GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Geobacter metallireducens GS-15

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004514090.1 GMET_RS03510 cystathionine gamma-synthase

Query= SwissProt::P55218
         (403 letters)



>NCBI__GCF_000012925.1:WP_004514090.1
          Length = 378

 Score =  266 bits (680), Expect = 7e-76
 Identities = 140/333 (42%), Positives = 208/333 (62%), Gaps = 3/333 (0%)

Query: 67  YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126
           Y+R  NPT    EE IA LEG  +  A ASGM+AI ++++ L S GDH++V   V+G T 
Sbjct: 44  YARSDNPTREALEETIAQLEGGTRGFAYASGMAAISSVLL-LFSPGDHLVVCEDVYGGTF 102

Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186
            +  + F R GI   +   +DL A  AA +P TK  F+ESPSNPL ++ D+   A IA  
Sbjct: 103 RVLTQLFSRLGITSTFVDATDLDAIAAAFRPETKGLFLESPSNPLLKITDLEGAARIARE 162

Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFL 246
           +GA+  VDN F TP LQ+PL++G D+V+HS TK+++G    + G    +  ++ + + F+
Sbjct: 163 RGAITLVDNTFMTPYLQRPLEVGCDIVLHSGTKFLNGHSDVICGFAVVKDPELGKRIRFI 222

Query: 247 RTA-GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305
           + A G  L P ++WL L+GL+TLR+RM+    SA  +A WL  +  + RV Y GLPSHP 
Sbjct: 223 QNAFGAILGPQDSWLVLRGLKTLRVRMEESQRSATRIASWLAGEKRVTRVLYPGLPSHPG 282

Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365
           H +  RQ SG GAV+SF +    +   R ++  ++ +   +LG  ++ I++PA  SH  +
Sbjct: 283 HAIHARQSSGPGAVLSFAL-DSLEVTRRLLEGMKLAAFAVSLGGVESIISYPARMSHAAM 341

Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMAR 398
            PE+RA  GIGD+L+R++VGLE+ DDL A+M R
Sbjct: 342 PPEERAARGIGDTLVRLSVGLEEADDLIAEMDR 374


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: 363
Number of extensions: 19
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: 378
Length adjustment: 31
Effective length of query: 372
Effective length of database: 347
Effective search space:   129084
Effective search space used:   129084
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 10 2024. The underlying query database was built on Apr 09 2024.

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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