GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Pseudomonas fluorescens FW300-N1B4

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Pf1N1B4_1065 Histidinol-phosphate aminotransferase (EC 2.6.1.9)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1065
          Length = 350

 Score =  182 bits (463), Expect = 9e-51
 Identities = 125/365 (34%), Positives = 187/365 (51%), Gaps = 23/365 (6%)

Query: 3   ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASE 62
           + F   +V+++ PY+ G+             A +VKL +NENP G    A  AM    ++
Sbjct: 2   SKFWSPFVKSLVPYVPGEQPKL---------AKLVKLNTNENPYGPSPKALAAMQTELND 52

Query: 63  -LGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFA 121
            L  YPD N+  LK A+++ YGV  + V LGNGS+++L    H  ++  Q +++   S++
Sbjct: 53  NLRLYPDPNSDLLKQAVAKYYGVQGNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYS 112

Query: 122 VYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAF 181
            Y +     G   I   AV          A  +     I   NPN PTG  +    +E  
Sbjct: 113 FYPVYC---GLYGIAFDAVPLDEQFQINPADYAKPNGGIIFPNPNAPTGCLLALDAVEQI 169

Query: 182 LDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIA 241
           L   P  VVVV DEAY ++  +     +I  V RYPNLLV++T SK+  LAGLRVG A+ 
Sbjct: 170 LKASPDSVVVV-DEAYIDFGGET----AITLVDRYPNLLVTQTLSKSRSLAGLRVGLAVG 224

Query: 242 QPELTDLLNRVRQPFN---VNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLG 298
            P+L + L R++  FN   ++ LA   A AA  D+ + +K+  L      ++    +  G
Sbjct: 225 HPDLIEALERIKNSFNSYPLDRLAIVGAAAAFEDREYFDKTCRLVIDSREKVVAQLEAKG 284

Query: 299 LEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEA 358
            E +PS  NF+  R    DAAG  +  +L ++GVIVR      + Q+LRI+IG PE+N+A
Sbjct: 285 FEVLPSAANFIFARHPKHDAAG--LAAKLRERGVIVRHFKQERIAQFLRISIGTPEQNQA 342

Query: 359 FIAAL 363
            I  L
Sbjct: 343 LIDGL 347


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: 365
Number of extensions: 21
Number of successful extensions: 6
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: 350
Length adjustment: 29
Effective length of query: 341
Effective length of database: 321
Effective search space:   109461
Effective search space used:   109461
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