Aligments for a candidate for ilvH in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Dinoroseobacter shibae DFL-12

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate 3607861 Dshi_1269 thiamine pyrophosphate protein central region (RefSeq)

Query= curated2:O08353
         (599 letters)



>lcl|FitnessBrowser__Dino:3607861 Dshi_1269 thiamine pyrophosphate
           protein central region (RefSeq)
          Length = 621

 Score =  152 bits (383), Expect = 5e-41
 Identities = 147/587 (25%), Positives = 262/587 (44%), Gaps = 58/587 (9%)

Query: 4   AEAMIKALEAEKVEI-------------LFGYPGGALLPFYDALH-HSDLIHLLT-RHEQ 48
           A+A+I+ L A+ +E              +FG+  G +    +ALH H + + L   ++EQ
Sbjct: 11  AQAIIRYLNAQFIETDGTRQRVCGGGFGIFGH--GNVTCLGEALHDHRETLPLYRGQNEQ 68

Query: 49  AAAHAADGYAR--ASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGN 106
           +   AA  YA+     +   C  ++GPG  NL+T  A AH++  PM+ L G      + +
Sbjct: 69  SMGFAAAAYAKYHLRRRFMFCTASAGPGTANLLTASALAHANRLPMLMLCGDTFLTRLPD 128

Query: 107 DAFQEID-----ALGL---FMPIVKHNFQIQKTCQIPEIFRSAFE-IAQTGRPGPVHIDL 157
              Q+++     ALGL   F  + ++  +I    Q+ +   +A   +      GP  + L
Sbjct: 129 PVLQQLEHYGNPALGLNDAFHAVTRYWDRITHPAQVIQSLPAALATMLDPADCGPAFLAL 188

Query: 158 PKDVQELELDIDKHPIPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLS 217
           P+DVQ    D  +     K   I           ++ +A  L+ SA+RP+I+AGGGV  S
Sbjct: 189 PQDVQGWAYDYPRAFFEEKTHRIR---RITPDADEVAEAAALLRSAERPVIIAGGGVQYS 245

Query: 218 GANEELLKLVELLNIPVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIG 277
           GA  EL    E   IPV  T+ G+  +  +HPL +G VG+ G+  AN    ++DV++++G
Sbjct: 246 GAVAELTGFAEAHGIPVIETIAGRANLLADHPLNIGPVGVTGSDSANAIAEQADVILAVG 305

Query: 278 CRFSDRITGDIKSFATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIIN 337
            R  D  TG   +FA  A+ I ++    + GK  +  +PIVGDAKL L  +   L     
Sbjct: 306 TRLQDFTTGSWTAFAQEARFIALNAARHDAGK--HRALPIVGDAKLGLVALEAAL----- 358

Query: 338 KDSKENNDKENISQWIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTI 397
                  D      W     + +K     +  +  P        + + V++ L   ++ +
Sbjct: 359 ------GDYRCPEAWRNYAQTERKGWDAYVADNVRPGNRPNSYAQAIGVVNALCEPRDRV 412

Query: 398 ITTDVGQNQMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVA----KPDSKVICIT 453
           +    G      A++ +T    +     G   MG+      GA++A    +P++  I   
Sbjct: 413 VAAAGGLPAEVTANW-RTLDIGTVDVEFGFSCMGYEIAGGWGARIAQTEVEPEADTIVFC 471

Query: 454 GDGGFMMNCQELGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAP---- 509
           GDG +++   ++ +       +++ + DN    ++ + QN   G    +     AP    
Sbjct: 472 GDGSYLLMNSDIYSSVLTRKKMIVLVLDNGGFAVINKLQN-NTGNESFNNLLADAPTIPE 530

Query: 510 ----DFIKLAESYGIKARRIESPNEINEALKEAINCDEPYLLDFAID 552
               DF+  A + G +A ++ + +E+ EA K A   D+  ++  ++D
Sbjct: 531 AFGVDFVAHAAAMGAEATQVANADELAEAFKAAKASDKTTVIVMSVD 577


Lambda     K      H
   0.319    0.137    0.405 

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: 775
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 599
Length of database: 621
Length adjustment: 37
Effective length of query: 562
Effective length of database: 584
Effective search space:   328208
Effective search space used:   328208
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 (21.7 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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Steps (tab-delimited)
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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 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

GapMind for Amino acid biosynthesis