GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Sphingomonas koreensis DSMZ 15582

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Ga0059261_2299 Ga0059261_2299 histidinol-phosphate aminotransferase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>FitnessBrowser__Korea:Ga0059261_2299
          Length = 376

 Score =  266 bits (680), Expect = 7e-76
 Identities = 151/363 (41%), Positives = 216/363 (59%), Gaps = 11/363 (3%)

Query: 9   YVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPD 68
           ++  IAPY+ GK  ++  R+        +KL+SNENPLG  + A+ A A AA+ L RYPD
Sbjct: 13  WIMDIAPYVPGKSKTDDGRK-------AIKLSSNENPLGTSDKARAAFATAANSLERYPD 65

Query: 69  ANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQ 128
           A+A EL+ AL+E +G+ A  +  GNGS+++L +AA AF   G  I+Y  Y F VY +AT+
Sbjct: 66  ASAVELREALAELHGLDAARIIYGNGSDEVLHLAAGAFAGPGDEIIYVNYGFTVYPIATK 125

Query: 129 GLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188
            +GA  +V     Y  D+DA+LA+V+D TR++FVANPNNPTGT+    ++      +   
Sbjct: 126 RVGATPVVAADADYATDVDAILASVTDRTRIVFVANPNNPTGTYASREEIARLHAGLRPD 185

Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDL 248
           +++VLD AY EY+  E     +   +  PN+LV+RTFSK +GLA  R+G+     E+ + 
Sbjct: 186 ILLVLDHAYAEYIEGEIDDGGMELAKTQPNVLVTRTFSKLYGLAAERIGWGYGSAEVIEA 245

Query: 249 LNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKL---GLEYVPSD 305
           ++R+R PF++     AAAIAAL+D AF+E + + NAQ  R   +   KL   GL  VPS 
Sbjct: 246 MHRIRLPFSITIAGTAAAIAALHDSAFVEHTRSHNAQWRRWFADEIAKLGNAGLRAVPSQ 305

Query: 306 GNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALER 365
            NFVLV +             L+ +G IVR +   GLP  LRITIG  EE  A  A L +
Sbjct: 306 ANFVLV-LFEGALTAEAAYKGLMDEGYIVRWLPGQGLPHGLRITIGTEEETRAVAAILNK 364

Query: 366 TLA 368
            +A
Sbjct: 365 LVA 367


Lambda     K      H
   0.318    0.135    0.385 

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: 380
Number of extensions: 16
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: 370
Length of database: 376
Length adjustment: 30
Effective length of query: 340
Effective length of database: 346
Effective search space:   117640
Effective search space used:   117640
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