Alignments for a candidate for ilvD in Rhizobium etli CFN 42

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Rhizobium etli CFN 42

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011426579.1 RHE_RS17115 dihydroxy-acid dehydratase

Query= curated2:Q8TW40
         (549 letters)



>NCBI__GCF_000092045.1:WP_011426579.1
          Length = 594

 Score =  286 bits (731), Expect = 2e-81
 Identities = 195/549 (35%), Positives = 286/549 (52%), Gaps = 32/549 (5%)

Query: 23  GLTDEEM--DRPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVETIALCDGI 80
           G+T EE+   +P + +  + S++ P +    ++ + V+ GIR AGG+P E  T  + +  
Sbjct: 37  GITPEELRAGKPIIGIAQSGSDLTPCNRVHVELAKRVRDGIRDAGGIPIEFPTHPIFENC 96

Query: 81  AMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARLDLPAAIV 140
              T  +  +L    LV      ++  +  DG V    CDK  P A+MAA+ +D+PA ++
Sbjct: 97  KRPTAALDRNLAYLGLVE-----ILYGYPLDGVVLTTGCDKTTPSAIMAASTVDIPAIVL 151

Query: 141 TGGPMEPGCVDGERVDLIDAFEAVGA-YEEGEISEEELEELEQRACPGPGSCAGMFTANT 199
           +GGPM  G  +GE          +   Y  GEI  EE  +    + P  G C  M TA+T
Sbjct: 152 SGGPMLDGWHEGELAGSGTVIWRMRRKYAAGEIGREEFLQAALDSAPSVGHCNTMGTAST 211

Query: 200 MACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTREAFLDAIR 259
           M  + E LG+S   C A PA   E+ ++A  TG R VE + E +   D+LTR AFL+AIR
Sbjct: 212 MNALAEALGLSLTGCGAIPAAYRERGQMAYRTGRRAVEIVFEDLKPSDILTRAAFLNAIR 271

Query: 260 VDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMRDLYEAGG 319
            + A+GGSTN   HL A+A+ A VEL  DD+     + P L  ++P G Y     + AGG
Sbjct: 272 TNSAIGGSTNAQPHLAAMAKHAGVELYPDDWQVHGFDIPLLANVQPAGAYLGERYHRAGG 331

Query: 320 VPAVMKEL--ADDLHLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEGGIVVLYGN 377
            PA+M EL  A  L  D     GR+M E ++  +  DREVIRP ++P+ E  G +VL GN
Sbjct: 332 TPAIMWELLQAGKLDGDCRTVTGRTMAENLKGRQASDREVIRPFDEPLKERAGFLVLKGN 391

Query: 378 LAPKGAVIKTAALSEEMYEH-----------EGPAVVFDSEEE----ATEAILGGDIDPG 422
           L    A++K + +SE+  +            EG AVVFD  E+      + +LG  ID  
Sbjct: 392 LF-DFAIMKMSVVSEDFRQRYLLEPGREGVFEGRAVVFDGSEDYHKRINDPVLG--IDEN 448

Query: 423 DVVVIRYEGPAGGPGMREM--LTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPE 480
            ++VIR  GP G PG  E+  + P   L   G+  S+  + DGR SG    P + + SPE
Sbjct: 449 TILVIRGAGPLGWPGSAEVVNMQPPDHLLKRGI-RSLPTIGDGRQSGTADSPSILNASPE 507

Query: 481 AYRGGPIAVVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPP-EDEVTGYLRRYRELV 539
           +  GG +A +  GD IR+D  + R ++ V D E+E R  +  PP   + T + + YR  V
Sbjct: 508 SAAGGGLAWLRTGDIIRIDFNQGRCDMLVSDAEIERRKGDGIPPVPADATPWQQIYRRSV 567

Query: 540 RGADEGAVL 548
               +GAVL
Sbjct: 568 TQLSDGAVL 576


Lambda     K      H
   0.317    0.137    0.396 

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: 808
Number of extensions: 45
Number of successful extensions: 6
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: 549
Length of database: 594
Length adjustment: 36
Effective length of query: 513
Effective length of database: 558
Effective search space:   286254
Effective search space used:   286254
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 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