GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Echinicola vietnamensis KMM 6221, DSM 17526

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Echvi_2458 Echvi_2458 histidinol-phosphate aminotransferase

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



>FitnessBrowser__Cola:Echvi_2458
          Length = 354

 Score =  149 bits (377), Expect = 9e-41
 Identities = 115/369 (31%), Positives = 187/369 (50%), Gaps = 32/369 (8%)

Query: 11  RAIAPYIAG-KPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69
           + + P+IA  KP S    E+   E   V L +NENP G         +  A    RYPD 
Sbjct: 7   KLLRPHIAQLKPYSSARDEYTGKEG--VFLDANENPFG---------SITAESFNRYPDP 55

Query: 70  NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQ-SIVYAQYSFAVYALATQ 128
               LK  +S    VP + + +GNGS++ +++   AF   G+ +I+    ++ +Y ++  
Sbjct: 56  YQHALKEKISAIKQVPVEQIFIGNGSDEAIDLLMRAFCRPGKDNIIILPPTYGMYEVSAD 115

Query: 129 GLGARAIVVPAVKYGHDL----DAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDK 184
                 I +  V    D     DA+L AV ++T++IF+ +PNNP+G  +    +   +  
Sbjct: 116 ---INDISIKRVNLSADFQLRPDAILEAVDENTKIIFICSPNNPSGNKVRRKDILKII-- 170

Query: 185 VPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPE 244
           V    +VV+DEAY ++  +       A + ++PNLLV +TFSKA+GLA LR+G A A   
Sbjct: 171 VGFDGLVVVDEAYIDFSDEPS---FTAELPQHPNLLVMQTFSKAWGLAALRLGMAFASLP 227

Query: 245 LTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKL-GLEYV- 302
           +  +LN+++ P+N++ L Q   + AL D + +++      Q    L  A  K+ G++ + 
Sbjct: 228 IIRILNKIKPPYNISGLTQETVLKALQDTSKMKQMVKEMLQERDYLLHALSKMDGIKKIH 287

Query: 303 PSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGL-PQWLRITIGLPEENEAFIA 361
           P+  NFVLV V     A       L++Q +IVR      L  Q LRI++G  EEN+  I 
Sbjct: 288 PTHANFVLVEV----PAAKETYDHLIEQQIIVRDRSKVVLCDQCLRISVGTREENDQLIG 343

Query: 362 ALERTLAAA 370
            L   +A +
Sbjct: 344 KLSEFIATS 352


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: 293
Number of extensions: 16
Number of successful extensions: 4
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: 354
Length adjustment: 29
Effective length of query: 341
Effective length of database: 325
Effective search space:   110825
Effective search space used:   110825
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: 49 (23.5 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