GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas putida KT2440

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate PP_0372 PP_0372 Acetylornithine aminotransferase 2

Query= curated2:Q9V1I4
         (364 letters)



>FitnessBrowser__Putida:PP_0372
          Length = 426

 Score =  195 bits (496), Expect = 2e-54
 Identities = 131/358 (36%), Positives = 190/358 (53%), Gaps = 19/358 (5%)

Query: 11  VRGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFEHEEKEE 70
           VRG+G ++WD+EG  YLD   G  V  LGH+    V+ +GNQ   L+  G  F +     
Sbjct: 47  VRGQGSWLWDNEGHAYLDFTQGGAVNSLGHSPSVLVKALGNQAQALINPGSGFHNRGLLG 106

Query: 71  MLEELSRWVNFEYVYMGNSGTEAVEAALKFARLY-----TGRKEIIAMTNAFHGRTMGAL 125
           ++  L +    +  Y+ NSG EA E A+K AR +      G   II  + A HGR++GAL
Sbjct: 107 LVNRLCQSTGSDQAYLLNSGAEACEGAIKLARKWGQLHRNGAYHIITASQACHGRSLGAL 166

Query: 126 SATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAVIFEPIQGESGIIPAKEEFV 185
           SA+      +  EP +PGF  +PFND+ A    +   T A++ EPIQGE+G+IPA +E++
Sbjct: 167 SASDPLPCNR-CEPGLPGFSKVPFNDLAALHAEVDSRTVAIMLEPIQGEAGVIPATQEYL 225

Query: 186 KTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNGVPVSLTLTN 244
           K +  L  ++G LLI DEVQ+G+ R G  LA E Y V  DI+TLGKG+G GVP++  L  
Sbjct: 226 KGVETLCRELGILLILDEVQTGIGRCGALLAEELYGVRADIITLGKGLGGGVPLAALLAR 285

Query: 245 FD---VERGKHGSTFGGNPLACKA-VAVTLRILRKERLVEKASEKFIKVKGKDVVT---- 296
                 E G+   +  GN L C A +AV   +L    L +         +G   +T    
Sbjct: 286 GKACCAEPGELEGSHHGNALMCAAGLAVLDSVLEPGFLAQVQDNGRHLREGLSRLTGRYG 345

Query: 297 ---TRGRGLMIGIVLKKPVGR-YVEELQNEGYLVHTSGQRVIRLLPPLIISKEKMMEV 350
               RG GL+  + LK+ + R  V    +EG L++     V+R  P L +SK  + E+
Sbjct: 346 QGEVRGHGLLWALQLKENLARELVAAALHEGLLLNAPQVDVVRFSPALTVSKGNIDEM 403


Lambda     K      H
   0.318    0.137    0.393 

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: 376
Number of extensions: 25
Number of successful extensions: 5
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: 364
Length of database: 426
Length adjustment: 31
Effective length of query: 333
Effective length of database: 395
Effective search space:   131535
Effective search space used:   131535
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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