GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Rhizorhabdus wittichii RW1

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012050345.1 SWIT_RS21085 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000016765.1:WP_012050345.1
          Length = 434

 Score =  206 bits (523), Expect = 1e-57
 Identities = 146/400 (36%), Positives = 203/400 (50%), Gaps = 51/400 (12%)

Query: 12  RGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIV-----VAGPMFEHD 66
           R E   +WD +GRRY+D  +GI V  +GH HP  +  +  QL +       V G  +E  
Sbjct: 34  RAENAEIWDVEGRRYIDFASGIAVLNVGHRHPRIIAAVEEQLGRFTHTAFQVVG--YEPY 91

Query: 67  ER-EEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSL 125
            R  E L  L+  V         +G EA E A+K AR A+GRS ++A  N FHGRTL + 
Sbjct: 92  VRLAERLNALAPVVGPAKTIFFTTGAEATENAVKIARYASGRSAVIAFVNGFHGRTLLAS 151

Query: 126 SATWKK-KYREGFGPLVPGFKHIPFNN------VEAAKEAITK---------ETAAVIFE 169
           + T K   Y++GFGPL     HIPF +      VE +  A+             AA+I E
Sbjct: 152 AMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGITVEHSLAALANVLSSDVEAANVAAIILE 211

Query: 170 PIQGEGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTM 228
           P+QGEGG   A  EF++ LR L ++ G  LIADEVQ+G+ RTGK  A+EH GVRPD++T+
Sbjct: 212 PVQGEGGFHVAPFEFLRALRSLCDEHGIALIADEVQTGIGRTGKLFAVEHAGVRPDLITV 271

Query: 229 GKGIGNGFPVSLTLTDL----EIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA-- 282
            K +G GFP+S  + +      +P G  G T+ G+P+AC A    L ++ +DRL ++A  
Sbjct: 272 AKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYAGSPIACAAGLAVLDVIEQDRLCDRAER 331

Query: 283 -----GEKFMEFSGER---VVKTRGRGLMIGIVLR------RPAGNYVKAL----QERGI 324
                 E+    +  R   +   RG G MI   +R      RP G   K +     E G+
Sbjct: 332 MGRRITERLSAVAARRELPIGLPRGLGAMIAFDIRAGLDDLRPDGAAAKRVCVRALELGL 391

Query: 325 LVNTAG--NRVIRLLPPLIIEGDTLEEARKEIEGVLNDIL 362
           ++ T G     IRLL PL      L+E    +   L D L
Sbjct: 392 ILLTCGQHGEAIRLLAPLTASDAVLDEGLDILAQALADTL 431


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: 387
Number of extensions: 15
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: 434
Length adjustment: 31
Effective length of query: 331
Effective length of database: 403
Effective search space:   133393
Effective search space used:   133393
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