GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Paraburkholderia bryophila 376MFSha3.1

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate H281DRAFT_00787 H281DRAFT_00787 tartronate-semialdehyde synthase

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__Burk376:H281DRAFT_00787
          Length = 591

 Score =  327 bits (837), Expect = 1e-93
 Identities = 181/553 (32%), Positives = 310/553 (56%), Gaps = 33/553 (5%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHS-DLIHLLTRHEQAAAHAADGYAR 59
           M   +A +  LE E ++  FG PG A+ PFY A+  + ++ H+L RH + A+H A+GY R
Sbjct: 4   MRAVDAAVLVLEKEGIDTAFGVPGAAINPFYSAMRRAGNISHVLARHVEGASHMAEGYTR 63

Query: 60  AS-GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118
           A  G +GVCIGTSGP  T+++TG+ +A +DS P++A+TGQ P   +  + FQ +D   + 
Sbjct: 64  AQPGNIGVCIGTSGPAGTDMITGLYSAQADSIPILAITGQAPRARLYKEDFQAVDIESIA 123

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQ--ELELDIDKH-PIPS 175
            P+ K    +++   +P +F+ AF + ++GRPGPV +DLP DVQ  E+E DID + P+P 
Sbjct: 124 KPVTKWAVTVREPALVPRVFQQAFHLMRSGRPGPVLVDLPIDVQLAEIEFDIDTYEPLPV 183

Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235
                 Y P      +QI+ A+ L+  +++P+I++GGGVL + A + L++  E + +PV 
Sbjct: 184 ------YKPKAT--RKQIEAALTLLNDSEKPLIVSGGGVLNAAAEDLLVRFAETVGVPVI 235

Query: 236 TTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSFATN 294
            TLM  G I ++HPL  GMVG+  + +  N  +  SD ++ IG R+++R TG I  +   
Sbjct: 236 PTLMSWGAIPDDHPLMAGMVGLQTSHRYGNATMLASDFVLGIGNRWANRHTGSIDVYTKG 295

Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIE 354
            K +H+DI+P +IG+    D+ IV DAK  L+  ++     +  + K     ++ S W+ 
Sbjct: 296 RKFVHVDIEPTQIGRVFGPDLGIVSDAKAALELFVE-----VASEWKAAGKLKDRSAWVA 350

Query: 355 NVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFK 414
           +    K++      +D++P+KPQ++ +E+  V       ++T   + +G +Q+  A +  
Sbjct: 351 DCQQRKQTMHRKTHFDNVPMKPQRVYEEMNQV-----FGRDTCYVSTIGLSQIAGAQFLH 405

Query: 415 TQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIP 474
               R++++ G  G +G+  P+A+G + A P   ++ ++GD  F    +EL   A++ +P
Sbjct: 406 VYKARNWINCGQAGPLGWTIPAALGVRAADPQRPIVALSGDYDFQFMIEELAAGAQFKLP 465

Query: 475 VVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKARRI 525
            V  + +N  LG++ Q Q  F       + F         G   D + +AE  G KA R+
Sbjct: 466 YVHVVVNNSYLGLIRQAQRAFDMDFCVQLGFENINSPETNGYGVDHVAVAEGLGCKAIRV 525

Query: 526 ESPNEINEALKEA 538
             P E+  AL++A
Sbjct: 526 FKPEELKPALQKA 538


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: 782
Number of extensions: 41
Number of successful extensions: 7
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: 591
Length adjustment: 37
Effective length of query: 562
Effective length of database: 554
Effective search space:   311348
Effective search space used:   311348
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