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 GFF1577 PS417_08025 acetylornithine aminotransferase

Query= curated2:Q5HJI8
         (394 letters)



>FitnessBrowser__WCS417:GFF1577
          Length = 389

 Score =  280 bits (716), Expect = 5e-80
 Identities = 158/378 (41%), Positives = 227/378 (60%), Gaps = 10/378 (2%)

Query: 16  YAPLKLVISKGKGVKVWDTDGKQYIDCISGFSVANQGHCHPTIVKAMTEQASKLSIISRV 75
           Y PL L  ++G G ++WD  G++Y+D ++G +V N GH HP +V A++EQA  L   S +
Sbjct: 10  YQPLALSFTRGLGTRLWDQQGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNL 69

Query: 76  LYSDNLGKWEEKICHLAKKDKVLPLNSGTEAVEAAIKIARKWGSEVKGITDGQVEIIAMN 135
              D   +  +++  L+  D+    NSG EA E A+K+AR  G + KGI    V  + M 
Sbjct: 70  YSIDWQQRLAQRLTQLSGLDRAFFNNSGAEANETALKLARLHGWK-KGIEAPLV--VVME 126

Query: 136 NNFHGRTLGSLSLSNHDAYKAGFHPLLQGTTTVDFGDI---EQLTQAISPNTAAIILEPI 192
           N FHGRTLG+L+ S+  + + GF  L      V FGD+   E +T+A  P   A++LEPI
Sbjct: 127 NAFHGRTLGTLAASDGPSVRLGFQQLPGDFLKVRFGDLAALEAITKAFGPRITAVLLEPI 186

Query: 193 QGEGGVNIPPKGYIQAVRQLCDKHQILLIADEIQVGLGRTGKWFAMEWEQVVPDIYILGK 252
           QGE GV   P GY+QA+R  C +   L++ DEIQ G+GRTG WFA + E +VPD+  L K
Sbjct: 187 QGESGVLPAPSGYLQALRDHCTRQGWLMMLDEIQTGIGRTGTWFAFQHEGIVPDVMTLAK 246

Query: 253 ALGGGLYPVSAVLANNDVMRVLTPGTHGSTFGGNPLAIAISTAALDVLKDEQLVERSERL 312
            LG G+ P+ A LA   V ++ TPG+HGSTFGGNPLA  +    LD+++++ L++ + + 
Sbjct: 247 GLGNGV-PIGACLARAAVAQLFTPGSHGSTFGGNPLACRVGCTVLDIIEEQGLLQNAAQQ 305

Query: 313 GSFLLKAL-LQL-KHPSIKEIRGRGLFIGIELNTDAAPFVDQLIQ-RGILCKDTHRTIIR 369
           G  LL  L ++L +H  +  IRG+GL IGIEL +       +  Q  G+L   T   IIR
Sbjct: 306 GERLLARLRVELNEHAQVVAIRGQGLMIGIELASPCRDLAQRAAQEHGLLINVTRGKIIR 365

Query: 370 LSPPLVIDKEEIHQIVAA 387
           L PPL +D +E+  IV A
Sbjct: 366 LLPPLTLDTQEVEMIVRA 383


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: 330
Number of extensions: 19
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: 389
Length adjustment: 31
Effective length of query: 363
Effective length of database: 358
Effective search space:   129954
Effective search space used:   129954
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.

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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