GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Paucidesulfovibrio gracilis DSM 16080

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_078718069.1 B5D49_RS12615 ornithine--oxo-acid transaminase

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_900167125.1:WP_078718069.1
          Length = 399

 Score =  244 bits (622), Expect = 4e-69
 Identities = 142/374 (37%), Positives = 207/374 (55%), Gaps = 24/374 (6%)

Query: 10  LVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDERE 69
           L +GEGV+VWD +  RY+D ++       GH HP  V  +  Q E++ +    F +D+  
Sbjct: 25  LSKGEGVWVWDVEDNRYMDCLSAYSAVNQGHCHPRIVAALQEQAERLPLTSRAFRNDQLG 84

Query: 70  EMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR--------LATGRSEIVAMTNAFHGRT 121
            + EEL    +   V   NSG EAVE AIK  R        +   ++EI+   N FHGRT
Sbjct: 85  LLYEELCRLTNSHKVLPMNSGAEAVETAIKAVRKWGYMEKGVPENQAEIIVCANNFHGRT 144

Query: 122 LGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPAD 181
           +  +S +     R GFGP  PGF+ IPF + +A ++AIT  T A++ EPIQGE G++   
Sbjct: 145 ISIVSFSTDSGARAGFGPFTPGFRVIPFGDAQAFEQAITPHTVALLVEPIQGEAGVIIPP 204

Query: 182 EEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNG-FPVS 239
           E +++ +R+L +  G  LI DE+Q+GL RTGK LA EH G+  DI  +GK +  G +PVS
Sbjct: 205 EGYLRRVRELCDTHGIQLILDEIQTGLGRTGKLLAEEHEGIEADITLIGKALSGGLYPVS 264

Query: 240 LTLTDLEI----PRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFME---- 288
             L++ E+      G+HGSTFGGNPLAC      L +L  + L+  A   G++FM+    
Sbjct: 265 AVLSNTEVLGILRPGEHGSTFGGNPLACAVARAALNVLVEEGLIANAELMGQRFMKGLRA 324

Query: 289 FSGERVVKTRGRGLMIGIVLRRPAGN---YVKALQERGILVNTAGNRVIRLLPPLIIEGD 345
            +   V   RGRGL++ + L   AG    Y + L+E G+L        IR  PPL+I  +
Sbjct: 325 IANPAVRDVRGRGLLLAVELDPSAGGARPYCERLKEAGLLCKETHENTIRFAPPLVITAE 384

Query: 346 TLEEARKEIEGVLN 359
            ++ A + I  VL+
Sbjct: 385 QVDWALERISSVLS 398


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: 378
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: 399
Length adjustment: 30
Effective length of query: 332
Effective length of database: 369
Effective search space:   122508
Effective search space used:   122508
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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