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 dihydroxyacid dehydratase (characterized)
to candidate WP_011424066.1 RHE_RS03550 phosphogluconate dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>NCBI__GCF_000092045.1:WP_011424066.1
          Length = 606

 Score =  190 bits (482), Expect = 2e-52
 Identities = 159/542 (29%), Positives = 257/542 (47%), Gaps = 49/542 (9%)

Query: 35  PIIAVVNSFTQFVPGHVHLRDLGKLVAEQIEAAGGVAKEFNTI-AVDDGIAMGHGGMLYS 93
           P + ++ ++   +  H        ++ E    AGGVA+    + A+ DG+  G  GM  S
Sbjct: 68  PNLGIITAYNDMLSAHQPFETYPSIIREAAAEAGGVAQVAGGVPAMCDGVTQGQPGMELS 127

Query: 94  LPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPVIFVSGGPMEAGK 152
           L SR+LIA +    ++ +  DA + +  CDKI PG+++A+L   ++P IFV  GPM  G 
Sbjct: 128 LFSRDLIAMAAGVGLSHNMFDAALFLGVCDKIVPGLVIAALSFGHLPSIFVPAGPMTTGL 187

Query: 153 TKLSDQIIKLDLVDAMIQGADPKVSDSQSDQVERSACPTCGSCSGMFTANSMNCLTEALG 212
                  ++          A+ KV  ++  + E  +    G+C+   TANS   L E +G
Sbjct: 188 PNDEKSRVRQLF-------AEGKVGRAELLEAESKSYHGPGTCTFYGTANSNQMLMEIMG 240

Query: 213 LSQPGNGSLLATHADRKQLFLNAGKRIVELTKRYYEQNDESALPRNIASKAAFENAMTLD 272
              PG+  +      R+ L   A KR + +T      N+ +     I  ++     + L 
Sbjct: 241 FHMPGSSFINPGTPLREALTREAAKRALAITAL---GNEFTPAGEMIDERSVVNGVVGLH 297

Query: 273 IAMGGSTNTVLHLLAAAQEAEIDFTMSDIDKLSRKVPQLCKVAPSTQKYHMEDVHR---A 329
            A GGSTN  LHL+A A+ A I  T  DI +LS  VP L +V P+     + DV+    A
Sbjct: 298 -ATGGSTNHTLHLVAMARAAGIQLTWQDIAELSEIVPLLARVYPN----GLADVNHFQAA 352

Query: 330 GGVIGILGELDRAGLLNRDVKNVLGLTLPQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQ 389
           GG+  ++ EL + GL++ DV+ V G    Q L  Y V                A +   +
Sbjct: 353 GGMGFLIKELLKHGLVHDDVRTVFG----QGLAAYTV---------------DARLGENR 393

Query: 390 AFSQDCRWDTLDDDRANGCIRSLEHAYSKDGGLAVLYGNFAENGCIVKTAGVDDSILKFT 449
              ++   D   D +    + ++E  +  +GGL +L GN  +   ++K + V        
Sbjct: 394 TVLREPSPDKSHDPKV---LSNIETPFQANGGLKMLRGNLGK--AVIKISAVKPERHIIE 448

Query: 450 GPAKVYESQDDAVEAILGGKVVAGDVVVIRYEGPK--GGPGMQEMLYPTSFLKSMGLGKA 507
            PA V+ SQ +  +A   GK+    V V+R++GPK  G P + ++  P   L+  G    
Sbjct: 449 APAIVFHSQQELQDAFKEGKLNRDFVAVVRFQGPKANGMPELHKLTPPLGVLQDRGF--R 506

Query: 508 CALITDGRFSGGTSGLSIG-HVSPEAASGGSIGLIEDGDLIAIDIPNRGIQLQVSDAELA 566
            AL+TDGR SG +  +    HV+PEA  GG I  I++GD+I +D     +++ V  A++A
Sbjct: 507 VALLTDGRMSGASGKVPAAIHVTPEAVDGGPIARIKNGDIIRLDAIKGTLEVLVDAADMA 566

Query: 567 AR 568
            R
Sbjct: 567 ER 568


Lambda     K      H
   0.317    0.134    0.386 

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: 911
Number of extensions: 52
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: 616
Length of database: 606
Length adjustment: 37
Effective length of query: 579
Effective length of database: 569
Effective search space:   329451
Effective search space used:   329451
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 (21.7 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