GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Sinorhizobium meliloti 1021

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate SMc02595 SMc02595 cystathionine gamma-synthase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__Smeli:SMc02595
          Length = 408

 Score =  257 bits (657), Expect = 4e-73
 Identities = 140/337 (41%), Positives = 197/337 (58%), Gaps = 2/337 (0%)

Query: 67  YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126
           Y R  NPT     + +A LEG   AV T SGM+A L L++        VL     +G T+
Sbjct: 72  YGRSGNPTRDLLAQALAKLEGGADAVVTPSGMAA-LDLLLGRLRRNHLVLAPHDCYGGTL 130

Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186
            L         +        D   +EAA      L  +ESPSNPL  + DIA L+ +A A
Sbjct: 131 RLLKARADLGHLTFRLTDQRDFGGFEAALSDAPALVLIESPSNPLMRVTDIARLSTLAKA 190

Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGG-VVAGRGEQMKEVVGF 245
            G+ +AVDN F +PALQQPL LGAD  IHSATK+++G    + G V+A   ++  ++  +
Sbjct: 191 AGSAVAVDNTFLSPALQQPLSLGADYAIHSATKFLNGHSDVIAGAVIAAEPQEAHDLKRW 250

Query: 246 LRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305
               G   +PF+AWL L+GL TL  RM +   SA+ +AE+L+  P +  V+YAGLP H  
Sbjct: 251 ANVTGAVAAPFDAWLTLRGLRTLFARMSSQERSAMTIAEYLDAHPAVRHVHYAGLPDHAD 310

Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365
           HE+ARRQQ GFGA++SF+++GG  A  RF+   R  ++  +LG  ++ +AHPAT +H  +
Sbjct: 311 HEVARRQQRGFGAMMSFELEGGVPAVRRFLAHIRCFTLAESLGGVESLVAHPATMTHLDM 370

Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402
            PE R RAGI D L+R+++GLE +DDL   +  GL A
Sbjct: 371 GPEARERAGIRDELLRLSIGLEHIDDLMEGLELGLGA 407


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: 395
Number of extensions: 13
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: 408
Length adjustment: 31
Effective length of query: 372
Effective length of database: 377
Effective search space:   140244
Effective search space used:   140244
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.

Links

Downloads

Related tools

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