GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Pseudomonas fluorescens GW456-L13

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate PfGW456L13_1928 Uncharacterized PLP-dependent aminotransferase YfdZ

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1928
          Length = 405

 Score =  359 bits (922), Expect = e-104
 Identities = 178/380 (46%), Positives = 249/380 (65%), Gaps = 3/380 (0%)

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

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

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

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

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

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

Query: 368 VRISLIADCDRLGEALDRIK 387
           VR +LI + DR+ +A+  I+
Sbjct: 372 VRFALIENQDRIRQAVRGIR 391


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: 495
Number of extensions: 26
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: 405
Length adjustment: 31
Effective length of query: 372
Effective length of database: 374
Effective search space:   139128
Effective search space used:   139128
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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