GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Cupriavidus basilensis 4G11

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate RR42_RS32610 RR42_RS32610 O-acetylhomoserine aminocarboxypropyltransferase

Query= BRENDA::P94890
         (442 letters)



>FitnessBrowser__Cup4G11:RR42_RS32610
          Length = 424

 Score =  436 bits (1122), Expect = e-127
 Identities = 228/429 (53%), Positives = 295/429 (68%), Gaps = 12/429 (2%)

Query: 14  KPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTD 73
           K ETIA+HGG  PDPTT + AVP+YQT +Y F +  H A LF L+  GNIY+R+MNPT D
Sbjct: 2   KIETIAVHGGYSPDPTTRAVAVPIYQTVAYAFDNAQHGADLFDLKVPGNIYSRIMNPTND 61

Query: 74  VLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKL 133
           VLE+R+AALEGGV ALA ASG +A   A+  I EAG  I+++S LYGGTYNL  +T P  
Sbjct: 62  VLEQRLAALEGGVGALALASGMAAITYAIQTIAEAGDNIISASQLYGGTYNLFAHTLPLS 121

Query: 134 GIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNT 193
           GI+  F D  +P  F    + +T+A + E++GNP  + +DI A++KVA   G+PL++DNT
Sbjct: 122 GIETRFADGRNPAAFGDLVDARTKAIFVESVGNPLGNIVDIEAIAKVAHSHGIPLIVDNT 181

Query: 194 MPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGK--FKNFTEPDPS 251
           +PSPYL  P +HGADIVVHSLTK+LGGHG S+GG I+D G F W   K  FK   EPD S
Sbjct: 182 VPSPYLCRPFEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFKRLNEPDVS 241

Query: 252 YHGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMER 311
           YHG+ + E  G          A+I +ARV  LR+ G A+SPFNA+ ILQG+ETL LR++R
Sbjct: 242 YHGVVYTEALGA--------AAYIGRARVVPLRNTGAALSPFNAFLILQGIETLALRLDR 293

Query: 312 HSGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIK-GGVEKA 370
            + NAL VA  L+  PK+EWVN+ GL    ++A  ++Y   G    I+ F +K GG E  
Sbjct: 294 ITENALAVARHLKASPKVEWVNFAGLPEHPDHALVQRY-LGGRGPGILSFGLKSGGREAG 352

Query: 371 KKFIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDD 430
            +F+D L+LF+ L NIGDAKSLA HPASTTH+QL   E  +AGV+   VRLS+G+E+IDD
Sbjct: 353 ARFLDALQLFTRLVNIGDAKSLATHPASTTHRQLDAAELKAAGVSEDMVRLSIGIEHIDD 412

Query: 431 ILVDLEEAL 439
           +L DLE AL
Sbjct: 413 LLEDLERAL 421


Lambda     K      H
   0.317    0.137    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: 535
Number of extensions: 17
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: 442
Length of database: 424
Length adjustment: 32
Effective length of query: 410
Effective length of database: 392
Effective search space:   160720
Effective search space used:   160720
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 (21.6 bits)
S2: 51 (24.3 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