GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Cupriavidus basilensis 4G11

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate RR42_RS19850 RR42_RS19850 glyoxylate carboligase

Query= curated2:O08353
         (599 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS19850 RR42_RS19850 glyoxylate
           carboligase
          Length = 591

 Score =  343 bits (881), Expect = 9e-99
 Identities = 194/604 (32%), Positives = 334/604 (55%), Gaps = 34/604 (5%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLI-HLLTRHEQAAAHAADGYAR 59
           M   +A I  LE E +   FG PG A+ PFY A+  +  I H L RH + A+H A+GY R
Sbjct: 4   MRAVDAAIAVLEKEGITTAFGVPGAAINPFYSAMRRAGTIDHFLARHVEGASHMAEGYTR 63

Query: 60  A-SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118
           A +G +GVCIGTSGP  T+++TG+ +A +DS P++ +TGQ P   +  + FQ +D   + 
Sbjct: 64  AEAGNIGVCIGTSGPAGTDMITGLYSAWADSIPILCITGQAPRARLYKEDFQAVDIESIA 123

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178
            P+ K    +++   +P++F+ AF + ++GRPGPV IDLP DVQ  E++ D     +   
Sbjct: 124 KPVTKWAVTVREPALVPQVFQQAFHLMRSGRPGPVLIDLPFDVQVAEIEFDPE---TYQP 180

Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238
           L  Y P  +    QI+KAI ++ +A+RP+I+ GGGV+ + A E L++  EL+N+PV  TL
Sbjct: 181 LAPYKP--VASRAQIEKAIAMLNAAERPLIVCGGGVINADAAELLVEFAELVNVPVVPTL 238

Query: 239 MGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKI 297
           MG G ++++HPL  GMVG+  + +  N  +  SD ++ IG R+++R TG ++ +    K 
Sbjct: 239 MGWGVLADDHPLQAGMVGLQTSHRYGNATMLASDFVLGIGNRWANRHTGSVEVYTKGRKF 298

Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357
           +H+DI+P +IG+    D+ IV DAK  L++ ++     + ++ K          W+ +V 
Sbjct: 299 VHVDIEPTQIGRVFGPDLGIVSDAKAALEQFVE-----VAREMKMAGRLPCRKSWVADVQ 353

Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417
             +++     D+D++P+KPQ++ +E+     +    ++    + +G +Q+  A +     
Sbjct: 354 KRRRTMQRKSDFDNVPVKPQRVYREM-----NQYFPRDVRYVSTIGLSQIAAAQFLSVNE 408

Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477
           PR +++ G  G +G+  P+AIG KVA P+S V+ I+GD  F    +EL   A++ +P + 
Sbjct: 409 PRHWINCGQAGPLGWTIPAAIGVKVASPESDVVAISGDYDFQFMIEELAVAAQFKVPYIH 468

Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKARRIESP 528
            + +N  LG++ Q Q  F       + F         G   D +K+ E  G KA R+  P
Sbjct: 469 LVVNNSYLGLIRQAQRNFEMDYCVQLAFDNVNSPELNGYGVDHVKVVEGLGCKAIRVFKP 528

Query: 529 NEINEALKEA----INCDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQEHPNEKIVCF 584
            +I  A  EA         P +++  ++  + ++M   G ++ NI +       E+ +  
Sbjct: 529 EDIAPAFAEARDLMAEFSVPVVVEVILERVTNIAM---GTEIDNINEFEPIEDIEEAILK 585

Query: 585 DEIK 588
           +E++
Sbjct: 586 EEVE 589


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: 753
Number of extensions: 32
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 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