GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Paraburkholderia bryophila 376MFSha3.1

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate H281DRAFT_06478 H281DRAFT_06478 succinylornithine aminotransferase apoenzyme

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__Burk376:H281DRAFT_06478
          Length = 411

 Score =  254 bits (649), Expect = 3e-72
 Identities = 151/379 (39%), Positives = 218/379 (57%), Gaps = 21/379 (5%)

Query: 33  RGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMRGEF 92
           RG G+RVWD +G +YID  GG  V  LGH +PE+++ +  Q   L  +            
Sbjct: 28  RGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLKVLHEQGSKLWHIGNGYTNEPVLRL 87

Query: 93  YRTLTAILPPELNRVFPVNSGTEANEAALKFARA-----HTGRK-KFVAAMRGFSGRTMG 146
            R L  +   +  R F  NSG EANEAALK AR      H   K + ++  + F GRT  
Sbjct: 88  ARRLEELTFAD--RAFFANSGAEANEAALKLARRVAFERHGADKYEIISFTQSFHGRTFF 145

Query: 147 SLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQGEGGVRPATPE 206
           ++SV  +PKY E F P+ + +  +PYND++A ++A+  +T AVI+EP+QGEGGV PA P 
Sbjct: 146 TVSVGGQPKYSEGFGPVPQGIVHLPYNDIQAAQKAIGAKTCAVIVEPIQGEGGVIPADPA 205

Query: 207 FLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGAAV 266
           FL+A RE   + GALLI DE+QTG+GR+G  +A++  G+ PDILT AKALG G P+GA +
Sbjct: 206 FLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQDTGVTPDILTTAKALGNGFPIGAML 265

Query: 267 MREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWE---RAAELGPWFMEKLRA 323
              E+A     G HGTT+GGNPL  A     +  +   +L E     +E+    + KL  
Sbjct: 266 TTNELAAHFKVGVHGTTYGGNPLGSAIAEKVVELISDPKLLEGVRTRSEVLKGHLAKLNE 325

Query: 324 IPSPKIREVRGMGLMVGLEL----KEKAAPYIARLEKEHRVLALQAGPTVIRFLPPLVIE 379
                  EVRG GL++G +L    K +A  ++     +H V+ L AGP V+RF+P L++ 
Sbjct: 326 -RFGLFDEVRGKGLLIGAQLTDAYKGRAKDFVT-AAGQHGVIMLMAGPDVLRFVPSLIMP 383

Query: 380 KEDL----ERVVEAVRAVL 394
            +D+    ER+ +A+  V+
Sbjct: 384 LDDMNEGFERLAKAIADVV 402


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: 406
Number of extensions: 17
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 411
Length adjustment: 31
Effective length of query: 364
Effective length of database: 380
Effective search space:   138320
Effective search space used:   138320
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