTKQSGDFMPIGEIVDECSLVNSIVALHATGGSTN 302

Query: 269 SVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAVLKELGE 328
             LH+ A+A   GI L  +   ++S  VP ++ + P+G+  +     AGG+  +++EL E
Sbjct: 303 HTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLE 362

Query: 329 AGLIHKDALTV---------------TGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLA 373
           AGL+H++  TV                G+ VW        LD  ++RP+   +SP GGL 
Sbjct: 363 AGLLHENVNTVLGHGLSRYTMEPFLENGELVWRE-GPIESLDETILRPVARAFSPEGGLR 421

Query: 374 ILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVIRYEGP 433
           +++G+L     V+K SAV  E    +  A VF  ++D   A + G +E   V V+R++GP
Sbjct: 422 VMEGNL--GRGVMKVSAVALENQVVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGP 479

Query: 434 RGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGGPIALV 491
           R   GM E+   T  +  L   G KVALVTDGR SGA+ + PA  HVSPEA  GG +A V
Sbjct: 480 RSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARV 538

Query: 492 QDGDEIVIDIEKRRLDLLVDEKELEER 518
           Q+GD I +D  K  L+L VD +E   R
Sbjct: 539 QEGDIIRVDGVKGTLELKVDAEEFAAR 565


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: 872
Number of extensions: 53
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: 608
Length adjustment: 36
Effective length of query: 516
Effective length of database: 572
Effective search space:   295152
Effective search space used:   295152
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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