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= 0055.0005.p (284 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KBT3.1 B3KBT3_9BACI Helix-turn-helix domain protein 341 5e-92 B1DMD7.1 B1DMD7_9BACL Helix-turn-helix domain protein 205 3e-51 B3K3Z9.1 B3K3Z9_9BACI Putative uncharacterized protein 174 1e-41 B1D5M4.1 B1D5M4_9BACL Helix-turn-helix domain protein 164 8e-39 Q9ADL0.1 Q9ADL0_STRCO Putative DNA-binding protein 160 1e-37 >B3KBT3.1 B3KBT3_9BACI Helix-turn-helix domain protein Length = 284 Score = 341 bits (874), Expect = 5e-92, Method: Compositional matrix adjust. Identities = 162/270 (60%), Positives = 202/270 (74%), Gaps = 2/270 (0%) Query: 1 MDNHHTSSALGEFIKSRRYRLQPEEAGIKPFPGRRRTPGLRREEVAFLANVSVTYYTWLE 60 M + +SSALG+F+KSRR RLQP EAGI+P PGRRRTPGLRREEV++LAN+SVTYY WLE Sbjct: 1 MKMNRSSSALGDFLKSRRERLQPSEAGIQPLPGRRRTPGLRREEVSYLANISVTYYAWLE 60 Query: 61 QGRERNPSPEVLSHISQALQLDEDERKHLFNLAAPEPANSYTAPKPEPHNTEFLQNLVNQ 120 QG+E NPSPEVL IS+ALQLDEDE+KHLF+LA + A+ T P +T LQ +VNQ Sbjct: 61 QGKEVNPSPEVLLSISKALQLDEDEQKHLFDLANVDVASVVTVPNNGGPDTGVLQKIVNQ 120 Query: 121 LRYPSFIANEVADVIVWNQGAKLVITDFGRLPEKERNMATLLFLDPEYPKRLINWEEFAR 180 L YPSFI +E DVI WN+ A+L++ DFG LP+ ERNM ++FL P+Y RL+NWE AR Sbjct: 121 LHYPSFITDEGTDVIAWNRAAELIVADFGSLPDNERNMMDIMFLKPDYRNRLVNWEGAAR 180 Query: 181 YMTGLIRASFDQNKENPMFMNRFDRL-KNSEEFLRLWEWHEIRHKTTAVPVQCRLADGPE 239 Y ++RA FD K NP++M RF+RL + S EF+ WE +EI+ K A + R+ D E Sbjct: 181 YSVAVLRAGFDLYKNNPLYMERFERLTRESVEFVHFWELYEIKQKRVATAL-FRVPDAQE 239 Query: 240 LAFTIHCAAAIDNDPGLHWCFFVPMPGSGT 269 + F +H AA IDNDPGLHWCFFVP+PGSGT Sbjct: 240 MEFELHSAAVIDNDPGLHWCFFVPVPGSGT 269 >B1DMD7.1 B1DMD7_9BACL Helix-turn-helix domain protein Length = 275 Score = 205 bits (522), Expect = 3e-51, Method: Compositional matrix adjust. Identities = 107/264 (40%), Positives = 162/264 (61%), Gaps = 11/264 (4%) Query: 10 LGEFIKSRRYRLQPEEAGIKPFPGRRRTPGLRREEVAFLANVSVTYYTWLEQGRERNPSP 69 LG+F+KSRR ++ P +AG+ P G+RRTPGLRREEVA LA+VS T+YTWLEQGR PS Sbjct: 9 LGQFLKSRREKMNPSDAGLPPGYGKRRTPGLRREEVAQLAHVSTTWYTWLEQGRASTPSR 68 Query: 70 EVLSHISQALQLDEDERKHLFNLAAPEPANSYTAPKPEPHNTEF---LQNLVNQLRYPSF 126 +VL ++QAL+L ++E H+ +LA E P P P + ++ L++QL YP+F Sbjct: 69 QVLDSVAQALKLSKNEHLHMLHLANLE------LPNPSPAVNQLSPDIEKLIDQLPYPAF 122 Query: 127 IANEVADVIVWNQGAKLVITDFGRLPEKERNMATLLFLDPEYPKRLINWEEFARYMTGLI 186 IA E +V+ WN A +I DF +P ++R+MA L F++ + + +WEE+A+Y G++ Sbjct: 123 IATERTEVLSWNAAACRIIFDFPSVPAEDRSMAWLTFMNENLRRSVPDWEEYAQYTAGVL 182 Query: 187 RASFDQNKENPMFMNRFDRLKN-SEEFLRLWEWHEIRHKTTAVPVQCRLADGPELAFTIH 245 R +++N + F DRL S EFL LW H+I KT ++ + L F I+ Sbjct: 183 RGRYEKNLNDLTFRKLIDRLTGASPEFLELWSTHDIMDKTIKT-IRLLHPEAGLLTFNIN 241 Query: 246 CAAAIDNDPGLHWCFFVPMPGSGT 269 + I+ + H C ++P+ G+GT Sbjct: 242 TFSQINGNSSAHCCVYIPVEGTGT 265 >B3K3Z9.1 B3K3Z9_9BACI Putative uncharacterized protein Length = 279 Score = 174 bits (440), Expect = 1e-41, Method: Compositional matrix adjust. Identities = 97/271 (35%), Positives = 151/271 (55%), Gaps = 5/271 (1%) Query: 1 MDNHHTSSALGEFIKSRRYRLQPEEAGIKPFPGRRRTPGLRREEVAFLANVSVTYYTWLE 60 M++ AL F+K +R ++ PE G+ P RRRTPGLRREEVA LA VS T+YTWLE Sbjct: 1 MNSQVRLQALSAFLKGQRAKISPESVGLPP-GTRRRTPGLRREEVAQLAGVSTTWYTWLE 59 Query: 61 QGRERNPSPEVLSHISQALQLDEDERKHLFNLAAPEPANSYTAPKPEPHNTEFLQNLVNQ 120 QGR+ S VL ++ ALQL+ DER++L++LA A YT + LQ ++ + Sbjct: 60 QGRDIQVSSSVLDCVASALQLNADERRYLYSLALESGAEPYTVKHEAVQISPSLQKIITE 119 Query: 121 LRY-PSFIANEVADVIVWNQGAKLVITDFGRLPEKERNMATLLFLDPEYPKRLINWEEFA 179 L+Y P I++ +++ WN+ A V DF R+P +ERNM LLF E+ + +NWE+FA Sbjct: 120 LKYCPVMISDRKCNIVGWNRAAAYVFLDFDRIPPEERNMIRLLFTRREFQRLAVNWEQFA 179 Query: 180 RYMTGLIRASFDQNKENPMFMNRFDRLKNSE-EFLRLWEWHEIRHKTTAVPVQCRLADGP 238 + R+ + Q E+ + + + +KN +F R+WE ++ + V ++ R A Sbjct: 180 SGFLSMFRSYYGQYVEDEWYDHFLEEMKNGHPDFNRMWEQSQVSY-APEVHLEFRHAKAG 238 Query: 239 ELAFTIHCAAAIDNDPGLHWCFFVPMPGSGT 269 ++ + + ND L + P P + T Sbjct: 239 KMVYELTSLKVYGND-DLRCSIYTPAPDTTT 268 >B1D5M4.1 B1D5M4_9BACL Helix-turn-helix domain protein Length = 285 Score = 164 bits (415), Expect = 8e-39, Method: Compositional matrix adjust. Identities = 103/275 (37%), Positives = 147/275 (53%), Gaps = 9/275 (3%) Query: 1 MDNHHTSSALGEFIKSRRYRLQPEEAGIKPFPGRRRTPGLRREEVAFLANVSVTYYTWLE 60 M+N +AL F+K++R +L PEE G P RRRTPGLRREEVA LA VS T+YTWLE Sbjct: 1 MNNKTRLTALSSFLKNQRAKLTPEEVGFPP-GSRRRTPGLRREEVAALAGVSTTWYTWLE 59 Query: 61 QGRERNPSPEVLSHISQALQLDEDERKHLFNLAA-PEPANSYTAPKPEPHNTEF---LQN 116 QGR+ SP VL I+ AL+L DER +L+ LA P S TA P + L+ Sbjct: 60 QGRDIQASPNVLDAIASALRLTHDERNYLYGLAIEPGAGPSITAEMPAYSSDAVSPPLRK 119 Query: 117 LVNQLRY-PSFIANEVADVIVWNQGAKLVITDFGRLPEKERNMATLLFLDPEYPKRLINW 175 ++ +LR PS I++ ++ WN+ A V DF ++PE+ERNM LLF E + +NW Sbjct: 120 ILQELRQCPSIISDRRCQIVGWNEAAAHVFVDFAQIPEQERNMIRLLFTRKELRRLAVNW 179 Query: 176 EEFARYMTGLIRASFDQNKENPMFMNRFDRLKNSE-EFLRLWEWHEIRHKTTAVPVQCRL 234 ++FA + RA + Q E+ + + +F LWE E+R V ++ R Sbjct: 180 KQFASGFLSIFRAYYGQYVEDNWYDQFLKEMTGLHPDFQELWEHSEVRTAPEVV-LEFRH 238 Query: 235 ADGPELAFTIHCAAAIDNDPGLHWCFFVPMPGSGT 269 A ++ F + + + L + P P S T Sbjct: 239 AKAGKMLFHL-TSLQLQGGSDLRCSIYTPAPDSET 272 >Q9ADL0.1 Q9ADL0_STRCO Putative DNA-binding protein Length = 291 Score = 160 bits (406), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 85/222 (38%), Positives = 135/222 (60%), Gaps = 3/222 (1%) Query: 10 LGEFIKSRRYRLQPEEAGIKPFPGRRRTPGLRREEVAFLANVSVTYYTWLEQGRERNPSP 69 L EF+++RR RL+PE+ G++ + +RR PGLRREE+A LA VSV YYT LEQG +N S Sbjct: 11 LSEFLRTRRARLKPEDVGLESYGRQRRVPGLRREELAQLAGVSVAYYTRLEQGNGQNVSA 70 Query: 70 EVLSHISQALQLDEDERKHLFNLAAPEPA--NSYTAPKPEPHNTEFLQNLVNQLRYPSFI 127 EVL I++AL+L + E+ HL +LA P+ + A +P LQ L + P+++ Sbjct: 71 EVLDAIARALRLTDAEQAHLTHLARPKQQRRRAGAARGKQPVRVALLQLLDSIDTVPAYV 130 Query: 128 ANEVADVIVWNQGAKLVITDFGRLPEKERNMATLLFLDPEYPKRLINWEEFARYMTGLIR 187 + ++++ WN+ A + D+G+LP ERN A L+FL+P+Y + ++W++ A M +R Sbjct: 131 SGRRSEILAWNRMAAALFGDWGKLPAAERNWARLVFLNPDYRELFVDWDQKAYDMVSFLR 190 Query: 188 ASFDQNKENPMFMNRFDRLK-NSEEFLRLWEWHEIRHKTTAV 228 ++ ++P L SEEF RLW H+++ K+ V Sbjct: 191 MDAGRHPDDPRLSALVGELSVKSEEFRRLWATHDVKEKSYGV 232 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.320 0.136 0.428 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,775,310,064 Number of extensions: 76188712 Number of successful extensions: 164739 Number of sequences better than 1.0e-05: 459 Number of HSP's gapped: 164019 Number of HSP's successfully gapped: 459 Length of query: 284 Length of database: 3,060,696,203 Length adjustment: 134 Effective length of query: 150 Effective length of database: 1,798,280,193 Effective search space: 269742028950 Effective search space used: 269742028950 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: 130 (54.7 bits)