GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Caulobacter crescentus NA1000

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate CCNA_02321 CCNA_02321 O-succinylhomoserine sulfhydrylase

Query= SwissProt::P9WGB5
         (406 letters)



>FitnessBrowser__Caulo:CCNA_02321
          Length = 394

 Score =  401 bits (1031), Expect = e-116
 Identities = 207/386 (53%), Positives = 272/386 (70%), Gaps = 5/386 (1%)

Query: 20  ATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTVSVFE 79
           AT  +RGG+ RS F ETAEA+YLT G+ Y SA  A++ FAGE   +VYSR+ NPTV +FE
Sbjct: 11  ATKLIRGGIARSQFMETAEALYLTQGFTYDSAEGADRRFAGEDPGFVYSRFNNPTVKMFE 70

Query: 80  ERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQ 139
           +RL L+EGA    A A+GMA++  +L  L+ AGD +VA R+LFGSC  + SE LPR+GV+
Sbjct: 71  DRLALLEGAEVCRAQATGMASIHAALMGLVRAGDHVVAGRALFGSCRWIVSEWLPRFGVE 130

Query: 140 TVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFAT 199
           T FVD  D   WE A+   T+AV  ETPSNP+  + DI AV+ELAHA GAKV++DNVFAT
Sbjct: 131 TTFVDATDPKAWEAAMRPNTKAVLVETPSNPVLEITDIRAVSELAHAVGAKVIVDNVFAT 190

Query: 200 PLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAFNA 259
           P+ Q+   LG DVVVYS TKHIDGQGRVLGGAIL      +   +  +RHTGP++S FNA
Sbjct: 191 PIFQKPLELGADVVVYSATKHIDGQGRVLGGAILTSEAINEEFYRDSLRHTGPSLSPFNA 250

Query: 260 WVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGT 319
           WV+LKGLETL +RV+    SA  +A  +  H  V+ V YP+ P HP +++AK QM+GGGT
Sbjct: 251 WVMLKGLETLDLRVRRQADSAFALANTIAEHKKVQTVLYPFRPDHPGHNVAKAQMTGGGT 310

Query: 320 VVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIG 379
           V+   L      +++ AF+ L+ + ++DISNNLGDAKS+ THP TTTHR++    R ++G
Sbjct: 311 VIALDLG-----SREAAFKFLNALEIVDISNNLGDAKSMATHPPTTTHRSVPEAERPSLG 365

Query: 380 LGDGVVRISVGLEDTDDLIADIDRAL 405
           + +G VR+SVGLE  +DL  D+ RAL
Sbjct: 366 VTEGGVRLSVGLESVEDLKRDVIRAL 391


Lambda     K      H
   0.319    0.135    0.395 

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: 436
Number of extensions: 18
Number of successful extensions: 2
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: 406
Length of database: 394
Length adjustment: 31
Effective length of query: 375
Effective length of database: 363
Effective search space:   136125
Effective search space used:   136125
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