GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Sinorhizobium meliloti 1021

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate SMa0958 SMa0958 acetolactate synthase catalytic subunit

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__Smeli:SMa0958
          Length = 570

 Score =  247 bits (631), Expect = 8e-70
 Identities = 178/566 (31%), Positives = 278/566 (49%), Gaps = 34/566 (6%)

Query: 4   AEAMIKALEAEKVEILFGY--PGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARAS 61
           A+ +   L    VE +FG   P   +L    A     +  +  R E      ADGYAR S
Sbjct: 11  AQRIANILRRHGVEFIFGQSLPSAVIL----AAEAIGIRQIAYRQENMGGAMADGYARVS 66

Query: 62  GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121
           GKVGV    +GP AT LV  +A A   S P+VAL   V       +AFQ++D + LF   
Sbjct: 67  GKVGVVAAQNGPAATLLVPPLAEALKASVPIVALVQDVERDQTDRNAFQDLDQIALFQSC 126

Query: 122 VKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIG 181
            K   ++    +I +   +AF  A +GR GP  + LP D+   E    K P   + K +G
Sbjct: 127 TKWVRRVTVPERIDDYVDAAFTAAASGRAGPAALLLPADLLRAEA---KSPAVVRSKQLG 183

Query: 182 YNPTTIGHPRQ--IKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239
           + P     P    + +   LIA+A  PII+AGGGV   GA  EL  L +   +PV TT M
Sbjct: 184 HWPLDRVRPSDDALAEVASLIAAAHAPIIIAGGGVHCGGATHELAALQQEACLPVFTTNM 243

Query: 240 GKGCISENHPLALG----MVGMHGTKPANYCLSE-SDVLISIGCRFSDRITGDIKSFATN 294
           GKG + E HPL+ G    +VG       +Y L E +D++I IG R +   T   +   ++
Sbjct: 244 GKGAVDEYHPLSAGVLGSLVGPRSLGRYSYGLVEDADLVILIGTRTNQNGTDTWRQIPSS 303

Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAK---LILKEVIKQLDYIINKDSKENNDKENISQ 351
           A+++HID+DP EIG+N    + +VGDA+     L+  + ++D      ++ + D+  + +
Sbjct: 304 ARVVHIDVDPVEIGRNYEA-IRLVGDARESLAALRAALTRVDL-----TRRHGDRARLEE 357

Query: 352 WIENV-NSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMA 410
            I       +     V+     PI+P++++ EL  +     +  +  +  D   + MW+ 
Sbjct: 358 CIAQYWKGFELDRHDVVTSRSRPIRPERVMAELQDL-----LTGDVTVVADASYSSMWVL 412

Query: 411 HYFKTQ-TPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIA 469
              + + +   F++  GL  +G+G P AIGAKVA+P   VI + GDGGF  +  EL T+ 
Sbjct: 413 GQLRARASGMRFITPRGLAGLGWGVPLAIGAKVARPGKPVIAVVGDGGFAHSWAELETMV 472

Query: 470 EYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPN 529
              +PV I + +N  LG     + + +G    + +F    D  KLAE+ G  A R+E P 
Sbjct: 473 RMKLPVTIVVLNNGILGFQRDAETVKFGTYTTACHFAEV-DHAKLAEACGCPAVRVEDPG 531

Query: 530 EINEALKEAINCDEPYLLDFAIDPSS 555
           E+   L   ++   P L++   DP++
Sbjct: 532 ELAFHLHRGMD-QGPLLIEVMTDPAA 556


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: 716
Number of extensions: 27
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: 570
Length adjustment: 37
Effective length of query: 562
Effective length of database: 533
Effective search space:   299546
Effective search space used:   299546
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