GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Marinobacter adhaerens HP15

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein

Query= uniprot:Q5JFW3
         (362 letters)



>FitnessBrowser__Marino:GFF3099
          Length = 404

 Score =  246 bits (627), Expect = 1e-69
 Identities = 154/376 (40%), Positives = 216/376 (57%), Gaps = 25/376 (6%)

Query: 11  VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE 70
           VRGEG  +WD++GR ++DL  GI V  LGH+HP  V  +  Q EKI     +  ++    
Sbjct: 27  VRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEPALR 86

Query: 71  MLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAMTNAFHGRTLGS 124
           + + L      E V+  NSG EA EAA K AR          ++EI++  N+FHGRTL +
Sbjct: 87  LAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTLFT 146

Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKE-TAAVIFEPIQGEGGIVPADEE 183
           +S   + KY EGF P   G  H  FN++E+ K+ I+KE T A++ EPIQGEGG++P D+ 
Sbjct: 147 VSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVMPGDQA 206

Query: 184 FVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL 242
           F++ LRDL ++  ALL+ DEVQSG+ R+G F A + YGV PDI++  KG+G GFPV+  L
Sbjct: 207 FLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAAML 266

Query: 243 TDLEIPR----GKHGSTFGGNPLAC----RAVATTLR--ILRRDRLVEKAGEKFMEFSGE 292
           T  ++      G HGST+GGN LAC    R V T  +  IL+  +       K M   GE
Sbjct: 267 TTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLRKGMMDIGE 326

Query: 293 R---VVKTRGRGLMIGIVL----RRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGD 345
           R     + RG GL++G VL    +  A +++ A  E G++V  AG  VIRL P LII   
Sbjct: 327 RYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEP 386

Query: 346 TLEEARKEIEGVLNDI 361
            +E A +  E  +  +
Sbjct: 387 DIELALERFEAAVKKL 402


Lambda     K      H
   0.320    0.140    0.410 

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: 391
Number of extensions: 24
Number of successful extensions: 6
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: 362
Length of database: 404
Length adjustment: 30
Effective length of query: 332
Effective length of database: 374
Effective search space:   124168
Effective search space used:   124168
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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