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

GapMind for Amino acid biosynthesis

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00787 H281DRAFT_00787
           tartronate-semialdehyde synthase
          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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis