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_014626023.1 RRU_RS04110 PLP-dependent transferase

Query= metacyc::MONOMER-17873
         (438 letters)



>NCBI__GCF_000013085.1:WP_014626023.1
          Length = 439

 Score =  645 bits (1664), Expect = 0.0
 Identities = 316/429 (73%), Positives = 358/429 (83%)

Query: 8   PKAAQYHQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTR 67
           P     + +TLALHGG+YRADPTTG+VAVPIYQTTSYQ  +T  AARL  L+E+G  Y+R
Sbjct: 9   PLTGLKNPETLALHGGTYRADPTTGSVAVPIYQTTSYQFENTGQAARLFALQELGNIYSR 68

Query: 68  IGNPTQDAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLF 127
           + NPT DAFEQR+AA+EGGVAALA++SGQAAS  AVL LAQAGDNIV+STDLYGGTW LF
Sbjct: 69  LTNPTTDAFEQRIAAIEGGVAALAVSSGQAASTFAVLNLAQAGDNIVSSTDLYGGTWALF 128

Query: 128 ANTLRTLGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGV 187
           A+T +  GIE RFVDP DPE FR+ATD RTR YY ETLPNPKL VFPI EVA IGRSLGV
Sbjct: 129 ASTFKQFGIEVRFVDPTDPENFRKATDERTRAYYAETLPNPKLNVFPIREVADIGRSLGV 188

Query: 188 PLIIDNTATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALL 247
           PLI+DNTA PLIARPFDHGAAVVVYSTTKYIGGHGTTIGG IID GTFPW D  +R   L
Sbjct: 189 PLIVDNTAAPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGVIIDSGTFPWEDFPDRFPTL 248

Query: 248 TGPEPSYHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLA 307
           T P+ SYH A WT+   P GP+AYI+RAR  +LRD+GA+I+P++ F LIQGLETLPLR+ 
Sbjct: 249 TEPDESYHGAVWTEATKPLGPVAYIIRARVKLLRDVGAAISPLAVFQLIQGLETLPLRIR 308

Query: 308 RHNANAIKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGR 367
           +HN NA+KVA +L  HPK++ V +PGLQ+GE RRRADAYL GGYGGL+GFEL GG EAGR
Sbjct: 309 QHNENALKVATFLKDHPKIARVIYPGLQTGELRRRADAYLTGGYGGLVGFELHGGAEAGR 368

Query: 368 RFIEALRLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDI 427
            FIE+LRLFYHV NIGDARSLAIHPATTTHSQLS EDQ  TGVTPG+VRLSIGIEHP DI
Sbjct: 369 AFIESLRLFYHVANIGDARSLAIHPATTTHSQLSEEDQLLTGVTPGYVRLSIGIEHPADI 428

Query: 428 IGDIAQALD 436
           I D++QALD
Sbjct: 429 IEDLSQALD 437


Lambda     K      H
   0.319    0.136    0.402 

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: 687
Number of extensions: 18
Number of successful extensions: 1
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: 438
Length of database: 439
Length adjustment: 32
Effective length of query: 406
Effective length of database: 407
Effective search space:   165242
Effective search space used:   165242
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: 51 (24.3 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