GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Dyella japonica UNC79MFTsu3.2

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate N515DRAFT_0378 N515DRAFT_0378 acetolactate synthase, large subunit (EC 2.2.1.6)

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0378
          Length = 547

 Score =  266 bits (681), Expect = 1e-75
 Identities = 175/562 (31%), Positives = 266/562 (47%), Gaps = 40/562 (7%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           MN A   +KALEAE V  +FG PG   L   +AL  S +  ++TRHEQAA   A  + R 
Sbjct: 1   MNAAALFVKALEAEGVRRIFGVPGEENLDLVEALRDSKIELIVTRHEQAAGFMAATWGRL 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +G+ GV + T GPGATNLVT  A A   + PM+ +TGQ P +      FQ +D + +  P
Sbjct: 61  TGEAGVALSTLGPGATNLVTAAAYAQLGAMPMLMITGQKPIRTHKQGLFQLVDVVDMMQP 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQE--------LELDIDKHP 172
           + K+  QI     IP   R AF  A+  RPG VH++LP+D+          L  +  + P
Sbjct: 121 LTKYTRQIVSAPTIPARVREAFRRAEEERPGAVHLELPEDIARDSVDEAILLPTEYARRP 180

Query: 173 IPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232
            P    L+              +A + I +AK PI++ G           L   ++ L I
Sbjct: 181 SPDDAALV--------------QAGEAITAAKHPILMIGAAANRQRTAVALRTFIDKLGI 226

Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFA 292
           P  TT MGKG + E+HPL LG   +      +  +  +DV++++G    ++         
Sbjct: 227 PFFTTQMGKGVVDEDHPLWLGNAALSDGDFVHRAIDAADVIVNVGHDVVEK--PPFFMHK 284

Query: 293 TNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352
               +IHI+   AE+       + +VGD    +   +++L      D+       N   +
Sbjct: 285 GRRTVIHINFSSAEVDTVYFPQIEVVGD----IAHTVERL-----TDALTPQAHWNFKYF 335

Query: 353 IENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412
            +   +  +      D    PI P ++V +    + D     + ++  D G  ++W A Y
Sbjct: 336 DQVREAFHRQLAEHADDPRFPIHPVRLVADTRRYMPD-----DGVLCLDNGMYKIWYARY 390

Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472
           ++ + P + L    L TMG G PSA+ AK+  P+ KV+ I GDGGFMMN QEL T     
Sbjct: 391 YRARQPNTVLLDNALATMGAGLPSAMAAKLVYPERKVLAICGDGGFMMNAQELETAVRLK 450

Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEIN 532
           + +VI +  +   GM+ +W+    G     + F   PDF+K AE++G    R ES +   
Sbjct: 451 MDLVILLLRDDAYGMI-RWKQAEMGYADFGMQFSN-PDFVKFAEAHGAHGHRPESADAFL 508

Query: 533 EALKEAINCDEPYLLDFAIDPS 554
             LK A      +L+D AID S
Sbjct: 509 PTLKRAFEQGGVHLIDLAIDYS 530


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: 667
Number of extensions: 32
Number of successful extensions: 5
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: 599
Length of database: 547
Length adjustment: 36
Effective length of query: 563
Effective length of database: 511
Effective search space:   287693
Effective search space used:   287693
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