GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Marinobacter adhaerens HP15

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate GFF3176 HP15_3118 acetolactate synthase, large subunit, biosynthetic type

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__Marino:GFF3176
          Length = 556

 Score =  281 bits (718), Expect = 7e-80
 Identities = 181/557 (32%), Positives = 281/557 (50%), Gaps = 31/557 (5%)

Query: 2   NGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARAS 61
           NGAE  I+ALE E VE +F  PG   L F +AL  S +  +L RHEQAA   A  Y R +
Sbjct: 10  NGAELFIRALENEGVEYIFAVPGEENLAFLEALRTSSIQLVLNRHEQAAGFMAATYGRLT 69

Query: 62  GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121
           G+VGVC+ T GPGATN VT  A A     PM+ ++GQ P K      FQ +D + L  P+
Sbjct: 70  GRVGVCLSTLGPGATNFVTAAAYAQLGGMPMMMISGQKPIKSSKQGLFQILDVVDLMRPL 129

Query: 122 VKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPI-PSKVKLI 180
            K+  QI     IP   R AF +A   RPG VH++LP+D+ +   + D H   PS  +  
Sbjct: 130 TKYTRQISNANTIPAKVREAFRLASEERPGAVHLELPEDIADEAPESDTHIFKPSDAR-- 187

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
              P+    P+ ++ A +++  A+ P+I+ G G      ++ LL LV +  IP  TT MG
Sbjct: 188 --RPS--ASPKSLEMACEMLREARHPLIMIGAGANRKRVSQALLHLVNVTGIPFFTTQMG 243

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFAT--NAKII 298
           KG + E HP  LG   +      +  +  +D++I++G      +      F T    K+I
Sbjct: 244 KGVVDERHPRYLGNAALSAGDFVHCAIDRADLVINVG----HDVVEKPPFFMTPGGKKVI 299

Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYII-NKDSKENNDKENISQWIENVN 357
           H++   A++         +VGD       +   ++Y+  N     N+D   + +  E V+
Sbjct: 300 HVNFSAADVDPVYFPQHEVVGD-------IANSVEYMAENCGQCANHDFTRLMEVKEAVD 352

Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417
           +  +      + D  P+ PQ+IV ++  V+ D     + IIT D G  ++W A  ++   
Sbjct: 353 AHLQER---AEDDRFPVIPQRIVHDVRQVMPD-----DGIITLDNGMYKLWFARNYRAYD 404

Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477
             + L    L +MG G PS + A +  PD KV+ I GDGGFMMN QEL T    N+ +V+
Sbjct: 405 NNTVLLDNALASMGAGLPSGMMASMLYPDLKVMAICGDGGFMMNSQELETAVRLNLNLVV 464

Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537
            I ++   GM+ +W+    G     +++   PDF+  A+SYG K  R+    ++   L+ 
Sbjct: 465 LIINDSAYGMI-KWKQGQEGYSDFGLDYRN-PDFVTYAQSYGAKGHRLTRTEDLRPTLEG 522

Query: 538 AINCDEPYLLDFAIDPS 554
           A+     +++D  +D S
Sbjct: 523 ALAEGGVHVVDVPVDYS 539


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: 750
Number of extensions: 38
Number of successful extensions: 4
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: 556
Length adjustment: 36
Effective length of query: 563
Effective length of database: 520
Effective search space:   292760
Effective search space used:   292760
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