GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Pseudomonas simiae WCS417

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__WCS417:GFF179
          Length = 425

 Score =  205 bits (521), Expect = 2e-57
 Identities = 137/400 (34%), Positives = 214/400 (53%), Gaps = 43/400 (10%)

Query: 27  KGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLS-IISRVLYSDNLGKWE 85
           K   V D +G+++ID   G +V N GH HP I+ A+TEQ +KL+    +VL  +   +  
Sbjct: 32  KNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYEPYVELC 91

Query: 86  EKICHLAKKD---KVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAMNNNFHGRT 142
           EKI      D   K L + +G+EAVE A+KIAR           G+  +IA    +HGRT
Sbjct: 92  EKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA--------ATGRAGVIAFTGAYHGRT 143

Query: 143 LGSLSLSNH-------------DAYKAGFHPLLQGTTTVD-FGDIEQL--TQAISPNTAA 186
           + +L L+                 ++A F   L G +  D    IE++    A   + AA
Sbjct: 144 MMTLGLTGKVVPYSAGMGLMPGGVFRALFPNELHGVSDDDAIASIERIFKNDAEPRDIAA 203

Query: 187 IILEPIQGEGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPD 246
           II+EP+QGEGG  + PK +++ +R+LCDKH ILLIADE+Q G GRTG +FAME   V  D
Sbjct: 204 IIIEPVQGEGGFYVAPKSFMKRLRELCDKHGILLIADEVQTGAGRTGTFFAMEQMGVAAD 263

Query: 247 IYILGKALGGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLV 306
           +    K++ GG +P++ V    + M  + PG  G T+ G+P+A A + A ++V ++E L+
Sbjct: 264 LTTFAKSIAGG-FPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLL 322

Query: 307 ERSERLGSFLLKAL--LQLKHPSIKEIRGRGLFIGIELNTD----------AAPFVDQLI 354
           +R + +G  L+  L  +Q K+P I E+R  G  I +EL  D           A  V +  
Sbjct: 323 DRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFDDGDTHKPNAAAVASVVAKAR 382

Query: 355 QRG--ILCKDTHRTIIRLSPPLVIDKEEIHQIVAAFQDVF 392
           ++G  +L   T+  ++R+  PL    E++ + +A  ++ F
Sbjct: 383 EKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECF 422


Lambda     K      H
   0.319    0.137    0.402 

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: 412
Number of extensions: 17
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: 394
Length of database: 425
Length adjustment: 31
Effective length of query: 363
Effective length of database: 394
Effective search space:   143022
Effective search space used:   143022
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: 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