GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 in Pseudomonas putida KT2440

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate PP_0817 PP_0817 aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>lcl|FitnessBrowser__Putida:PP_0817 PP_0817 aminotransferase
          Length = 402

 Score =  366 bits (939), Expect = e-106
 Identities = 182/381 (47%), Positives = 251/381 (65%), Gaps = 3/381 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI +LPPYVF    ELK  AR +G D+IDL MGNPDGATP  +V+  +Q  Q    HGY 
Sbjct: 12  RIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGATPPHIVEKLVQVAQREDTHGYS 71

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
              G    RRAI+NWY  RY V +DP+SEA+  +GSKEGL+HL +A ++ GD VLVP+P+
Sbjct: 72  TSRGIPRLRRAISNWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPS 131

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G VIAG  V S+ L P  D+  +L     E   K K++   +PSNPT      +
Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVPGVDFFNELERAIRESIPKPKMMILGFPSNPTAQCVELD 191

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           FFE +VA A++Y +L+VHDL YA++ +DG++  S++++PGAKDI VEF TLSK+YNMAGW
Sbjct: 192 FFERVVALAKQYNVLVVHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKSYNMAGW 251

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           R+GF+VGN  ++  L  +K+  DYG F  LQ AA  AL+     + ++ ++YR RR+ L+
Sbjct: 252 RIGFMVGNPELVSALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYRQRRNLLV 311

Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +GL ELGW V   KA+MY+W K P     +GS +F+  LL +T V V+PG  FG  G+ +
Sbjct: 312 KGLHELGWMVENPKASMYVWAKIPPEYAHLGSLEFSKKLLAETKVCVSPGIGFGDYGDDH 371

Query: 368 VRISLIADCDRLGEALDRIKQ 388
           VR +LI + DR+ +A+  I+Q
Sbjct: 372 VRFALIENQDRIRQAIRGIRQ 392


Lambda     K      H
   0.321    0.140    0.427 

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: 501
Number of extensions: 23
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: 403
Length of database: 402
Length adjustment: 31
Effective length of query: 372
Effective length of database: 371
Effective search space:   138012
Effective search space used:   138012
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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