GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Sphingomonas koreensis DSMZ 15582

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__Korea:Ga0059261_3205
          Length = 398

 Score =  271 bits (692), Expect = 3e-77
 Identities = 156/385 (40%), Positives = 223/385 (57%), Gaps = 21/385 (5%)

Query: 23  VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82
           VY + ++  VRG+G  +    G  Y+D   G  V  LGHG+P+  +A+  QA TLM +  
Sbjct: 9   VYPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAATLMHVSN 68

Query: 83  TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAH------TGRKKFVAA 136
              +P      + +  +     + VF  NSG EA E A+K AR +        R K +  
Sbjct: 69  LYGSPQGEALAQRI--VDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNPQRHKLITF 126

Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEPVQG 196
              F GR++G++S T +PK R+ F PL+   +++ +ND+E     +D+ETA  ++E VQG
Sbjct: 127 KNAFHGRSIGAISATDQPKMRDGFEPLLPGFDYVKFNDLEGAIAKIDDETAGFLVETVQG 186

Query: 197 EGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKAL 256
           EGG+   T EF++  R+   E G LLILDEIQ G GRTGK +A+EH+GI PDILT AK +
Sbjct: 187 EGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYGRTGKMWAYEHYGITPDILTAAKGI 246

Query: 257 GGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPW 316
           G G PLGA +  EE A+ M  G HG+T+GGNPLAMAAG A +  +     +E   ++G  
Sbjct: 247 GNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMAAGQAVLDVMLEPGFFEHVEKMG-- 304

Query: 317 FMEKLRA-----IPSPK--IREVRGMGLMVGLELKEKAA--PYIARLEKEHRVLALQAGP 367
             E+LRA     IP+      E+RG GLM+G++LKE A    ++A L + H +L + AG 
Sbjct: 305 --ERLRAGFEQLIPNHDHLFDEIRGKGLMLGIKLKEPAVSRDFVAHLRENHGLLTVAAGE 362

Query: 368 TVIRFLPPLVIEKEDLERVVEAVRA 392
            V R LPPLVIE+  +   +E + A
Sbjct: 363 NVFRVLPPLVIEESHIAECIEKLSA 387


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: 414
Number of extensions: 23
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: 398
Length adjustment: 31
Effective length of query: 364
Effective length of database: 367
Effective search space:   133588
Effective search space used:   133588
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