GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Novosphingobium barchaimii LL02

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_059150016.1 V474_RS02810 acetolactate synthase large subunit

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_001046635.1:WP_059150016.1
          Length = 557

 Score =  268 bits (686), Expect = 3e-76
 Identities = 171/556 (30%), Positives = 273/556 (49%), Gaps = 30/556 (5%)

Query: 4   AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHL-LTRHEQAAAHAADGYARASG 62
           ++  I+ LE E VE +FG PG   L F D+L  S  I L LTRHEQ A   A  Y R +G
Sbjct: 10  SDLFIECLEQEGVEYIFGVPGEENLDFLDSLSRSKQIKLILTRHEQGAGFMAATYGRHTG 69

Query: 63  KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122
           K GVC+ T GPGATN VT  A A     PM+ +TGQ P K      FQ +D + +  PI 
Sbjct: 70  KAGVCLSTLGPGATNFVTAAAYATLGGMPMLMITGQKPIKKSKQGRFQILDVVSMMQPIT 129

Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGY 182
           K+  Q+  +  IP   R AF IA+  +PG  HI+LP+D+ +     D  P+P   + I  
Sbjct: 130 KYAHQMASSDNIPSRVREAFRIAEEEKPGATHIELPEDIADEH--TDSRPVP---RSIVR 184

Query: 183 NPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKG 242
            PT     + I +A+  +  AKRP+++ G G      ++ L + VE   IP  TT +GKG
Sbjct: 185 RPT--ADVKSIVQAVDALQKAKRPVLVIGAGANRKMTSKMLGEFVEKTGIPFLTTQLGKG 242

Query: 243 CISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDR----ITGDIKSFATNAKII 298
            I E HP  LG   +      +  + ++D +++IG    ++    +T D      +  +I
Sbjct: 243 VIDERHPKFLGCAALSAGDFVHRAIEDADCIVNIGHDVIEKPPFFMTND--GTRDDRTVI 300

Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358
           H+    AE+       + ++GD    + ++         K++   ++K +    +    +
Sbjct: 301 HVSTKTAEVDPVYFPHIEVIGDIANAMWQI---------KEAITPSEKWSFDAMLRYRQA 351

Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
             + +  +   +  PI P   V+++   + D     + II  D G  ++W A  +  + P
Sbjct: 352 EVEHTAKLAADERFPIFPPHAVQQVRDALPD-----DAIICLDNGIYKIWFARGYSARGP 406

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
            + L    L TMG G PSA+ + +  P  KV+ + GDGGFMMN QE+ T     + + + 
Sbjct: 407 NTVLLDNALATMGAGLPSAMASAMVYPGRKVLAVCGDGGFMMNSQEVETAVRLGLDLTVL 466

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           I ++   GM+ +W+    G     +++G  PDF+K AE+YG    R+ES   + E L   
Sbjct: 467 ILNDNAYGMI-RWKQANMGFADFGLSYGN-PDFVKYAEAYGANGYRVESSGHLQELLVHC 524

Query: 539 INCDEPYLLDFAIDPS 554
            +    +++D  +D S
Sbjct: 525 RDTPGVHIIDCPVDYS 540


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: 761
Number of extensions: 39
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: 557
Length adjustment: 36
Effective length of query: 563
Effective length of database: 521
Effective search space:   293323
Effective search space used:   293323
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 Jul 26 2024. The underlying query database was built on Jul 25 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:

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