Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate HSERO_RS16440 HSERO_RS16440 hypothetical protein
Query= SwissProt::Q83A83 (387 letters) >FitnessBrowser__HerbieS:HSERO_RS16440 Length = 413 Score = 214 bits (546), Expect = 3e-60 Identities = 140/413 (33%), Positives = 214/413 (51%), Gaps = 33/413 (7%) Query: 5 NNKKSH-IDTRVIHAGQKPDPLTGAVMTPIYTASTY--------AQKSPGVHQGYEYSRS 55 N+KK++ T ++H+ ++ G++ PI+T+ T+ A+ G GY Y R Sbjct: 2 NDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQ 61 Query: 56 QNPTRFAYERCVADLESGQHGFAFASGMAATATILE-LLQPGDHVVVMDDVYGGSYRLFE 114 NPT A E + +E G+ FA+GMAA I++ LL+ GDHVV ++G + L+ Sbjct: 62 GNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM 121 Query: 115 NVRKRSAGLSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNI 174 V + G S VD TD V A+TA T++++VE+ +NPR ++ DL +I E+ +E+ I Sbjct: 122 TVGAQ--GAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 Query: 175 IAVADNTFATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAV------------VGDN 222 + V DNT +P + RP +G +V +S TK + GH + +GG + +N Sbjct: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAEN 239 Query: 223 --KTLAEQLKYLQ------NAIGAIAAPFDSFMVLRGLKTLAIRMERHCENAMQLAQWLE 274 K A Q Q G P + + G +T+A+R ER C+NA+ LAQ L+ Sbjct: 240 YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQ 299 Query: 275 KHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVELKCDLNETKKVLERCQLFTLAESL 334 +V VYYPGL SHPQH+++K R FG ++S ELK D + L R +L +L Sbjct: 300 ADERVAAVYYPGLESHPQHALSKALFRSFGSLMSFELK-DGIDCFDYLNRLRLAIPTSNL 358 Query: 335 GGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAAL 387 G +L+ A + R +GI + IR+SVG+E DL D AL Sbjct: 359 GDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 Lambda K H 0.319 0.134 0.385 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: 365 Number of extensions: 15 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 387 Length of database: 413 Length adjustment: 31 Effective length of query: 356 Effective length of database: 382 Effective search space: 135992 Effective search space used: 135992 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