Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Cup4G11:RR42_RS31610 Length = 402 Score = 143 bits (361), Expect = 9e-39 Identities = 128/451 (28%), Positives = 195/451 (43%), Gaps = 62/451 (13%) Query: 1 MPSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGY---VYS 57 M H DT +HAG P H VP+ T++ FENS + G Y Sbjct: 1 MSHHRDTQLIHAGTP-PFVQGHGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYG 59 Query: 58 RFQNPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQ 117 R T LE+ IA LEGG A SG AA +L L GD+ + +Y Sbjct: 60 RHGMDTHRALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRL 119 Query: 118 FKISFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHG 177 + +R GIE + + ++ + + T+ +YLE+ + Y V D ++V IAH+HG Sbjct: 120 EQTLLRRLGIEVSYFS-PSQDDLDALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHG 178 Query: 178 IPVVVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKF 237 + V DNT+ A G+ QP+ G DI ++TK+I GH + G +V Sbjct: 179 VVVATDNTW-ASGHALQPLALGVDISILASTKYISGHSDLMQGAVV-------------- 223 Query: 238 PQFSQPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAE 297 + +EA H G ++ ++L L+G+ TL++R Sbjct: 224 -------------VKDEALARRIADAH------DGFGLAISADDAYLALRGIRTLAVRLA 264 Query: 298 RHGENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADK 357 +H NAL +A++LE V V YP L S H + S G G++SF LP AD Sbjct: 265 QHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWLRDFS-GANGLVSF---SLPTAD- 319 Query: 358 ETDPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGV----TKD 413 + ++VD+L L A+ G ++LV Q+ E+LA + Sbjct: 320 -----VAAARKLVDSLSLFGLGASWGGYESLV---------QVAAPERLAEHSYWRGAEP 365 Query: 414 LIRVSVGIEFIDDIIADFQQSFETVFAGQKP 444 +IR+ +G+E +D+IAD Q P Sbjct: 366 VIRLHIGLEAPEDLIADLAQGLAATVQASVP 396 Lambda K H 0.317 0.136 0.402 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: 442 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: 444 Length of database: 402 Length adjustment: 32 Effective length of query: 412 Effective length of database: 370 Effective search space: 152440 Effective search space used: 152440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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