GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens FW300-N2C3

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate AO356_17010 AO356_17010 acetylornithine aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17010
          Length = 391

 Score =  256 bits (655), Expect = 6e-73
 Identities = 149/382 (39%), Positives = 207/382 (54%), Gaps = 12/382 (3%)

Query: 24  YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83
           Y    L    G G R+WD +G EY+D V G  V N+GH +P +V A+  QA  L+     
Sbjct: 10  YQPLALNFTHGLGTRLWDQDGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLHTSNL 69

Query: 84  LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKF-----VAAMR 138
                +    + LT +   E  R F  NSG EANE ALK AR +   K       V    
Sbjct: 70  YSIDWQQRLAQKLTQLSGME--RAFFNNSGAEANETALKLARLYGWHKGIEQPLVVVMDN 127

Query: 139 GFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKR---AVDEETAAVILEPVQ 195
            F GRT+G++S +  P  R  +  L      +P+ D+ AL++   A  E   AV++EP+Q
Sbjct: 128 AFHGRTLGTMSASDGPSVRLGYNRLPGDFIKVPFGDLAALEQIQQAHAERIVAVLVEPIQ 187

Query: 196 GEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKA 255
           GE GV+ A P +L+A R++   +  LL+LDEIQTG+GRTG+ FAF+H GIVPD++TLAK 
Sbjct: 188 GESGVQLAPPGYLKALRQLCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 247

Query: 256 LGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGP 315
           LG GVP+GA + R + A     G HG+TFGGNPLA   G   +  +E   L   A   G 
Sbjct: 248 LGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIIEEQALVGNARHQGE 307

Query: 316 WFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFL 373
             + +LR     +P +  +RG GLM+G+ELK+       R  ++H +L        IR L
Sbjct: 308 QLLSRLRTELAENPNVLAIRGQGLMIGIELKQPVRDLTLRAARDHGLLINVTRGQTIRLL 367

Query: 374 PPLVIEKEDLERVVEAVRAVLA 395
           PPL I+  ++E +V  V   LA
Sbjct: 368 PPLTIDGREVEMIVRGVSRCLA 389


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: 370
Number of extensions: 21
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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