BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0444.0025.p (476 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_yvfP_2 [TK] COG2208 Serine phosphatase RsbU, regulator of sig... 77 5e-14 BS_rsbU [TK] COG2208 Serine phosphatase RsbU, regulator of sigma... 72 2e-12 all1703_3 [TK] COG2208 Serine phosphatase RsbU, regulator of sig... 67 9e-11 alr1086_2 [TK] COG2208 Serine phosphatase RsbU, regulator of sig... 52 2e-06 RSc0588_1 [T] COG2202 FOG: PAS/PAC domain 52 2e-06 >BS_yvfP_2 [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 77.0 bits (188), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 12/185 (6%), Positives = 28/185 (15%), Gaps = 8/185 (4%) Query: 261 SKKEVERAVKLQNHRHTVVFPL-EDKAELEKLYIPARTLSGDFFIFHKIDEERVIGMIGD 319 + + + + V + + Sbjct: 40 VAQGINLIDVAE--MYPVPPRPETQGLTETYVGNWLAKHGSREKLIIASKVSGPSRNNDK 97 Query: 320 VTGKGITAALNISALRVLFADCLEVTVDPLQAIKELNQKAMLHLGED-----YIAGCCFQ 374 + + T Q+ G+ A Sbjct: 98 GIRPDQALDRKNIREALHDSLKRLQTDYLDLYQVHWPQRPTNCFGKLGYSWTDSAPAVSL 157 Query: 375 LDFGAGVLKAAGAGINEFIYVPKDQESQCLTVRGAPLGMFGNSEFEEITVPFSSGDRFCF 434 LD + + AG +I V + + F Sbjct: 158 LDTLDALAEYQRAGKIRYIGVSNETAFGVMRYLHLADKHDLPRIVTIQNPYSLLNRSFEV 217 Query: 435 YSDGM 439 + Sbjct: 218 GLAEV 222 >BS_rsbU [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 72.4 bits (176), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 15/207 (7%), Positives = 39/207 (18%), Gaps = 16/207 (7%) Query: 240 GVPIIYEEEKALQLVLRDITESKKEVERAVKLQNHRHTVVFPLEDKAELEKLYIPARTLS 299 +I + + D ++A+ +N R + L+ Sbjct: 79 REKLIIASKVSGPSRNNDK---GIRPDQALDRKNIREALHDSLKRLQTDYLDLYQVHWPQ 135 Query: 300 GDFFIFHKIDEERVIGMIGDVTGKGITAALNISALRVLFADCLEVTVDPLQAIKELNQKA 359 F K V+ AL ++ L+ Sbjct: 136 RPTNCFGK-LGYSWTDSAPAVSLLDTLDALAEYQRAGKIRYIGVSNETAFGVMRYLHL-- 192 Query: 360 MLHLGEDYIAGCCFQLDFGAGV------LKAAGAGINE-FIYVPKDQESQCLTVRGAPLG 412 + + + + + A + + LT + Sbjct: 193 ---ADKHDLPRIVTIQNPYSLLNRSFEVGLAEVSQYEGVELLAYSCLGFGTLTGKYLNGA 249 Query: 413 MFGNSEFEEITVPFSSGDRFCFYSDGM 439 + + + Sbjct: 250 KPAGARNTLFSRFTRYSGEQTQKAVAA 276 >all1703_3 [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 66.6 bits (161), Expect = 9e-11, Method: Compositional matrix adjust. Identities = 13/194 (6%), Positives = 24/194 (12%), Gaps = 28/194 (14%) Query: 264 EVERAVKLQNHRHTVVFPLEDKAELEKLYIPARTLSGDFF-IFHKIDEERVIGMIGDVTG 322 L T + +L R T Sbjct: 9 SSLEVSTLGLGTMTFGEQNSEADAHAQLDYAVAQGINLIDVAEMYPVPPRPETQGLTETY 68 Query: 323 KGITAAL----NISALRVLFADCLEVTVDPLQAIKELNQKAMLHLGEDYIAGCCFQLDFG 378 G A + + + + A L Sbjct: 69 VGNWLAKHGSREKLIIASKVSG--PSRNNDKGIRPDQALD----RKNIREALHDS-LKR- 120 Query: 379 AGVLKAAGAGINEFIYV------PKDQESQC-------LTVRGAPLGMFGNSEFEEITVP 425 + K S L L + + Sbjct: 121 --LQTDYLDLYQVHWPQRPTNCFGKLGYSWTDSAPAVSLLDTLDALAEYQRAGKIRYIGV 178 Query: 426 FSSGDRFCFYSDGM 439 + + Sbjct: 179 SNETAFGVMRYLHL 192 >alr1086_2 [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit Length = 346 Score = 52.4 bits (124), Expect = 2e-06, Method: Compositional matrix adjust. Identities = 11/170 (6%), Positives = 28/170 (16%), Gaps = 16/170 (9%) Query: 281 PLEDKAELEKLYIPARTLSGDFFIFHKIDEERVIGMIGDVTGKGITAAL-NISALRVLFA 339 E+ L + T + G Sbjct: 6 IPHSSLEVSTLGLGTMTFGEQNSEADAHAQLDYAVAQGINLIDVAEMYPVPPRPETQGLT 65 Query: 340 DCLEVT--VDPLQAIKELNQKAMLHLGEDYIAGCCFQLDFGA-----GVLKAAGAGINEF 392 + K + + + + + +A + Sbjct: 66 ETYVGNWLAKHGSREKLIIASKVSGPSRNND----KGIRPDQALDRKNIREALHDSLKRL 121 Query: 393 IYV----PKDQESQCLTVRGAPLGMFGNSEFEEITVPFSSGDRFCFYSDG 438 + Q T LG +++ + + G Sbjct: 122 QTDYLDLYQVHWPQRPTNCFGKLGYSWTDSAPAVSLLDTLDALAEYQRAG 171 >RSc0588_1 [T] COG2202 FOG: PAS/PAC domain Length = 179 Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust. Identities = 33/121 (27%), Positives = 67/121 (55%), Gaps = 7/121 (5%) Query: 153 LVELCPEAILVYSGGMILFANKQSEKMFGK-KKKEMIGQRIEAFFSEEYLKSAKYKK--L 209 LV P+A+ + + +I+F N+ ++ G +++G+ ++AF E+ ++ A+ ++ + Sbjct: 33 LVRQMPDALYIVADDIIVFINEAGVRLLGADSASDIVGRELDAFVHEDSVQLARQRREWM 92 Query: 210 MTWGSTAKERFRIEQRLIRYDNRIFDVEISGVPIIYEEEKALQLVLRDITESKKEVERAV 269 + G+ +EQ L+R D DVEI P+ A+Q+V RDI + +K E+A+ Sbjct: 93 IEHGAGLPP---VEQTLLRCDGTPVDVEILSAPVQLGWRTAVQVVARDIRQ-RKHAEQAL 148 Query: 270 K 270 + Sbjct: 149 R 149 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.322 0.139 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 33,038,339 Number of extensions: 1379037 Number of successful extensions: 3103 Number of sequences better than 1.0e-05: 11 Number of HSP's gapped: 3103 Number of HSP's successfully gapped: 11 Length of query: 476 Length of database: 38,378,431 Length adjustment: 110 Effective length of query: 366 Effective length of database: 25,691,691 Effective search space: 9403158906 Effective search space used: 9403158906 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 (21.9 bits) S2: 118 (50.1 bits)