GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate AZOBR_RS07830 AZOBR_RS07830 aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__azobra:AZOBR_RS07830
          Length = 424

 Score =  340 bits (872), Expect = 5e-98
 Identities = 173/388 (44%), Positives = 244/388 (62%), Gaps = 10/388 (2%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI++LPPYVFA ++ +KA+AR  G D+IDLGMGNPD  TPQ +VD  I+A++DPK H Y 
Sbjct: 8   RIKRLPPYVFAEVNAMKARARAAGEDIIDLGMGNPDQPTPQHIVDKLIEAVRDPKTHRYS 67

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
              G    R+A   +Y RR+ V +DP+SE +  +GSKEGL++LA A  +PGD++LVP+P+
Sbjct: 68  NSRGIPGLRKAHAAYYKRRFNVDVDPESECIVTIGSKEGLANLAQAITSPGDIILVPNPS 127

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVAR-------KAKILYFNYPSNPT 183
           YP H  G ++AG +V  L +   N    D+ +    + R       K   L  NYPSNPT
Sbjct: 128 YPIHPFGFILAGASVRHLPVGQANGTSTDIDSFMIMLERAVRHSVPKPLALVLNYPSNPT 187

Query: 184 GATAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSK 243
                 +F+  IV F RK+ I ++ DL YAE+ FDG  P S+LEIP A+++ VEF ++SK
Sbjct: 188 AEVVGLDFYRPIVEFCRKHGIYILSDLAYAEVFFDGEPPPSILEIPEAREVAVEFTSMSK 247

Query: 244 TYNMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYR 303
           TY+MAGWR+GF  GN+ +I  L  +K+ LDYG F  +Q AA  AL  P   + +V+  YR
Sbjct: 248 TYSMAGWRIGFATGNKKLITALARIKSYLDYGAFTPIQVAATAALNGPQECVEQVRTMYR 307

Query: 304 TRRDFLIQGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAF 360
            RRD +I+GL   GW VP   A+M+ W   P     +GS +F+  LLQ+  V V PG  F
Sbjct: 308 QRRDVMIEGLASAGWTVPSPSASMFAWAPIPEPFAHLGSLEFSKLLLQEAKVAVAPGIGF 367

Query: 361 GVAGEGYVRISLIADCDRLGEALDRIKQ 388
           G  G+G+VR++L+ +  R+ +A   IK+
Sbjct: 368 GEYGDGHVRLALVENVHRIRQATRNIKE 395


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: 483
Number of extensions: 21
Number of successful extensions: 3
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: 424
Length adjustment: 31
Effective length of query: 372
Effective length of database: 393
Effective search space:   146196
Effective search space used:   146196
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 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