GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Rhodospirillum rubrum ATCC 11170

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011389828.1 RRU_RS10755 O-acetylhomoserine aminocarboxypropyltransferase

Query= BRENDA::L7N4M1
         (449 letters)



>NCBI__GCF_000013085.1:WP_011389828.1
          Length = 612

 Score =  438 bits (1127), Expect = e-127
 Identities = 225/427 (52%), Positives = 291/427 (68%), Gaps = 3/427 (0%)

Query: 10  ADPTAHWSFETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTR 69
           AD  A + FET+ +HAG  PDPTT ARA PIY TTSY F+DT  AAALF L   G +Y+R
Sbjct: 184 ADKPAPFGFETRAVHAGAAPDPTTGARATPIYQTTSYVFEDTDQAAALFNLHTFGYLYSR 243

Query: 70  IGNPTTDVVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLF 129
           + NPT  V+E+RIA+LEGG AA+  +SG AA+      L   GDH V+S  LYGG+   F
Sbjct: 244 LTNPTVSVLEERIASLEGGRAAVCCASGHAAQFLTFFTLLEPGDHFVASRALYGGSLTQF 303

Query: 130 HYSLAKLGIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNG 189
             S  KLG E SFVD P D+D ++AA+ P TKA F E ++NP   ++D   V+ VA + G
Sbjct: 304 GQSFRKLGWECSFVD-PTDIDAFRAAIGPRTKAIFLELLANPGGVIVDVEQVARVAQQAG 362

Query: 190 VPLIVDNTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWTQG-RFPG 248
           +PLIVDNT+ATPYL +P   GAD+VVHS TK+L GHG A+ G +V+ G F+W+   +FPG
Sbjct: 363 IPLIVDNTLATPYLCRPFDWGADLVVHSTTKFLSGHGNAVGGAVVESGRFNWSASDKFPG 422

Query: 249 FTTPDPSYHGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERH 307
            + P+P+YHG+ F E  G  AF  KAR   LRD+G A +P NAFL   G+ETL LR++RH
Sbjct: 423 LSQPEPAYHGMTFHETFGDFAFTTKARAVALRDFGPAMAPQNAFLTLTGIETLPLRMDRH 482

Query: 308 VANAQRVAEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAF 367
           V NA++VA FLAA   V  V+YAGLP SP+H  A +  PKG GAV +F + GG EAGK  
Sbjct: 483 VENAKKVAAFLAAHPKVSWVSYAGLPDSPFHGLAGKYLPKGPGAVFTFGVVGGFEAGKKV 542

Query: 368 VNALKLHSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILA 427
           V  ++L SH+AN+GD RSL++HPASTTH QLS  ++ A G    ++RL+VGIE   D++A
Sbjct: 543 VEGVRLFSHLANVGDTRSLILHPASTTHRQLSDDQRQAAGAGDEVIRLSVGIETAADLIA 602

Query: 428 DLELGFA 434
           DL+   A
Sbjct: 603 DLDQALA 609


Lambda     K      H
   0.318    0.134    0.394 

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: 757
Number of extensions: 40
Number of successful extensions: 4
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: 449
Length of database: 612
Length adjustment: 35
Effective length of query: 414
Effective length of database: 577
Effective search space:   238878
Effective search space used:   238878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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