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= 0548.0027.p (274 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KJR3.1 B3KJR3_9BACI Helix-turn-helix-domain containing protein... 156 2e-36 B1DCE8.1 B1DCE8_9BACL Transcriptional regulator, AraC family 143 2e-32 B3KJU6.1 B3KJU6_9BACI AraC protein arabinose-binding/dimerisation 140 2e-31 B1D654.1 B1D654_9BACL Transcriptional regulator, AraC family 94 1e-17 A9U6B0.1 A9U6B0_PHYPA Predicted protein 90 2e-16 >B3KJR3.1 B3KJR3_9BACI Helix-turn-helix-domain containing protein AraC type Length = 275 Score = 156 bits (395), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 91/265 (34%), Positives = 134/265 (50%), Gaps = 4/265 (1%) Query: 9 RLLQNLNVTVTYAQLSTKYPGWNRTNETPSFNRLYFIDRGEGKVIINGVAYYPRPGQLMI 68 ++L N+ V + A+ + +P W + T S+N+LYFI GEG V I YP PGQL++ Sbjct: 13 QMLLNMQVQIWEAERTQCWPEWKEFDYTVSYNKLYFILDGEGWVKIGDEELYPVPGQLVL 72 Query: 69 MPAGSTQTTETSPDNPYARYFCHFDAHIGEWPLFHSANKLYISDAADPDGVRAVFTEMIS 128 MPA + Q+ PY +Y+ HF A +G+ +F N + D + + A+F +++ Sbjct: 73 MPARTRQSYSVISGRPYLKYWSHFSATVGDSDVFSWLNVPHCYDLSGNAEMPALFQQLVD 132 Query: 129 LFQDDSFLSKIRXXXXXXXXXXXXXXXXXYSDFIDELLHSSDQRKLAHVLEYIDQRLMRP 188 + D+ +++R D++ D +L V +YI L Sbjct: 133 AHRSDTLAARLREKSVMLDILSRVFEHQQPQIHADKM---EDMGRLHKVQQYIKNHLHEE 189 Query: 189 XXXXXXXXXXXXXPNYFIPYFKKFMGVTPMHYVQLKRMELAKKQLSYTSFSISDIAEQVG 248 PNYFI YFK+ G+TP Y+ LKRME AK L TS SI +IA+ G Sbjct: 190 ITLEQMAGTLHLHPNYFIKYFKRHFGITPQKYLSLKRMEQAKLMLRTTSLSIKEIADATG 249 Query: 249 LELA-HFSKTFKKTTGVSPSAYRNS 272 E A +FSKTF+K G SPS YRN+ Sbjct: 250 FESANYFSKTFRKEVGYSPSEYRNN 274 >B1DCE8.1 B1DCE8_9BACL Transcriptional regulator, AraC family Length = 281 Score = 143 bits (361), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 86/268 (32%), Positives = 129/268 (48%), Gaps = 6/268 (2%) Query: 8 GRLLQNLNVTVTYAQLSTKYPGWNRTNETPSFNRLYFIDRGEGKVIINGVAYYPRPGQLM 67 +LQ+L V + A + P W + PS+N+ Y I GEG + I+G Y P PGQL+ Sbjct: 11 NEMLQHLQVHLEEAYYTQCSPQWRELDYIPSYNKFYLICEGEGWLNIDGQDYRPVPGQLV 70 Query: 68 IMPAGSTQTTETSPDNPYARYFCHFDAHIGEWPLFHSANKLYISDAA--DPDGVRAVFTE 125 MPA Q+ D PY++Y+CHF A +GE LF I D + D + +F E Sbjct: 71 HMPAHVLQSYSAVSDRPYSKYWCHFTATMGEMDLFQWLEIPPILDISPDHTDSLTKLFRE 130 Query: 126 MISLFQDDSFLSKIRXXXXXXXXXXX-XXXXXXYSDFIDELLHSSDQRKLAHVLEYIDQR 184 ++ L+Q+ S+L++IR + F+ L + +L + +I+ Sbjct: 131 LVELYQNRSYLARIREKAILLEIIALFLSHSDTHLKFVPGRL--GEIERLKQIEAFIEAN 188 Query: 185 LMRPXXXXXXXXXXXXXPNYFIPYFKKFMGVTPMHYVQLKRMELAKKQLSYTSFSISDIA 244 L PNY + YF K V P+ Y+ KRM+ AK L T +I +IA Sbjct: 189 LSEALTLEQLAKHVHLHPNYLVRYFNKHFAVPPLKYLNRKRMQKAKSLLGTTDLAIKEIA 248 Query: 245 EQVGL-ELAHFSKTFKKTTGVSPSAYRN 271 E VG + HF+K F+K SP+ YR+ Sbjct: 249 ELVGFPDTNHFAKAFRKEASCSPTEYRH 276 >B3KJU6.1 B3KJU6_9BACI AraC protein arabinose-binding/dimerisation Length = 277 Score = 140 bits (352), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 79/276 (28%), Positives = 132/276 (47%), Gaps = 10/276 (3%) Query: 1 MDHFNTPGRLLQNLNVTVTYAQLSTKYPGWNRTNETPSFNRLYFIDRGEGKVIINGVAYY 60 ++H L N N+ ++ A++ W N PS+N LYFI GEG + I+ Y Sbjct: 3 INHLKLIQNYLANANLRLSIAKVDKVSQNWRFFNMRPSYNALYFIREGEGWIKIDDQEYR 62 Query: 61 PRPGQLMIMPAGSTQTTETSPDNPYARYFCHFDAHIGEWPLFHSANKLYISDAADPDGVR 120 P PGQ+++MPAGS + DN Y +++CHF A + LF + ++ D D + Sbjct: 63 PSPGQIVLMPAGSLHSISVVNDNTYRKFWCHFTAKVDTLNLFQLIHLPHVLDVPDESYME 122 Query: 121 AVFTEMISLFQDDSFLSKIRXXXXXXXXXXXXXXXXXYSDFIDE----LLHSSDQRKLAH 176 +F E+I ++ ++ + ++ Y D + + L D +KL Sbjct: 123 QLFKELIDAYRSSAWTAPLQ------RNEILMKLVRHYLDIVPDRQISLSMLPDMQKLNT 176 Query: 177 VLEYIDQRLMRPXXXXXXXXXXXXXPNYFIPYFKKFMGVTPMHYVQLKRMELAKKQLSYT 236 V +YI++ + PNYFI +FK M +TP+ Y+ R+E K L T Sbjct: 177 VFQYIEEHINDNVSVEQLAGLIHYNPNYFIRFFKSKMKMTPVQYIIKVRIEKTKGLLMTT 236 Query: 237 SFSISDIAEQVGLELAHFSKTFKKTTGVSPSAYRNS 272 ++ +I QVG+E+ + + FK+ T +SP +RN Sbjct: 237 DLTLEEIGRQVGMEVHYLCRVFKQFTNMSPGEFRNQ 272 >B1D654.1 B1D654_9BACL Transcriptional regulator, AraC family Length = 297 Score = 94.0 bits (232), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 68/267 (25%), Positives = 109/267 (40%), Gaps = 5/267 (1%) Query: 9 RLLQNLNVTVTYAQLSTKYPGWNRTNETPSFNRLYFIDRGEGKVIINGVAYYPRPGQLMI 68 R +L + V A S + GW N+ + R++++ G + GV Y PG++ + Sbjct: 10 RQFDHLKIDVIMAAYSEREAGWLNNNDEIDYYRVFYLMEGHAVLETKGVGYDLLPGRIYV 69 Query: 69 MPAGSTQTTETSPDNPYARYFCHFDAHIGEWPLFHSANKLYIS---DAADPDGVRAVFTE 125 + + Y+CHF + F KL S + D V + + Sbjct: 70 LRPKQKVSYNIVIKQTIKAYWCHFRIRNPDDMKFMKLPKLPFSSSVEVQDEYHVVEIMQK 129 Query: 126 MISLFQDDSFLSKIRXXXXXXXXXXXXXXXXXYSDFIDELLHSSD--QRKLAHVLEYIDQ 183 MI + + S +R + D D ++ + K V+ YI+Q Sbjct: 130 MIHAQEFQTVSSNLRLHSGILELIAYLLDHSSWDDLNDAYFIGNEVGKEKWDDVILYIEQ 189 Query: 184 RLMRPXXXXXXXXXXXXXPNYFIPYFKKFMGVTPMHYVQLKRMELAKKQLSYTSFSISDI 243 L PNY I FK MG +P+ YV +R+ELAKK L T IS+I Sbjct: 190 NLHHNIQIEDLAKVAYLHPNYLITSFKSIMGCSPIQYVTERRLELAKKLLKETDLPISEI 249 Query: 244 AEQVGLELAHFSKTFKKTTGVSPSAYR 270 A +VG+ + + K+ TG++P YR Sbjct: 250 AGKVGMLNHYLPRLLKRHTGITPKQYR 276 >A9U6B0.1 A9U6B0_PHYPA Predicted protein Length = 404 Score = 90.1 bits (222), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 71/261 (27%), Positives = 108/261 (41%), Gaps = 6/261 (2%) Query: 11 LQNLNVTVTYAQLSTKYPGWNRTNETPSFNRLYFIDRGEGKVIINGVAYYPRPGQLMIMP 70 L+ + V A S PG N + + L G + + PG + +P Sbjct: 31 LRQMQVIYAMAARSEWKPGSVIENSSLGHHCLALPITGSVSLNASDGCLQAGPGHMYCIP 90 Query: 71 AGSTQTTETSPDNPYARYFCHFDAHIGEWPLFHSANKLYISDAAD-PDGVRAVFTEMISL 129 GS T P+ Y+ F+ G F S +L +S A D PD + A + +ISL Sbjct: 91 PGSKHTYTVDKGVPFRCYWVRFELDAGSTEFFKSL-QLPLSAAVDEPDQLEARYRRLISL 149 Query: 130 FQDDSFLSKIRXXXXXXXXXXXXXXXXXYSDFIDELLHSSDQRKLAHVLEYIDQRLMRPX 189 + + + R +S +S+ + +LEYI+Q Sbjct: 150 SGNITDELRARAIIMELIAVYLQRGLEGHSS----AAVASELSLFSEILEYIEQHPAENL 205 Query: 190 XXXXXXXXXXXXPNYFIPYFKKFMGVTPMHYVQLKRMELAKKQLSYTSFSISDIAEQVGL 249 PNYFI F+ F G TP+ YV ++ME A+K L ++ + DIA +VGL Sbjct: 206 SVDDLARQMYLHPNYFISLFRSFTGCTPIQYVNQRKMEHARKLLEESTLPVRDIASEVGL 265 Query: 250 ELAHFSKTFKKTTGVSPSAYR 270 +FS+ FK+ G SP YR Sbjct: 266 TGPYFSRMFKQLIGTSPRRYR 286 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 0.321 0.136 0.410 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: 1,450,503,311 Number of extensions: 53761708 Number of successful extensions: 135887 Number of sequences better than 1.0e-05: 473 Number of HSP's gapped: 140619 Number of HSP's successfully gapped: 473 Length of query: 274 Length of database: 3,060,696,203 Length adjustment: 134 Effective length of query: 140 Effective length of database: 1,798,280,193 Effective search space: 251759227020 Effective search space used: 251759227020 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: 130 (54.7 bits)