Align Putative cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; ORF5 (uncharacterized)
to candidate Ac3H11_4146 Cystathionine beta-lyase (EC 4.4.1.8)
Query= curated2:Q52811 (396 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4146 Length = 412 Score = 234 bits (597), Expect = 3e-66 Identities = 157/417 (37%), Positives = 214/417 (51%), Gaps = 32/417 (7%) Query: 1 MKDKDSLLQNAGINTRLTHIGNDPFDYHGFINPPVVHASTVLFPNARAMETRTQK----Y 56 MKD D+ L TR+ H G P P V ASTV+FPN AM +R K Y Sbjct: 4 MKDHDTDLA-----TRIVHHGYLPPAGFEAPQPGVYKASTVIFPNVAAMRSREWKDKSGY 58 Query: 57 TYGTRGTPTTDALCEAIDALEGSAGTILVPSGLAAVTIPFLGFVAAGDHALVVDSVYGPT 116 TYG GTPTT L E + LEG +LVPSGLAA+ L + GD L+ D+ YGP Sbjct: 59 TYGLHGTPTTFILEERLCTLEGGLQCVLVPSGLAAIANVGLALLKPGDEVLIPDNAYGPG 118 Query: 117 RHFCDTMLKRLGVEVEYYHPEIGAGIETLFRSNTKLVHTEAPGSNTFEMQDIPAISAVAH 176 + F + L R G+ +Y P A + T+LV EAPGS + E D+ + Sbjct: 119 KDFANGELARFGITHVFYDPLDPADLAARITPATRLVWLEAPGSVSMEFPDLCEQVRICR 178 Query: 177 RHGAVVMMDNTWATPVYFRPLD------HGVDISIHASTKYPSGHSDILLGTV-SANAEH 229 G +DNTW + F P D GVDIS HA TKYPSG D+L+G+V + + Sbjct: 179 ARGVTTALDNTWGAGLAFAPFDLTGDGSLGVDISAHALTKYPSGGGDVLMGSVITRDLGL 238 Query: 230 WERLKEANGVLGICGAPDDAYQILRGLRTMGLRLERHYESALDIAKWLEGRDDVARVLHP 289 ++K + LG+ +D +LR L ++GLR H E+A +A+WL+ + +A+VLHP Sbjct: 239 HMKIKLTHMRLGLGVGVNDVEAVLRALPSIGLRYRAHDEAARVLARWLQQQPAIAQVLHP 298 Query: 290 ALPSFPSHHLWKR-------DFKGASGIFSFVLAADGPEKSRAKAHAFLDALRIFGLGYS 342 AL P H WK A+G+FS ++ A ++ + AF D LR+F LGYS Sbjct: 299 ALEGAPGHAHWKALCGAAQGGQGAAAGLFSVMIDA---RYTQQQVDAFCDGLRLFKLGYS 355 Query: 343 WGGFESLALHAYLNDRTVAKAP--TDGPVIRLQIGIEDVADLKADI----ERGFAAA 393 WGG SL + + +P G ++R IG+E V DL+ D+ ER F AA Sbjct: 356 WGGPMSLVVPYTIGSMRSRPSPQLQPGTLVRFSIGLEAVEDLQRDLQQAMERAFPAA 412 Lambda K H 0.320 0.137 0.417 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: 516 Number of extensions: 25 Number of successful extensions: 6 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: 396 Length of database: 412 Length adjustment: 31 Effective length of query: 365 Effective length of database: 381 Effective search space: 139065 Effective search space used: 139065 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