GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Caulobacter crescentus NA1000

Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate CCNA_01491 CCNA_01491 cystathionine beta-lyase

Query= reanno::Korea:Ga0059261_3194
         (402 letters)



>FitnessBrowser__Caulo:CCNA_01491
          Length = 386

 Score =  145 bits (366), Expect = 2e-39
 Identities = 106/349 (30%), Positives = 173/349 (49%), Gaps = 15/349 (4%)

Query: 51  DAAARFSGDQQGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAG 110
           DAA+ +  DQ  +TY      T   L+  +A LEGA       SG+AA+T A+L  L AG
Sbjct: 35  DAASLYDDDQ--LTYGITGLSTPVALQNALAELEGATNVTLYPSGLAAITGAMLAVLKAG 92

Query: 111 DHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDAR-DPQQFIDAIRPNTKVFFFETPANPT 169
           D ++   +A+   R   D  L +FG+ T   D +  P+  +  +  +T++   E P + T
Sbjct: 93  DEVLVVDSAYKPTRRFCDRVLGRFGVTTRYYDPKLSPEALMGLVTSSTRLIVLEAPGSLT 152

Query: 170 MDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGA 229
            ++ D+ A+ A A  RG++T++DN +A   L +P+  G  +   + TK + G      G+
Sbjct: 153 FEMQDIPAIAAAANARGVLTLIDNTWAAGLLFKPLAHGVTMSVQALTKYVGGHSDCFMGS 212

Query: 230 VCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR- 288
           V   ++ +   L     + G ++S  +A+ +L+GL TL  R+ R +EN L +AR+L+ R 
Sbjct: 213 VATCDDAVAKLLGDAMWDIGWSVSSDDAYTMLRGLRTLATRLPRHAENGLAIARWLQERP 272

Query: 289 -VPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGGRTQA-HGLLDALGLIDISNNIG- 345
            V RV  P LP    H +       A  +F + L     +A H  LD+L L  +  + G 
Sbjct: 273 EVARVLHPALPGDAGHAIWKRDFTGACGLFGVVLKPCSQKAVHAFLDSLKLFGLGFSWGG 332

Query: 346 -DSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADL 393
            +S +L   P     S       + + +   +LR ++GLE  EDL ADL
Sbjct: 333 YESLALNCDPQLGARS-------IPVDLEGPLLRFHIGLEGIEDLKADL 374


Lambda     K      H
   0.319    0.134    0.396 

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: 15
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: 402
Length of database: 386
Length adjustment: 31
Effective length of query: 371
Effective length of database: 355
Effective search space:   131705
Effective search space used:   131705
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