Alignments for a candidate for ilvI in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI 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)



>NCBI__GCF_000009985.1:WP_011383235.1
          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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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