GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Herbaspirillum seropedicae SmR1

Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate HSERO_RS15835 HSERO_RS15835 aspartate aminotransferase

Query= reanno::Cup4G11:RR42_RS33490
         (400 letters)



>FitnessBrowser__HerbieS:HSERO_RS15835
          Length = 405

 Score =  421 bits (1083), Expect = e-122
 Identities = 210/397 (52%), Positives = 261/397 (65%), Gaps = 1/397 (0%)

Query: 1   MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60
           +F  I+  P DPIL + E++  D    K NL +G+Y+DD G++P+++ V++AEA L A +
Sbjct: 9   LFSAIEMAPRDPILGVTEAYNADQNPAKTNLGVGVYYDDNGKVPLLECVKKAEAELAAKL 68

Query: 61  GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFP- 119
            PR YLP+ G A Y  AVQ LVFG       E R  TVQ LGG+GAL++GADFLK + P 
Sbjct: 69  APRTYLPIDGLATYDRAVQELVFGAGSAVVTEKRAITVQALGGTGALKLGADFLKHFSPA 128

Query: 120 DAQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHA 179
             +VWISDPSWENHR +FE  GF VN YPYYD AT G+ F  MLDAL+ +   S+VLLHA
Sbjct: 129 GTEVWISDPSWENHRALFEMAGFKVNAYPYYDPATRGVNFAGMLDALKTMKSGSVVLLHA 188

Query: 180 CCHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCL 239
           CCHNPTG DL  DQW Q+I ++    L+PF+DMAYQGFG G+ +D   VR     G P  
Sbjct: 189 CCHNPTGADLTDDQWTQVIEVVTSRGLVPFLDMAYQGFGDGIAEDGQVVRRFAEAGGPLF 248

Query: 240 VANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLT 299
           V+NSFSK+FSLYGER G LS+   SAEE  RVL QL   VR NYSNPP HG +VVA  L 
Sbjct: 249 VSNSFSKSFSLYGERVGALSIAAASAEEAARVLSQLKRVVRTNYSNPPIHGGQVVATALA 308

Query: 300 TPALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVD 359
           +P LR +WE ELA    RI +MR  +   L     G      + QRGMF+Y+GLT  QVD
Sbjct: 309 SPELRKLWEDELAEMRVRIREMRQLLVAKLKEKAPGHDFDFVIKQRGMFSYSGLTKAQVD 368

Query: 360 RLRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396
           RLR E  +Y + +GR+CVA LN +N+  V  AIA VL
Sbjct: 369 RLRNEFSIYAVDTGRICVAALNTKNIDVVVDAIAKVL 405


Lambda     K      H
   0.323    0.137    0.417 

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: 446
Number of extensions: 14
Number of successful extensions: 2
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: 400
Length of database: 405
Length adjustment: 31
Effective length of query: 369
Effective length of database: 374
Effective search space:   138006
Effective search space used:   138006
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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