Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate CCNA_02321 CCNA_02321 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Caulo:CCNA_02321 Length = 394 Score = 402 bits (1034), Expect = e-117 Identities = 204/391 (52%), Positives = 277/391 (70%), Gaps = 11/391 (2%) Query: 13 QNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPT 72 ++W AT+ IRGG ARS++ ET+EAL+LT G+ YD A A RF+G+ G YSR NPT Sbjct: 6 KDWDVATKLIRGGIARSQFMETAEALYLTQGFTYDSAEGADRRFAGEDPGFVYSRFNNPT 65 Query: 73 VEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLP 132 V+M E R+ALLEGAE CRA A+GMA++ AAL+ + AGDH++ GRA FGSCRW+ LP Sbjct: 66 VKMFEDRLALLEGAEVCRAQATGMASIHAALMGLVRAGDHVVAGRALFGSCRWIVSEWLP 125 Query: 133 KFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVD 192 +FG+ETT VDA DP+ + A+RPNTK ETP+NP +++ D++AV +A G +VD Sbjct: 126 RFGVETTFVDATDPKAWEAAMRPNTKAVLVETPSNPVLEITDIRAVSELAHAVGAKVIVD 185 Query: 193 NAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTE----EFINNTLLPFHRNT 248 N FATP Q+P++ GADVV YSATK +DGQGRVL GA+ +E EF ++L R+T Sbjct: 186 NVFATPIFQKPLELGADVVVYSATKHIDGQGRVLGGAILTSEAINEEFYRDSL----RHT 241 Query: 249 GPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLA 306 GP+LSPFNAWV+LKGLETLDLR++RQ+++A +A + +V V +P P HP HN+A Sbjct: 242 GPSLSPFNAWVMLKGLETLDLRVRRQADSAFALANTIAEHKKVQTVLYPFRPDHPGHNVA 301 Query: 307 MSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQ 366 +QM G + +++L G R A L+AL ++DISNN+GD++S+ THP +TTH V E + Sbjct: 302 KAQMTGGGTVIALDL-GSREAAFKFLNALEIVDISNNLGDAKSMATHPPTTTHRSVPEAE 360 Query: 367 RLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 R +GV EG +RL+VGLE EDL D+ +AL Sbjct: 361 RPSLGVTEGGVRLSVGLESVEDLKRDVIRAL 391 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: 460 Number of extensions: 21 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: 394 Length adjustment: 31 Effective length of query: 371 Effective length of database: 363 Effective search space: 134673 Effective search space used: 134673 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.
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:
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