GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Shewanella sp. ANA-3

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__ANA3:7025943
          Length = 425

 Score =  210 bits (534), Expect = 7e-59
 Identities = 143/393 (36%), Positives = 200/393 (50%), Gaps = 34/393 (8%)

Query: 22  GVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMP 81
           GV   H +   R + A VWD EG E+ID  GG  V N GH +P+V  AV  Q E      
Sbjct: 19  GVGQIHPVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFS--- 75

Query: 82  QTLPTPMRGEFY----RTLTAILPPELNRVFPV-NSGTEANEAALKFARAHTGRKKFVAA 136
            T    +  E Y      L  ++P +  +   +  SG+EA E A+K ARA+T R   +A 
Sbjct: 76  HTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAF 135

Query: 137 MRGFSGRTMGSLSVTWEPKYREPFLPLVE--------PVEFIPYNDVEALKR-------- 180
             G+ GRTM +L++T +       + L+         P      +D +A+          
Sbjct: 136 TSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVSDDDAMASIERIFKND 195

Query: 181 AVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAF 240
           A     AA+ILEPVQGEGG   A+PEF++  R +   +G +LI DE+QTG GRTG  FA 
Sbjct: 196 AEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAM 255

Query: 241 EHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRY 300
           E  G+  DI T AK++ GG PL     + EV  ++  GG G T+GGNPLA AA +A +  
Sbjct: 256 EQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAVLEV 315

Query: 301 LERTRLWERAAELGPWFMEKLRA--IPSPKIREVRGMGLMVGLELKEKAAP---YIARLE 355
            E  +L ERA  +G      L    +  P+I +VRG+G M+ +EL E+  P   Y A++ 
Sbjct: 316 FEEEKLLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIELMEEGKPAPQYCAQIL 375

Query: 356 KEHR---VLALQAGP--TVIRFLPPLVIEKEDL 383
            E R   ++ L  G    V+R L PL +  E L
Sbjct: 376 AEARNRGLILLSCGTYGNVLRILVPLTVPDEQL 408


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: 382
Number of extensions: 16
Number of successful extensions: 4
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: 425
Length adjustment: 31
Effective length of query: 364
Effective length of database: 394
Effective search space:   143416
Effective search space used:   143416
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