GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Methanococcus aeolicus Nankai-3

Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_011973392.1 MAEO_RS03365 aspartate kinase

Query= reanno::Pedo557:CA265_RS23475
         (817 letters)



>NCBI__GCF_000017185.1:WP_011973392.1
          Length = 468

 Score =  315 bits (806), Expect = 5e-90
 Identities = 184/468 (39%), Positives = 294/468 (62%), Gaps = 22/468 (4%)

Query: 3   VLKFGGTSVGSAENIKTLLRLVGEEKQKNSP--VVVLSAMSGVTNLLTEMAEMAERGEDY 60
           V+KFGGTSVG  + I+ + +++ ++  K +   VVV SAMS +TN L  M++ A    D 
Sbjct: 4   VMKFGGTSVGDGQRIRNVAKIIVDKSNKENTDIVVVTSAMSQITNALVNMSKQALNVRDI 63

Query: 61  ---DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFN----ELEDLLQAVANLRELSL 113
              +  ++E++ KH   I     A   + + T ++   N    EL  +L  V+ L EL+ 
Sbjct: 64  AKINNFVEELKEKHAIAIDE---AVKNDDIRTEVRHVINSSIDELGKVLVGVSYLGELTP 120

Query: 114 QTKDQILSYGERCSTFMISHIASKNIG-DSIYVNGSDL-IKTDSNFGQAKVETELTEMLI 171
           ++KD ILS+GER S  ++S  A +++G +S+++ G +  + TD N+G A+      +  +
Sbjct: 121 KSKDYILSFGERLSAPILSG-AVRDLGKNSLFLLGGEAGLITDENYGCARPIKIKIKEKV 179

Query: 172 NNFYQENKDKVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMM 231
           N   +EN   +  +TGF+A    G +TT GRGGSDY+AA+ GA L+A+ +EIWTDV+G++
Sbjct: 180 NPLLEENI--IPIITGFVAGTENGDITTFGRGGSDYSAALVGAGLDADTVEIWTDVSGIL 237

Query: 232 TADPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGT 291
           T+DPR+VK    +P++SY EAMEL+YFGAKV++P T+ P   K IP+ IKNTFEP+  GT
Sbjct: 238 TSDPRIVKNVKRIPKMSYIEAMELAYFGAKVLHPRTVEPLMEKNIPLRIKNTFEPENEGT 297

Query: 292 YIKSDVKASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSS 351
           +I +  + S+  +K +S+I  + +IN+ G+GMVG +G + R+FS L R   NV+LITQ S
Sbjct: 298 FITNCKELSNSVMKAVSAIRDVFLINIFGAGMVGVSGTAARIFSALGRADANVLLITQGS 357

Query: 352 SEHSITFAV--KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPG 409
           SE +++  +     DA+  +  ++KEF+     K + + E   N+AV++ VG  MK + G
Sbjct: 358 SETNVSVVIYGDEVDANNCMKELRKEFKNSNLVKDISIDE---NVAVISAVGVGMKGSKG 414

Query: 410 MSGRLFNALGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAF 457
           ++G+LF A+  +G N++ IAQGSSE NIS +I +++L   +  +H  F
Sbjct: 415 IAGKLFGAVAESGANIKMIAQGSSEVNISFVIGEEELENCLRILHGRF 462


Lambda     K      H
   0.316    0.133    0.369 

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: 968
Number of extensions: 51
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: 817
Length of database: 468
Length adjustment: 37
Effective length of query: 780
Effective length of database: 431
Effective search space:   336180
Effective search space used:   336180
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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