GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Dyella japonica UNC79MFTsu3.2

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate N515DRAFT_4363 N515DRAFT_4363 cystathionine gamma-synthase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4363
          Length = 399

 Score =  267 bits (682), Expect = 5e-76
 Identities = 154/383 (40%), Positives = 223/383 (58%), Gaps = 11/383 (2%)

Query: 21  TLAVRAG-QRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79
           T AVRAG +  T  G     L  +++Y F       A          YSR  NPT     
Sbjct: 12  TCAVRAGIESDTQHGAVVPPLHLSTNYAFEGLGGKRAYD--------YSRSGNPTRDLLG 63

Query: 80  ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139
             +A LE    AV TASGM+A+ AL + L  +G  VL +   +G T  L D + K+    
Sbjct: 64  NALAELEQGAGAVVTASGMAAV-ALALELVPAGGRVLAAHDCYGGTWRLLDAWAKKGRFT 122

Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199
           +++  L+D  A  A       L +VE+PSNPL  + D+  +A+ AHA GAL+ VDN F +
Sbjct: 123 LEFADLTDRVALAAGLASKPSLVWVETPSNPLLRITDVRHVAQAAHAAGALVVVDNTFLS 182

Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GPTLSPFNA 258
           PALQQPL LGADVV+HS TKYI+G    +GG V  R + + + + +     G T +PF++
Sbjct: 183 PALQQPLVLGADVVVHSTTKYINGHSDVVGGAVVARDQAVADQLKWWGNCNGLTGAPFDS 242

Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318
           +L L+GL TL +R++ H  +A  +A  L+    + +VYY GL SHP H LA RQQ+GFGA
Sbjct: 243 FLTLRGLRTLSVRLRQHQENAQRIATLLDGHAAVRKVYYPGLESHPGHALAARQQAGFGA 302

Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378
           ++SF+++G       F++  +  S+  +LG  ++ +AHPA+ +H  ++PE R  AGI DS
Sbjct: 303 MLSFELEGDVAQIEAFVNELKYFSLAESLGGVESLVAHPASMTHASMAPEARRTAGIADS 362

Query: 379 LIRVAVGLEDLDDLKADMARGLA 401
           L+R++VG+ED DDL  D+  GLA
Sbjct: 363 LLRISVGIEDGDDLVRDVDAGLA 385


Lambda     K      H
   0.319    0.133    0.392 

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: 413
Number of extensions: 19
Number of successful extensions: 3
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: 403
Length of database: 399
Length adjustment: 31
Effective length of query: 372
Effective length of database: 368
Effective search space:   136896
Effective search space used:   136896
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 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