Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_044408637.1 NA59_RS04485 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q83A83 (387 letters) >NCBI__GCF_000934765.1:WP_044408637.1 Length = 425 Score = 228 bits (581), Expect = 2e-64 Identities = 149/421 (35%), Positives = 220/421 (52%), Gaps = 46/421 (10%) Query: 11 IDTRVIHAGQKPDPLTGAVMTPIYTASTYA----QKSPGVHQ----GYEYSRSQNPTRFA 62 ++T +H G +P+ T +V PIY +++A Q + + G YSR NPT Sbjct: 3 LETIALHGGYQPEDTTKSVAVPIYQTTSFAFDDAQHAADLFDLKVAGNIYSRIMNPTNAV 62 Query: 63 YERCVADLESGQHGFAFASGMAA-TATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSA 121 E +A +ESG A ASGM+A T TI L + GD++V ++YGGSY LF + R Sbjct: 63 LESRIAAMESGIAALAVASGMSAITYTIQTLAEAGDNIVSTGELYGGSYNLFAHTLPRQ- 121 Query: 122 GLSFSFV--DFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVAD 179 GL F D +D + + + + +KTKML+ E+ NP I D+ ++A +A + I V D Sbjct: 122 GLDVRFFNKDASDAD-IAKLIDSKTKMLYCETVGNPSGGIADIERLANLAHQHGIPLVVD 180 Query: 180 NTFATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQ----------- 228 NT +PI+ RP+E G DIV H+ATKY+ GH IGGV V AE Sbjct: 181 NTVPSPILWRPIEQGADIVVHAATKYIGGHGTTIGGVIVDSGKFPWAEHADRFPLLNTPD 240 Query: 229 -----LKYLQN----------------AIGAIAAPFDSFMVLRGLKTLAIRMERHCENAM 267 + Y Q+ +GA +P ++F +L+GL+TLA+RMER CEN Sbjct: 241 ISYHGVTYTQDFGAAAFIARARVVPLRNMGAALSPMNAFQLLQGLETLALRMERVCENTQ 300 Query: 268 QLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMR-YFGGMISVELKCDLNETKKVLERCQ 326 ++A++L HP V V Y GL SH H++ +K M G++S LK T+K + Sbjct: 301 KVAEFLVAHPLVSWVNYAGLASHKDHALTQKYMNGKASGILSFGLKSGREGTRKFYDALA 360 Query: 327 LFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAA 386 + ++G +S PA TH + AE + G++ +RLS+GIE I D+ D+E A Sbjct: 361 MIIRLVNIGDAKSCASIPAETTHRQLNDAELKAAGVSPDMVRLSIGIEHIDDILADIEQA 420 Query: 387 L 387 L Sbjct: 421 L 421 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: 407 Number of extensions: 22 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: 2 Length of query: 387 Length of database: 425 Length adjustment: 31 Effective length of query: 356 Effective length of database: 394 Effective search space: 140264 Effective search space used: 140264 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