GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Methanobacterium lacus AL-21

Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_013644806.1 METBO_RS06070 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein

Query= reanno::HerbieS:HSERO_RS16440
         (413 letters)



>NCBI__GCF_000191585.1:WP_013644806.1
          Length = 439

 Score =  214 bits (546), Expect = 3e-60
 Identities = 138/430 (32%), Positives = 229/430 (53%), Gaps = 21/430 (4%)

Query: 2   NDKKTYGFTTTILHSDRQK-GIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60
           N+ +  G +T  LH  +++     GS   PI+ + ++ + D    A +F  ++ G  Y R
Sbjct: 8   NEWQGPGLSTIGLHVGQEEPDSATGSRAVPIYLTSSYVFNDTEHAANLFGLREFGNIYTR 67

Query: 61  QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW 120
             NPT    E ++  +E G + +  A+GM+AI   V  +   G+++VS   L+G T  L+
Sbjct: 68  IMNPTTDVFEKRVAAVEGGATALGVASGMSAIFLAVLNVSELGENIVSGDNLYGGTYELF 127

Query: 121 -MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179
             T+   G  V  V++   +  EAAI   TR ++VE++ NP+  V D +++ ++  +  I
Sbjct: 128 NYTLPRLGRTVKFVNSEKPEEFEAAIDEKTRAIYVESLGNPKLDVPDFEKLAKIAHDHDI 187

Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIA 237
             +VDNT T   L RP   GA + V S TK IGGHG ++GG + D+G+F+W   ++P   
Sbjct: 188 PLIVDNTSTVG-LLRPIDYGADITVISATKYIGGHGTSIGGVIVDSGKFNWGNGKFPQFT 246

Query: 238 ------------ENYKKNPAPQWGMAQIRAKA--LRDFGGSLGPEAAHHIAVGAETIALR 283
                       E +   P        IRA+   LRD G +L P  A     G ET+ LR
Sbjct: 247 DPDPSYHGLKYWETFGDFPGAGNIAFTIRARVVLLRDLGPALSPFNAFQFLQGLETLELR 306

Query: 284 QERECKNALALAQMLQADERVAAVYYPGLESHPQHAL-SKALFRSFGSLMSFELKDGIDC 342
             +  +NAL +A+ L+   +V+ + YPGLE  P+H + SK L   +G L+ F ++ G++ 
Sbjct: 307 VLKHAENALKVAKHLKNHPKVSWINYPGLEEDPRHEVASKYLKGGYGGLIGFGIEGGLES 366

Query: 343 FD-YLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTD 401
              ++  + L    +N+GD+++LVI  A T   ++  E + + G+ E  +R+S+GLED +
Sbjct: 367 GKKFIENVELFSHLANIGDSKSLVIHPASTTHQQLTREEQETTGVTEDFVRLSIGLEDVE 426

Query: 402 DLVADFRQAL 411
           D++AD  QAL
Sbjct: 427 DIIADIDQAL 436


Lambda     K      H
   0.319    0.134    0.391 

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: 470
Number of extensions: 20
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: 413
Length of database: 439
Length adjustment: 32
Effective length of query: 381
Effective length of database: 407
Effective search space:   155067
Effective search space used:   155067
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 (21.8 bits)
S2: 51 (24.3 bits)

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

Links

Downloads

Related tools

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