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= 0340.0045.p (333 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_yfiF [K] COG2207 AraC-type DNA-binding domain-containing prot... 74 3e-13 RSp0044 [K] COG4977 Transcriptional regulator containing an amid... 71 2e-12 CAC1451 [K] COG2207 AraC-type DNA-binding domain-containing prot... 69 1e-11 PA4436 [K] COG4977 Transcriptional regulator containing an amida... 69 1e-11 BH3679 [T] COG4753 Response regulator containing CheY-like recei... 68 2e-11 >BS_yfiF [K] COG2207 AraC-type DNA-binding domain-containing proteins Length = 345 Score = 74.3 bits (181), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 10/267 (3%), Positives = 44/267 (16%), Gaps = 18/267 (6%) Query: 60 HQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNCM 119 Q + ED ++G ++ Sbjct: 44 ADGGRRPARDDKQSQPRDRKWEDSPWRTVSRAPGDET--PEKADHGGISG---KSFIDPE 98 Query: 120 LRPELCRIPGELPGQYSEEDMVPLLKLLELKQWFGYRENNVELSFLLRRMQGIHNNGSAE 179 + + G+ + + + + + + +V F + Sbjct: 99 VLRRQRAEETRVYGENACQALFQSRPE-AIVR--AWFIQSVTPRFKEALRWMA----ANR 151 Query: 180 DQQQL----YPLLFELAKLILPAASVPFTQQP-QINEDPLHDVILYMISNFSEKITLKEI 234 + + + + + + + + + Sbjct: 152 KAYHVVDEAELTKASGTEHHGGVCFLIKKRNGTTVQQWVSQAGAQDCVLALENESNPHNL 211 Query: 235 SRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIYDMKY 294 + + + ++ + + L+ Y Sbjct: 212 GGMMRSCAHFGVKGVVVQDAALLESGAAIRTAEGGAEHVQPITGDNIVNVLDDF-RQAGY 270 Query: 295 FYRLFREYSGMTPACYRNRFHSHFLSA 321 G + Sbjct: 271 TVVTTSSEQGKPLFKTSLPAKMVLVLG 297 >RSp0044 [K] COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain Length = 387 Score = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 32/97 (32%), Positives = 56/97 (57%) Query: 217 VILYMISNFSEKITLKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFT 276 IL M + + L+E++ ++ +S+RQ +RLFK +TG+S +++R++ + LL + Sbjct: 238 AILLMEQHIGRPLPLEELAHKLDLSARQLERLFKAETGKSPQTFAKQVRLRTAAWLLTSS 297 Query: 277 KLGIQAIALEVGIYDMKYFYRLFREYSGMTPACYRNR 313 G+ IA G D + R FR+ GM PA YR++ Sbjct: 298 DRGVADIAFSCGFADASHLGREFRKQFGMPPAAYRDK 334 >CAC1451 [K] COG2207 AraC-type DNA-binding domain-containing proteins Length = 295 Score = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 62/268 (23%), Positives = 114/268 (42%), Gaps = 19/268 (7%) Query: 59 RHQHDFLELAYVVQGEGIHLAAEDKMQVVQGDLLVIPPGVSHVFQPLDLTGSEPLIILNC 118 RH H+ L++ Y G A++K V G + +I H + + S L Sbjct: 35 RHWHEHLQIYYFTAGTAYLECAQNKFDVTTGSIAIINSNELHYLE----SHSNNLKFYTI 90 Query: 119 MLRPELCRIPGE--LPGQYSEEDMVPL-LKLLELKQWFGYRENNVELSFLLRRMQGIHNN 175 + P E L +Y + PL L + K EN++++ ++ + +++ Sbjct: 91 RIEPTFLFSNKEDLLQTKY----LAPLALNRITFKNLI---ENDLQILECIKTILKEYSS 143 Query: 176 GSAEDQQQLYPLLFELAKLILPAASVPFTQQPQINE-----DPLHDVILYMISNFSEKIT 230 + + + +++L +L + + E + V + ++EK+T Sbjct: 144 KNIGYELAVKANIYQLIVYLLRGYVDKILNENEFEERKRILNKFQCVFRLIEEKYTEKLT 203 Query: 231 LKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIY 290 L E++ + S+ F R FK TG++ + IR+ S L T L I IA++ G Sbjct: 204 LNELADCVNFSTHHFCRTFKQMTGKTTTDYINGIRLYKSTNYLKQTDLNITEIAIKCGFD 263 Query: 291 DMKYFYRLFREYSGMTPACYRNRFHSHF 318 + YF RLF+++ MTP YR + HF Sbjct: 264 NNNYFSRLFKKHYDMTPTKYRKLYAGHF 291 >PA4436 [K] COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain Length = 299 Score = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 38/128 (29%), Positives = 73/128 (57%), Gaps = 3/128 (2%) Query: 188 LFELAKLILPAASVPFTQQPQINEDP-LHDVILYMISNFSEKITLKEISRQIAMSSRQFQ 246 L+E+ + P + F Q +++ DP + + ++ +F++K ++++R MS R F Sbjct: 169 LYEVQRSYTPG-RIGFGGQ-KLHHDPTILQIQQWLEDHFADKFRFEDVARDHGMSIRNFM 226 Query: 247 RLFKIKTGRSYIQMLQEIRMKYSCMLLMFTKLGIQAIALEVGIYDMKYFYRLFREYSGMT 306 R F+ TG + LQ +R++ + +L T+ I+ I+ EVG D +F RLFR+++ ++ Sbjct: 227 RRFQAATGDKPLHYLQRLRIETAKGMLSSTRKSIKTISYEVGYDDASFFARLFRQHTELS 286 Query: 307 PACYRNRF 314 P YR +F Sbjct: 287 PHHYRRQF 294 >BH3679 [T] COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain Length = 257 Score = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust. Identities = 32/103 (31%), Positives = 60/103 (58%) Query: 210 NEDPLHDVILYMISNFSEKITLKEISRQIAMSSRQFQRLFKIKTGRSYIQMLQEIRMKYS 269 + D +H+ + Y+ ++ +KI LK++++ + ++ LFK KT ++ + L R++++ Sbjct: 152 SSDSIHEALHYIDAHLDQKIGLKDVAKSVHLNPSYLSALFKEKTNMTFSEYLTRKRLQHA 211 Query: 270 CMLLMFTKLGIQAIALEVGIYDMKYFYRLFREYSGMTPACYRN 312 LL+ T I IA + G KYF ++F+E+ GMTP YR Sbjct: 212 KHLLVSTDRPISDIAEKCGYQTAKYFIKIFKEHEGMTPTQYRK 254 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 0.324 0.139 0.416 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: 23,875,030 Number of extensions: 998601 Number of successful extensions: 2378 Number of sequences better than 1.0e-05: 55 Number of HSP's gapped: 2385 Number of HSP's successfully gapped: 55 Length of query: 333 Length of database: 38,378,431 Length adjustment: 107 Effective length of query: 226 Effective length of database: 26,037,693 Effective search space: 5884518618 Effective search space used: 5884518618 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 116 (49.3 bits)