GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dino:3607861
          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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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:

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