GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Herbaspirillum seropedicae SmR1

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate HSERO_RS16670 HSERO_RS16670 acetylornithine aminotransferase

Query= curated2:Q5SHH5
         (395 letters)



>FitnessBrowser__HerbieS:HSERO_RS16670
          Length = 400

 Score =  229 bits (585), Expect = 8e-65
 Identities = 143/386 (37%), Positives = 207/386 (53%), Gaps = 16/386 (4%)

Query: 23  VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82
           V N+ +L+   G G  + D  G  Y+D + G+ V  LGH    + +A+  Q++ L+    
Sbjct: 14  VTNRPELVFTEGHGMWLTDHNGKRYLDYLQGWAVNTLGHAPQCIADALAAQSKKLINPSP 73

Query: 83  TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFAR-------AHTGRKKF-- 133
                   E  + LTA      +RVF  NSG EANE A+K AR       A  G  +F  
Sbjct: 74  AFYNEPSIELAKLLTA--NSVFDRVFFANSGGEANEGAIKLARKWGKKNPAADGSARFEI 131

Query: 134 VAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEETAAVILEP 193
           +     F GRT+ ++S + +  +   F P V        ND+E++K  + E T AV+LEP
Sbjct: 132 ITFKHSFHGRTLATMSASGKDGWDTMFAPQVPGFPKAVLNDLESVKALIGEHTVAVMLEP 191

Query: 194 VQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLA 253
           VQGEGGV PA+ EF++  R +T+EK  LLI+DE+Q+GMGRTG+ FA++H GI PDI+TLA
Sbjct: 192 VQGEGGVIPASKEFMQGLRSLTKEKNLLLIVDEVQSGMGRTGQLFAYQHSGIEPDIMTLA 251

Query: 254 KALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAEL 313
           K +GGGVPL A + REE+A     G  G T+ GNPL  A GVA I+ L +    E   E 
Sbjct: 252 KGIGGGVPLAALLAREEIA-CFEAGEQGGTYNGNPLMTAVGVAVIKELLKPGFMESVRER 310

Query: 314 GPWFMEK-LRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLAL---QAGPTV 369
           G +  ++ L           RG GL+  L+L     P I    +    + L      P +
Sbjct: 311 GQYLRQRSLEISEKYGFEGERGEGLLRALQLGRDIGPQIVEAARNLEPVGLLLNSPRPNL 370

Query: 370 IRFLPPLVIEKEDLERVVEAVRAVLA 395
           +RF+P L + KE+++++   +  VLA
Sbjct: 371 LRFMPALNVTKEEIDQMFSMLEEVLA 396


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: 398
Number of extensions: 22
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: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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