GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens FW300-N2E3

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate AO353_28215 AO353_28215 4-aminobutyrate aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_28215
          Length = 430

 Score =  231 bits (588), Expect = 4e-65
 Identities = 155/426 (36%), Positives = 224/426 (52%), Gaps = 31/426 (7%)

Query: 1   METRTLEDWRALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLG 60
           M ++  E    L + ++ +  G+   H L+I R QGA +WD +G  Y+D VGG GV N+G
Sbjct: 1   MNSKVDETPHLLRQRDQFVPRGLVTAHPLVIDRAQGAELWDVDGKRYLDFVGGIGVLNIG 60

Query: 61  HGNPEVVEAVKRQAETLM--AMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANE 118
           H +P+VV AV+ Q + +           P      R    I   E  +     SG EA E
Sbjct: 61  HNHPKVVAAVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGNEAYKAAFFTSGAEAVE 120

Query: 119 AALKFARAHTGRKKFVAAMRGFSGRTMGSLSVT-WEPKYREPFLPLVEPVEFIPYNDV-- 175
            A+K ARAHT R   +A   GF GRT+   ++T     Y++ F P    V   PY +   
Sbjct: 121 NAVKIARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYR 180

Query: 176 ----EALKRAVDE---------ETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALL 222
               E   +A+DE           AA+I+EPVQG+GG   A  EFL+A R +T++ G +L
Sbjct: 181 GVSSEMALKALDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQALRALTEKHGIVL 240

Query: 223 ILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGT 282
           ILDEIQTG GRTGK F F+H GI PD++T+AK+L GG+PL   V +  +  +   GG G 
Sbjct: 241 ILDEIQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAGIMDAPLPGGLGG 300

Query: 283 TFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVG 340
           T+GGN L+ AA +A I   E+ +L  R   LG    + L  + +   +I +VRG G M+ 
Sbjct: 301 TYGGNALSCAAALAVIDAYEQEQLLARGDALGERLRQGLLRLQARHRQIGDVRGSGFMLA 360

Query: 341 LEL------KEKAAPYIARLEKEHR---VLALQAG--PTVIRFLPPLVIEKEDLERVVEA 389
           +EL      +   A    RL  E R   +L ++ G    V+RFL PLV  ++ ++  ++ 
Sbjct: 361 IELIKDDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTTEDQIDEALQI 420

Query: 390 VRAVLA 395
           + A LA
Sbjct: 421 LEAALA 426


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: 420
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: 430
Length adjustment: 31
Effective length of query: 364
Effective length of database: 399
Effective search space:   145236
Effective search space used:   145236
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