Alignments for a candidate for ilvI in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sphingomonas koreensis DSMZ 15582

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate Ga0059261_0603 Ga0059261_0603 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

Query= curated2:Q02137
         (575 letters)



>FitnessBrowser__Korea:Ga0059261_0603
          Length = 607

 Score =  240 bits (613), Expect = 1e-67
 Identities = 176/579 (30%), Positives = 267/579 (46%), Gaps = 37/579 (6%)

Query: 13  SQLVLQTLKELGVEIIFGYPGGAMLPLYDAIHNFEGIQHILARHEQGATHEAEGYAKSSG 72
           S  V  TL + G+  +F   GG  + L  ++     ++     HEQ     AE Y + + 
Sbjct: 7   SDWVADTLAQRGIRDVFMLTGGGAMHLNHSLGTHPALKTTFTHHEQALAMAAEAYYRLTN 66

Query: 73  KVGVVVVTSGPGATNAVTGIADAYLDSVPLLVFTGQVGP--------LSIGKDAFQEADT 124
           ++ VV VTSGPG TNA+TG+  AY+DS+ +LV +GQV          L + +   QE D 
Sbjct: 67  RLAVVNVTSGPGGTNAITGVYGAYVDSIGMLVISGQVKTETTVRHTGLPLRQFGDQELDI 126

Query: 125 VGITAPITKYNYQIRETADIPRIVTEAYYLARTGRPGPVEIDLPKDVSTLEVTEINDPSL 184
             +  PITKY   + +   I   + +A +LA +GRPGPV +D+P DV   ++    DP  
Sbjct: 127 EELVRPITKYATMVLDPRSIRYHLEKAIHLATSGRPGPVWLDIPLDVQAAKI----DPDD 182

Query: 185 NLPHYHESE-------KATDEQLQELLTELSVSKKPVIIAGGGINYSGSVDIFRAFVEKY 237
            LP +  +E          D     +L +L+ +++PV+ AGGG+  SG+ D F   +E+ 
Sbjct: 183 LLPGFDPAELDQPWQAADLDATADAILAKLAAAQRPVVFAGGGVRLSGAHDAFLKLIERL 242

Query: 238 QIPVVSTLLGLGTLPISHELQLGMAGMHGSYAANMALVEADYIINLGSRFDDRVVS-NPA 296
            IPVV+       L   H L  G  G  G    NM    AD ++ LGSR + R VS N  
Sbjct: 243 GIPVVTGWNAHDVLWNDHPLYCGRPGTVGDRGGNMVTQSADLLLVLGSRLNIRQVSYNWK 302

Query: 297 KVAKNAVVAHIDIDAAELGK-IVKTDIPILSDLKAALSRLLQL-----NKVRTDFNDWIK 350
             A+ A    +DID  EL K  V  D+P+++DL   +  LL            ++ DW +
Sbjct: 303 SFAREAYKIWVDIDPVELAKPTVTPDMPVVADLADLIPALLDRPYAGPTPAHDEWLDWSR 362

Query: 351 TVTKNKEKAPFTYEPQNHDIRPQETIKLIGEYTQGDAIIVTDVGQHQMWVAQYYPYKNAR 410
               N       Y      I P   +  +      D ++VT  G   +   Q    K  +
Sbjct: 363 ERVFNFPAVLPEYRHHGPSIHPYVAMDELFVQLGEDDVVVTGNGSACVVSFQTANLKQGQ 422

Query: 411 QLITSGGMGTMGFGIPAAIGAKLA-QPNKNVIVFVGDGGFQMTNQELALLNGYGIAIKVV 469
           +L T+ G  TMG+ +PAAIG   A    K +I   GDG   M  QEL  + GY + +KV 
Sbjct: 423 RLWTNSGCATMGYDLPAAIGVWAATNGEKRIIAIAGDGSIMMNIQELQTIAGYDMPVKVF 482

Query: 470 LINNHSLGMVRQWQESFYE------ERRSQSVFDVEPNFQLLAEAYGIKHVKLDNPKTLA 523
           L+NN     + Q   +F+         +S   F   P+F  +A A+G  + + ++   L 
Sbjct: 483 LVNNSGYVSIFQTHRNFFNGVEVGGGPKSNVTF---PDFGKVATAFGFAYFRAESHNDLP 539

Query: 524 DDL-KIITEDEPMLIEVLISKSEHVLPMIPAGLHSDEMI 561
             +   +  D P+L E++I +     P + A  H D  I
Sbjct: 540 GTIAAALAADGPVLCELIIDEHVGFAPKLGAKAHPDGRI 578


Lambda     K      H
   0.316    0.135    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: 878
Number of extensions: 41
Number of successful extensions: 6
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: 575
Length of database: 607
Length adjustment: 37
Effective length of query: 538
Effective length of database: 570
Effective search space:   306660
Effective search space used:   306660
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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Protein sequences (fasta format)
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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