Align Putative cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; ORF5 (uncharacterized)
to candidate WP_011801276.1 PNAP_RS09440 cystathionine beta-lyase
Query= curated2:Q52811 (396 letters) >NCBI__GCF_000015505.1:WP_011801276.1 Length = 397 Score = 259 bits (662), Expect = 9e-74 Identities = 157/399 (39%), Positives = 215/399 (53%), Gaps = 29/399 (7%) Query: 14 NTRLTHIGNDPFDYHGFINPPVVHASTVLFPNARAMETRTQK----YTYGTRGTPTTDAL 69 +T+L H P ++P V AST++FP+ A+ R K YTYG GTPTT L Sbjct: 5 STQLIHHPYTPPAGFEAVSPAVHKASTIIFPSVAALRNRDWKHKTGYTYGLHGTPTTFTL 64 Query: 70 CEAIDALEGSAGTILVPSGLAAVTIPFLGFVAAGDHALVVDSVYGPTRHFCDTMLKRLGV 129 E I LEG LVPSGLAA+ + + + AGD L+ D+ YGP + F L G+ Sbjct: 65 EERIATLEGGQFCTLVPSGLAAIVLVDMALLKAGDEVLIPDNAYGPNKAFAQAELASWGI 124 Query: 130 EVEYYHPEIGAGIETLFRSNTKLVHTEAPGSNTFEMQDIPAISAV----------AHRHG 179 + Y P A + T+LV EAPGS T E D+PA++A AH G Sbjct: 125 TCQMYDPMNPADLAAKLTLKTRLVWLEAPGSITLEFPDLPALAAAVRAHNASPGQAHPQG 184 Query: 180 AVVMMDNTWATPVYFRPLDHGVDISIHASTKYPSGHSDILLGTVSANAE------HWERL 233 V +DNTW + F G DIS+ A TKYPSG +D+L+G+V N+E H+ + Sbjct: 185 VVTALDNTWGAGLAFNAFALGADISVQALTKYPSGGADVLMGSVVTNSEALHLLVHFCHM 244 Query: 234 KEANGVLGICGAPDDAYQILRGLRTMGLRLERHYESALDIAKWLEGRDDVARVLHPALPS 293 + GV G +DA +LRGL +M LR + +A W++G+ +A VLHPALP Sbjct: 245 RVGYGVSG-----NDAELVLRGLNSMALRYAAQDAATRQLAGWMQGQPQIAAVLHPALPD 299 Query: 294 FPSHHLWKRDFKGASGIFSFVLAADGPEKSRAKAHAFLDALRIFGLGYSWGGFESLALHA 353 P H WKRD GA+ +FS V PE ++A+ F D+L++F LGYSW G SL + Sbjct: 300 SPGHAQWKRDCLGAACLFSAVFR---PEFTQAQIDRFCDSLQLFRLGYSWAGPMSLCVPY 356 Query: 354 YLNDRTVAKA-PTDGPVIRLQIGIEDVADLKADIERGFA 391 + VAK P G ++R +G+E VADL+ADI + A Sbjct: 357 DMPALRVAKPWPHKGGLVRFSVGLEAVADLQADIAQALA 395 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: 428 Number of extensions: 21 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: 397 Length adjustment: 31 Effective length of query: 365 Effective length of database: 366 Effective search space: 133590 Effective search space used: 133590 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 10 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