GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Cupriavidus basilensis 4G11

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate RR42_RS36655 RR42_RS36655 hypothetical protein

Query= BRENDA::O53554
         (515 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS36655 RR42_RS36655 hypothetical
           protein
          Length = 512

 Score =  459 bits (1180), Expect = e-133
 Identities = 258/516 (50%), Positives = 329/516 (63%), Gaps = 10/516 (1%)

Query: 1   MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60
           MNGA++L+ TL+  GVD CFANPGTSEMHFVAALD +P MR +L LFEGV TGAADGYAR
Sbjct: 1   MNGAESLVKTLLACGVDTCFANPGTSEMHFVAALDRIPGMRCVLGLFEGVVTGAADGYAR 60

Query: 61  IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120
           +A +PAA LLH GPGL NGLANLHNARRA+ P++ +VGD ATYH+ +DAPL +D +  A 
Sbjct: 61  MADKPAATLLHCGPGLANGLANLHNARRAQTPVINIVGDQATYHRPFDAPLTADTEGWAR 120

Query: 121 TVSGWVRRTEAAADVGADAEAAI-AASRSGSQIATLILPADVCWSDGAHAAAGVPAQ--- 176
            VS W R    AA VGADA  A+ AA  +   +A+LILP+DVCW  G     GVP     
Sbjct: 121 PVSVWTRTATDAASVGADAATAVQAACAAPGGVASLILPSDVCWDAG--GKVGVPLAPLP 178

Query: 177 -AAAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLE 235
               +P  V   A +LRSG+P ++++ G A R   L  A RI  AT AR +       + 
Sbjct: 179 VPKVSPDAVQQAARLLRSGQPTLIVLAGTALREVPLADAHRIAAATDARLITPMSNARVS 238

Query: 236 RGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLA 295
           RG G   V+R+ Y  + A  +L G+++++L GA  PV+FFAYPG      P   E+HVLA
Sbjct: 239 RGRGRFNVDRVPYSGDVARDKLAGIRNVILVGAPPPVTFFAYPGKSPRPYPEDAEIHVLA 298

Query: 296 EP-GGAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDE 354
            P    A+ALA LADE+   +V+  A  +   +  G +TS + A  + ALLPE+AIVV+E
Sbjct: 299 RPEQDLAEALARLADELGAPSVSVPASVAPRGIAKGAVTSEAVAQTLTALLPEQAIVVEE 358

Query: 355 SNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTI 414
           S + G      T  A  HDWL LTGGAIG G+P A GAAVAAP R V+ L++DGS MYT+
Sbjct: 359 SVSFGRAFYPGTVHAAPHDWLQLTGGAIGDGLPLATGAAVAAPGRRVVALQADGSGMYTL 418

Query: 415 SGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIA 474
             LW+ ARE LDVT VI  N  Y IL  EL   G G++PG  ALD+LDI  P +D+V++A
Sbjct: 419 QSLWTMAREKLDVTVVILANRKYAILLGEL--AGVGANPGKTALDMLDIGNPDLDWVQLA 476

Query: 475 EGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510
            GMGV A R    E FA+    A    GP +I++V+
Sbjct: 477 NGMGVEAARAEDMERFAELFGMANGRRGPFVIELVI 512


Lambda     K      H
   0.318    0.134    0.402 

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: 640
Number of extensions: 24
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: 515
Length of database: 512
Length adjustment: 35
Effective length of query: 480
Effective length of database: 477
Effective search space:   228960
Effective search space used:   228960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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