Alignments for a candidate for ilvD in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Sinorhizobium medicae WSM419

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate YP_001325992.1 Smed_0298 phosphogluconate dehydratase

Query= BRENDA::Q8NQZ9
         (613 letters)



>NCBI__GCF_000017145.1:YP_001325992.1
          Length = 606

 Score =  198 bits (503), Expect = 6e-55
 Identities = 167/541 (30%), Positives = 250/541 (46%), Gaps = 49/541 (9%)

Query: 37  VAIVNSYTQFVPGHVHLKNVGDIVADAVRKAGGVPKEFNTI-AVDDGIAMGHGGMLYSLP 95
           + I+ SY   +  H   +    ++ +A  +AGGV +    + A+ DG+  G  GM  SL 
Sbjct: 70  LGIITSYNDMLSAHQPFETYPALIREAAHEAGGVAQVAGGVPAMCDGVTQGQPGMELSLF 129

Query: 96  SREIIADSVEYMVNAHTADAMVCISNCDKITPGMLNAAMRL-NIPVVFVSGGPMEAGKAV 154
           SR++IA +    ++ +  DA V +  CDKI PG+  AA+   ++P VF+  GPM +G   
Sbjct: 130 SRDVIAMAAGIGLSHNMFDAAVYLGVCDKIVPGLAIAALTFGHLPAVFIPAGPMTSG--- 186

Query: 155 VVDGVAHAPTDLITAI-SASASDAVDDAGLAAVEASACPTCGSCSGMFTANSMNCLTEAL 213
                   P D    I    A   V    L   E+ +    G+C+   TANS   L E +
Sbjct: 187 -------LPNDEKAKIRQLFAEGKVGRDELLEAESKSYHGPGTCTFYGTANSNQMLMEIM 239

Query: 214 GLSLPGNGSTLATHAARRALFEKAGETVVELCRRYYGEEDESVLPRG-IATKKAFENAMA 272
           G  LPG          R AL ++A +  + +     G E     P G +  +++  N + 
Sbjct: 240 GFHLPGASFINPGTPLRDALTKEATKRALAITA--LGNE---FTPAGEMIDERSIVNGVV 294

Query: 273 LDMAMGGSTNTILHILAAAQEGEVDFDLADIDELSKNVPCLSKVAPNSDYHMEDVHRAGG 332
              A GGSTN  LH++A A+   +     DI ELS  VP L++V PN    +   H AGG
Sbjct: 295 GLHATGGSTNHTLHLVAMARAAGIVLTWQDISELSDLVPLLARVYPNGLADVNHFHAAGG 354

Query: 333 IPALLGELNRGGLLNKDVHSVHSNDLEGWLDDWDIRSGKTTEVATELFHAAPGGIRTTEA 392
           +  ++ +L   GLL+ DV +V+   L  +    D++ G+   V  E    AP      + 
Sbjct: 355 MGFMIAQLLSKGLLHDDVRTVYGQGLSAYA--IDVKLGEKGSVKRE---PAPAVSADPKV 409

Query: 393 FSTENRWDELDTDAAKGCIRDVEHAYTADGGLVVLRGNISPDGAVIKSAGIEEELWNFTG 452
            +T                  ++  +   GGL +L GNI    AVIK + ++ E      
Sbjct: 410 LAT------------------IDRPFQHTGGLKMLSGNIGK--AVIKISAVKPESHVIEA 449

Query: 453 PARVVESQEEAVSVILTKTIQAGEVLVVRYEGPSGGPGMQEMLHPTAFLKG--SGLGKKC 510
           PA++   Q E  +      ++   V VVR++GP    GM E LH    + G     G+K 
Sbjct: 450 PAKIFNGQGELNAAFKAGKLEGDFVAVVRFQGPKAN-GMPE-LHKLTTVLGILQDRGQKV 507

Query: 511 ALITDGRFSGGSSGLSIG-HVSPEAAHGGVIGLIENGDIVSIDVHNRKLEVQVSDEELQR 569
           A++TDGR SG S  +    HV+PEA  GG I  I+ GDIV ID    K+EV V D  L+ 
Sbjct: 508 AILTDGRMSGASGKVPAAIHVTPEAKEGGPIARIQEGDIVRIDAIKGKIEVLVEDIALKT 567

Query: 570 R 570
           R
Sbjct: 568 R 568


Lambda     K      H
   0.315    0.132    0.385 

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: 905
Number of extensions: 46
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: 613
Length of database: 606
Length adjustment: 37
Effective length of query: 576
Effective length of database: 569
Effective search space:   327744
Effective search space used:   327744
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