GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metB in Paraburkholderia bryophila 376MFSha3.1

Align cystathionine γ-lyase (EC 2.5.1.48) (characterized)
to candidate H281DRAFT_06059 H281DRAFT_06059 O-succinylhomoserine sulfhydrylase

Query= metacyc::HP0106-MONOMER
         (380 letters)



>FitnessBrowser__Burk376:H281DRAFT_06059
          Length = 396

 Score =  255 bits (651), Expect = 2e-72
 Identities = 140/371 (37%), Positives = 217/371 (58%), Gaps = 15/371 (4%)

Query: 22  SVPIYQTSTY----RQDAIGRHKG----YEYSRSGNPTRFALEELIADLEGGVKGFAFAS 73
           S  I+ TS++      DA  R K     Y YSR  NPT    ++ +A LEGG    A AS
Sbjct: 25  SEAIFLTSSFVFASAADAAERFKNSEDYYTYSRFTNPTVSMFQDRLAALEGGEACMATAS 84

Query: 74  GLAGIHAV-FSLLQSGDHVLLGDDVYGGTFRLFNQVLVKNGLSCTIIDTSDISQIKKAIK 132
           G+A I +V  S LQ+GDH++    ++G T  +F+Q+  K G++ T +D +++   K A++
Sbjct: 85  GMAAIMSVVMSTLQAGDHLVSSQALFGSTLGMFSQIFSKFGITTTFVDPTNLDAWKNAVR 144

Query: 133 PNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVAHS 192
           P TK  +LETPSNPL ++ D+   + +AK    L +VDN F +P  Q PL LGAD+V HS
Sbjct: 145 PETKMFFLETPSNPLTEVADIEAISKIAKAANALFVVDNCFCSPALQQPLKLGADVVMHS 204

Query: 193 GTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIKTLGLRMEAH 252
            TK+L G   V+ G +  + + + +++  F  + G  L   ++W+L +G++TL LR+E  
Sbjct: 205 ATKFLDGQGRVLGGALVGSKKFIMEKVFPFVRSAGPTLSAFNAWVLLKGMETLSLRVEKQ 264

Query: 253 QKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKND------SE 306
             NAL +A +L+ HP V+RV+YPGL +HP + LA +Q +    ++SF LK D      + 
Sbjct: 265 SANALEIARWLDDHPSVKRVFYPGLESHPQHALAMRQQKAGGAIVSFELKGDTPEQMRAN 324

Query: 307 AVAFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAAGIRDGLVRLSVGIEHEQ 366
           A   ++S K+  +  +LG   + +  PA  TH  +    R AAGI +GL+RL+VG+E+  
Sbjct: 325 AWRVIDSTKICSITGNLGDTRTTITHPATTTHGRVTPEARAAAGITEGLIRLAVGLENAA 384

Query: 367 DLLEDLEQAFA 377
           D+  DLE+  A
Sbjct: 385 DIRADLERGLA 395


Lambda     K      H
   0.319    0.137    0.394 

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: 362
Number of extensions: 14
Number of successful extensions: 3
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: 380
Length of database: 396
Length adjustment: 30
Effective length of query: 350
Effective length of database: 366
Effective search space:   128100
Effective search space used:   128100
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: 50 (23.9 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:

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