GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas stutzeri RCH2

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate GFF3586 Psest_3653 4-aminobutyrate aminotransferase, prokaryotic type

Query= uniprot:Q5JFW3
         (362 letters)



>FitnessBrowser__psRCH2:GFF3586
          Length = 426

 Score =  175 bits (443), Expect = 2e-48
 Identities = 126/378 (33%), Positives = 195/378 (51%), Gaps = 48/378 (12%)

Query: 18  VWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIV-VAGPMFEHDEREEMLEELS 76
           V D +GR ++D   GI V   GH HP+ +  +  QL K+      +  ++   E+ E+++
Sbjct: 36  VVDVEGREFIDFAGGIAVLNTGHLHPKIIKAVEDQLHKLTHTCFQVLAYEPYVELCEKIN 95

Query: 77  HWVDYEYV---YMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSATWK-KK 132
             V  ++     +  +G+EAVE A+K AR ATGR+ ++A T A+HGRT+ +L  T K   
Sbjct: 96  ARVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVAP 155

Query: 133 YREGFGPLVPG----------FKHIPFNNVEAAKEAITK------ETAAVIFEPIQGEGG 176
           Y  G G L+PG             +  ++  A+ E I K      + AA+I EP+QGEGG
Sbjct: 156 YSAGMG-LMPGGIFRALYPCAIYGVSVDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGG 214

Query: 177 IVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNG 235
              A ++F+  LR L ++ G LLIADEVQ+G  RTG F A+E  GV  D+ T  K +G G
Sbjct: 215 FNVAPKDFMARLRALCDEHGILLIADEVQTGAGRTGTFFAMEQMGVVADLTTFAKSVGGG 274

Query: 236 FPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEK---------A 282
           FP++      E    I  G  G T+ GNPL+C A    L +   ++L+++          
Sbjct: 275 FPIAGVCGKAEIMDAIAPGGLGGTYAGNPLSCAAALAVLEVFEEEKLLDRCKAVAERLTT 334

Query: 283 GEKFMEFSGERVVKTRGRGLMIGIVL------RRPA----GNYVKALQERGILVNTAGN- 331
           G K ++   + + + RG G MI I L       RPA       V   +++G+++ + G  
Sbjct: 335 GLKAIQTKHKEIGEVRGLGAMIAIELFEDGDHARPAAALTSQIVARARDKGLILLSCGTY 394

Query: 332 -RVIRLLPPLIIEGDTLE 348
             V+R+L PL  E + L+
Sbjct: 395 YNVLRVLVPLTAEDELLD 412


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: 352
Number of extensions: 17
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: 362
Length of database: 426
Length adjustment: 31
Effective length of query: 331
Effective length of database: 395
Effective search space:   130745
Effective search space used:   130745
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.

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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