GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Cupriavidus basilensis 4G11

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate RR42_RS30610 RR42_RS30610 cystathionine beta-lyase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__Cup4G11:RR42_RS30610
          Length = 405

 Score =  167 bits (424), Expect = 4e-46
 Identities = 108/338 (31%), Positives = 170/338 (50%), Gaps = 7/338 (2%)

Query: 67  YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126
           Y    NPT    E+ +  LE   +     SG++A    +++    G HVL+   V+    
Sbjct: 57  YGARGNPTAFALEDMVTELEAGYRTRLFPSGLAAAAMTLLAYLRPGQHVLLPDCVYEPVR 116

Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186
            L + +  + GI   +   +D    +A  +  T+L +VE+P +   E+ D+ A+A+IAH 
Sbjct: 117 KLAEGFLAQHGIAASFYA-ADGHDLQARLRRETRLVYVEAPGSLAYEMCDLPAIADIAHR 175

Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFL 246
            GAL+A DN + +  L QPL LGAD+ + +ATKY+ G    M G V         +    
Sbjct: 176 HGALVAADNTWGSGLLYQPLALGADISLMAATKYLSGHSDVMMGTVCTLEAAWPALAAVA 235

Query: 247 RTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQH 306
              G ++SP +A+L  +G+ +L  R+  H  SALA+A WL  +P +  V+   LP  P H
Sbjct: 236 DAFGISVSPDDAYLVQRGMRSLGARLSQHERSALAVAHWLRTRPEVAEVFCPALPGDPGH 295

Query: 307 ELARRQQSGFGAVVSFDVKG-GRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365
            L +R   G   ++SF ++    DAA RFID+  +  I  + G  ++          G  
Sbjct: 296 ALWQRDCHGTNGLLSFALRAVAPDAAERFIDSLALFGIGASWGGFESLAV--IADMRGAR 353

Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403
           S  D +  G    +IR+ +GLED+DDL AD+ARG   +
Sbjct: 354 SVTDWSGRG---QVIRLHIGLEDVDDLLADLARGFEVI 388


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: 370
Number of extensions: 23
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: 405
Length adjustment: 31
Effective length of query: 372
Effective length of database: 374
Effective search space:   139128
Effective search space used:   139128
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