GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Shewanella loihica PV-4

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 5209311 Shew_1789 cystathionine beta-lyase (RefSeq)

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__PV4:5209311
          Length = 395

 Score =  150 bits (378), Expect = 8e-41
 Identities = 117/390 (30%), Positives = 179/390 (45%), Gaps = 17/390 (4%)

Query: 20  DTLAVRAGQ-RRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNV-YSRYTNPTVRT 77
           +T  V  G+ ++  +G     +F  S+ VF T  D          G + Y R   PT   
Sbjct: 4   ETKIVSVGRDKKWSKGVINPPVFRASTVVFDTIEDMRHATKNRANGAMFYGRRGTPTHFA 63

Query: 78  FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137
           F+  IA LEG        SG +AI   ++S   +GDH+L+  + +  T  L DK  K FG
Sbjct: 64  FQAAIAELEGGVGTALYPSGSAAISGALLSFLKAGDHLLMVDTAYEPTRDLCDKLLKGFG 123

Query: 138 IQVDY--PPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDN 195
           I+  Y  P + D    EA  +PNTK+ F+ESP +   E+ D+  L+ IAH    ++ +DN
Sbjct: 124 IETTYYDPLIGD--GIEALIRPNTKVLFLESPGSITLEVQDVPTLSAIAHRHNLVVMLDN 181

Query: 196 CFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSP 255
            + +P   +P +LG D+ I +ATKYI G    M G          ++       G   S 
Sbjct: 182 TWASPINCRPFELGVDISIQAATKYIVGHSDVMLGTATANQAHWDQLRENSYLMGQCTSA 241

Query: 256 FNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSG 315
            + +L  +GL TL +RM  H  + L +A  L  +P ++ + +    S P HE  +R  S 
Sbjct: 242 DDIYLASRGLRTLGVRMAQHEKNGLEVANLLATRPEVDHLRHPAFASCPGHEFFKRDFSA 301

Query: 316 FGAVVSFDVKGGR-DAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAG 374
              + SF +K G   A   F++      +  + G  ++ I        G    +    A 
Sbjct: 302 SNGLFSFVLKRGNIKAITAFVEGMDHFKMGFSWGGYESLIL-------GVFGIDKLRTAT 354

Query: 375 IGDS---LIRVAVGLEDLDDLKADMARGLA 401
             DS   LIR+ VGLE+ +DL  D+  G A
Sbjct: 355 QWDSSKPLIRLHVGLENPEDLIKDLEAGFA 384


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: 322
Number of extensions: 16
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: 403
Length of database: 395
Length adjustment: 31
Effective length of query: 372
Effective length of database: 364
Effective search space:   135408
Effective search space used:   135408
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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