GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Streptacidiphilus oryzae TH49

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_037576212.1 BS73_RS25220 thiamine pyrophosphate-binding protein

Query= BRENDA::O06335
         (552 letters)



>NCBI__GCF_000744815.1:WP_037576212.1
          Length = 554

 Score =  144 bits (364), Expect = 7e-39
 Identities = 167/564 (29%), Positives = 241/564 (42%), Gaps = 54/564 (9%)

Query: 4   GDHLVARMRAAGISVVCGLPTSRLDSLLVRLSRDAGFQIVLARHEGGAGYLADGFARASG 63
           GD LV  +RA G   V G+ +     L+  + R A  + V  RHE  A   ADG+ARA+G
Sbjct: 11  GDLLVEVLRAHGCDTVFGIVSVHNLPLVEAVDRSADVRFVPVRHEAAAVNAADGYARATG 70

Query: 64  K-SAAVFVAGPGATNVISAVANASVNQVPMLILTGEVAVGEFGL-HSQQDTSDDGLGLGA 121
           +   A+   G GA N   ++  +      +L +TG++     GL       + D LG+  
Sbjct: 71  RLGCALTSTGTGAGNAAGSLIESLSAGTSVLHVTGQIDSPYLGLGRGFIHETKDQLGMLT 130

Query: 122 TFRRFCRCSVSIESIANARSKIDSAFRALASIPRGPVHIALPRDL---VDERLPAHQLGT 178
              +    +V I S A A   + +A +A  + P GP  +  P DL        P   L T
Sbjct: 131 AVSKH---AVRIGSAAEAEGVLLAAAQAALTAPGGPASVEWPIDLQYAAQRPRPLTALDT 187

Query: 179 AAAGLGGLRTLAPCGPDVADEVIGRLDRSRAPMLVLGNGCRLDGIGEQIVAFCEKAGLPF 238
           A        T  P G D A E++     +R P++  G G      GE + A  E  G   
Sbjct: 188 APV------TALPDGLDAAAELLAA---ARRPVIWAGGGAAR--AGEPLRALAELLGAGL 236

Query: 239 ATTPNGRGIVAETHPLSLGVLGIFGDGRADEYLFDTPCDLLIAVGVSFGGLVTRSFSPRW 298
            T+ +GRG V E HPL +G       G+A         D +++VG  F    T  +  + 
Sbjct: 237 FTSNSGRGAVGEDHPLVIGNYATSPGGKA----LLAEADAILSVGTHFRSNETGDYRLQ- 291

Query: 299 RGLKADVVHVDPDPSAVGRFVATSLGITTSGRAFVNALNCGRPPRFCRRVGVRPPAPAAL 358
             L A  V VD DP+A+GR    ++G+     A + AL         R++ V     A  
Sbjct: 292 --LPAAHVQVDLDPAALGRVYPATVGLAGESGAVLAAL---LQKLSGRQLSVEEGWSARA 346

Query: 359 PGTPQARGE----SIHPLELMHELDRELAPNATICADVGTCIS--WTFRGIPVRRPGRFF 412
             T +   E    +I P   + E  R   P A++ A   T  S  W  R +P+  P    
Sbjct: 347 TETREEVRERQRWAIGPQAAVCEAIRAHYPAASVIARDVTIPSSTWGNRLLPLTDP---- 402

Query: 413 ATVDF---SPMGCGIAGAIGVALARPEEHVICIAGDGAFLMHGTEISTAVAHGIRVTWAV 469
           AT  F     +G G+A AIG A  RPE   + IAGDG F +H  E+ T      R+T AV
Sbjct: 403 ATNVFPRGGGIGQGLAMAIGAACGRPEVPTVLIAGDGGFAVHLGELLTVAQERPRLTLAV 462

Query: 470 LNDGQMSASAGPVSGRMDPSPVARIGANDLAA-----MARALGAEGIRVDTRCELRAGVQ 524
            NDG      G +    +     R G  DL A     +A A+G +  R+    E     +
Sbjct: 463 FNDG----GYGVLRNMQEAGGGDRHGV-DLTAPAFDRLAAAVGIDYARIGAEAEADPVFK 517

Query: 525 KALAATGPCV--LDIAIDPEINKP 546
            A AA GP +  +D+A    +N+P
Sbjct: 518 AAAAAEGPVLVEIDLAALGPMNQP 541


Lambda     K      H
   0.322    0.139    0.425 

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: 849
Number of extensions: 44
Number of successful extensions: 5
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: 554
Length adjustment: 36
Effective length of query: 516
Effective length of database: 518
Effective search space:   267288
Effective search space used:   267288
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 (21.9 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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