Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate Echvi_4510 Echvi_4510 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Cola:Echvi_4510 Length = 403 Score = 241 bits (615), Expect = 3e-68 Identities = 142/399 (35%), Positives = 219/399 (54%), Gaps = 18/399 (4%) Query: 13 QNWKPATQAIRGGTARSE-WGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNP 71 +N T+AI G G +S L +++ Y + + ++ Y+R NP Sbjct: 7 KNLGEQTRAIHAGELPDPVTGASSPNLVMSTTYLAEAGTGFSVEGHDEEDPWIYTRWGNP 66 Query: 72 TVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQL 131 TV LE+++A+LE AE A ASGM A+T L AGDH I A+ + +T+ + Sbjct: 67 TVHQLEEKLAVLEEAETAVAFASGMGAITVLFFHLLKAGDHAIVSDVAYAALSEMTNEMV 126 Query: 132 PKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVV 191 P I+ T VD D A++ NT++ + ETP NP + + D++AV IAR G V Sbjct: 127 PSLNIQITKVDTSDLSAVKAAVKNNTRLIYIETPCNPILRLTDIEAVAGIARGAGARLAV 186 Query: 192 DNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNT--- 248 D+ FATPA +P+ GAD + +S TK + G G L GA+ G + L P + T Sbjct: 187 DSTFATPAATKPLQLGADFIVHSLTKYLGGHGDALGGAILGRKA----DLAPLRKKTAIR 242 Query: 249 -GPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLE--GRVPRVNFPGLPSHPQHNL 305 G +SPFNAW++L+GL T +R++ +NALKVA FLE +V RV +PGLPSHPQH L Sbjct: 243 MGAVISPFNAWLILRGLATFPIRMRAHEKNALKVAAFLEKHPKVKRVIYPGLPSHPQHEL 302 Query: 306 AMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTH-------PASTT 358 A QM + + +++ G+ ++ D L ++ + ++G RSL+ + +S Sbjct: 303 AKKQMKNFSGMLTFQVENGKKRSGIFADKLRIVHYAVSLGHHRSLIFYLDSADLKESSFK 362 Query: 359 HSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 + +D+ + G+G+ RL+VGLED +D+I DL++AL Sbjct: 363 FATGKQDESWEIYAGDGIFRLSVGLEDSKDIIDDLNRAL 401 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: 343 Number of extensions: 13 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: 402 Length of database: 403 Length adjustment: 31 Effective length of query: 371 Effective length of database: 372 Effective search space: 138012 Effective search space used: 138012 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