GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Magnetospirillum magneticum AMB-1

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_011383235.1 AMB_RS04050 thiamine pyrophosphate-binding protein

Query= curated2:P37251
         (574 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383235.1 AMB_RS04050 thiamine
           pyrophosphate-binding protein
          Length = 613

 Score =  259 bits (662), Expect = 2e-73
 Identities = 171/558 (30%), Positives = 278/558 (49%), Gaps = 39/558 (6%)

Query: 24  LIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLV-HILPRHEQGAIHAAEGYARVSGKPG 82
           +I  L +E ++ IF   G A   + D    +    ++   HEQG   AAE YA++ G PG
Sbjct: 7   VINRLAEEGIDKIFVVYGAANGDLIDAFTRTNKTEYVATMHEQGGGFAAEAYAKIKGIPG 66

Query: 83  VVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSD------AFQEADILGITM 136
             IATSGPG  NL+T + +   DS+P V  TGQ+ +  +  D       FQE DI+G+  
Sbjct: 67  ATIATSGPGGQNLLTSMGNCFYDSIPCVFMTGQINSQFLRPDPSIRQVGFQETDIVGMAK 126

Query: 137 PVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGE----FSYD---- 188
           PVTK++  +    ++   +++A  IA  GRPGPVL+DIP ++   + +    F +D    
Sbjct: 127 PVTKYAKMITSAAEIRYEVEKALFIAKEGRPGPVLLDIPLNIQKQDIDPDKLFGFDTVAA 186

Query: 189 -HEMNLPGYQPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIP 247
               NL       +     + K       +K+P I+ G GV    A ++L    E   +P
Sbjct: 187 QRSWNLDAVDAAIDTYLADLAK-------SKRPTIMVGGGVRLANAVDDLVELGEVLGVP 239

Query: 248 VAHTLLGLGGFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTG-NLKHFA 306
           +  T   L    +D P + G  G +G    N  +   DLL+++G+R   R+TG N+  FA
Sbjct: 240 MFPTWNALDVVTSDLPQYGGRIGTYGGAGRNFGIQNSDLLLAVGSRISGRITGGNIHSFA 299

Query: 307 RNAKIAHIDIDPAEIGKIMKTQIP----VVGDSKIVLQELI------KQDGKQSDSSEWK 356
           R AK   +D+D   + K ++ Q+P    V+ D+ I L+ L+      + +G   D   W 
Sbjct: 300 REAKKYVVDVDETLLQKHLQ-QVPLDVNVLCDAGIFLRRLVARAKALRANGGLGDHKAWL 358

Query: 357 KQLAEWKEEY-PLWYVDNEEEG-FKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPF 414
            ++ +W++ Y P+     E++G   P   +  + +  KG  IV  D G + + ++  +  
Sbjct: 359 SKVLDWRDRYDPVLPEFFEQKGTVHPYAFVRKLSEMMKGGDIVVGDCGGNIVVTSHAFET 418

Query: 415 QKADKWVTSGGLGTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPV 474
           ++  + +T+ G   MGF    A+GA  A  +  VV ++GDGG  M +QEL       + V
Sbjct: 419 KRGQRLLTNNGNSPMGFSFAGAMGAWFAAPNNQVVCIIGDGGMNMNIQELQTFVNYGVKV 478

Query: 475 KVVILNNACLGMVRQWQEIFYEERYSE--SKFASQPDFVKLSEAYGIKGIRISSEAEAKE 532
           K  ILNN   G+ + +QE  +  R      K  + PDFVK+++AYG+K + I ++ E + 
Sbjct: 479 KTFILNNHIYGITKAYQETNFNGRAEACGPKGYAPPDFVKIAQAYGVKTVTIETQQEMEA 538

Query: 533 KLEEALTSREPVVIDVRV 550
           K+ E L +   VV DV +
Sbjct: 539 KIAEVLAADCAVVCDVNM 556


Lambda     K      H
   0.317    0.135    0.391 

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: 807
Number of extensions: 40
Number of successful extensions: 7
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: 574
Length of database: 613
Length adjustment: 37
Effective length of query: 537
Effective length of database: 576
Effective search space:   309312
Effective search space used:   309312
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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