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 isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate Ga0059261_0285 Ga0059261_0285 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__Korea:Ga0059261_0285
          Length = 552

 Score =  220 bits (561), Expect = 1e-61
 Identities = 163/546 (29%), Positives = 250/546 (45%), Gaps = 36/546 (6%)

Query: 2   NGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD-GGVEHLLCRHEQGAAMAAIGYARA 60
           NG + +V  L AQG + +F  PG + + V DAL+D   ++ + CR E GAA  A      
Sbjct: 6   NGGRILVDNLVAQGCDRIFHVPGESFLAVLDALHDVPEIDLVTCRQEGGAAFMACADGTM 65

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           TGK GVC  T GPGATN   G+  A+ DS P++   G V       + FQEVD   +   
Sbjct: 66  TGKPGVCFVTRGPGATNASIGVHVAMQDSQPMLLFIGDVDRSMRDREGFQEVDFPAMFAP 125

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
             K +  ++    +P  +A A++VA SGRPGPV++ +P+D+ L   +       V+  V+
Sbjct: 126 LAKWATRIEDARRIPEYVARAWNVATSGRPGPVVIALPEDMLLDEVE------AVDRPVS 179

Query: 181 FPHA--------EVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLK 232
            P+            Q  + +  A++PM  VGG             F     +P     +
Sbjct: 180 TPYPLMPDVNEDAAHQIVERIRAAKRPMAIVGGAGWDISTGRDFATFAERWGIPVAGAFR 239

Query: 233 GLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPH---AS 289
              A+      + G LG          +++ DLL+ VGAR  +  T       P     +
Sbjct: 240 RQDAIANTSSAWAGNLGYGPNPKLVQRIRDADLLLVVGARLGEATTDGYTLVTPDHPGQT 299

Query: 290 VIHMDIDPAEMNKLRQAHVA------LQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSW 343
           +IH+  DP E+N++  A +A      +  D+ + L  L  P +    + H   L     W
Sbjct: 300 LIHVHPDPEELNRVYHADMAVCCDVGIFADMLSSLKPLDTPFSGAA-EAHAEWL----DW 354

Query: 344 RYDHPGDAIYAPL--LLKQLSDR-KPADCVVTTDVGQHQMWAAQHIAH-TRPENFITSSG 399
               P + +   L   +  + +R  P D ++    G    W  ++  +  +P     +S 
Sbjct: 355 STPKPREGVTLDLGQCVAAMRERLGPDDAIICNGAGNFSGWWHRYWHYGAQPTQLAPTS- 413

Query: 400 LGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLG 459
            G MG+G PAAV A +   +   V ++GDG FMMN QEL T  +    L ++++DN   G
Sbjct: 414 -GAMGYGTPAAVAAALRLRDRLAVALAGDGDFMMNGQELATAIQHDADLLVLIIDNGAYG 472

Query: 460 MVRQWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYL 519
            +R  Q+  F  R S TTL  NPDF  LA A+G   + + + D+   ALD  L   G  L
Sbjct: 473 TIRMHQEREFPARLSGTTL-HNPDFAALARAYGCWAETVVKTDEFAPALDRALAQTGVRL 531

Query: 520 LHVSID 525
           LH+  D
Sbjct: 532 LHLKTD 537


Lambda     K      H
   0.320    0.135    0.410 

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: 754
Number of extensions: 40
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: 548
Length of database: 552
Length adjustment: 36
Effective length of query: 512
Effective length of database: 516
Effective search space:   264192
Effective search space used:   264192
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 (21.8 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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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