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= 0001.0538.p (250 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspir... 353 8e-99 gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspir... 333 6e-93 gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [... 134 9e-33 gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 113 1e-26 gi|300310696|ref|YP_003774788.1| hypothetical protein Hsero_1364... 97 1e-21 >gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 250 Score = 353 bits (906), Expect = 8e-99, Method: Compositional matrix adjust. Identities = 170/246 (69%), Positives = 200/246 (81%) Query: 1 MGRAVPSDDNDMPPSDPAMTSREAAKMLGVSITTAQMWMESGMLASWKTPGGHRRTRLSS 60 MGRA S ++D PPSDPAMTSREAA+MLGVSITTAQMWME+GMLASWKTPGGHRRTRLSS Sbjct: 1 MGRAARSHESDAPPSDPAMTSREAARMLGVSITTAQMWMETGMLASWKTPGGHRRTRLSS 60 Query: 61 VMTLLGHREVKQPEPTAGPSAPPIEVPYPVSQNEPERARFVEQIMEDVHCEARFQRLTWL 120 VM+LLGH KQ P A A + P S +E +A + Q EARF RLTWL Sbjct: 61 VMSLLGHNGAKQSGPAAVQPAAVAQTPEAASTDEARQAPLMAQAKTGTQAEARFHRLTWL 120 Query: 121 ASELLDVPIALVTFLTSELQIFRAAHGLNISSTPRSWAFCNYAVMQEDIFTVPDATRDAR 180 ASELL+VPIALVTF T+ELQIF AAHGLNI++TPRSWAFCNYA M ED+FTV DA++DAR Sbjct: 121 ASELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDEDVFTVADASKDAR 180 Query: 181 FVNNPMVTSDPYIRFYAGIRLMHQGKAFGSLCVIDTEPRILRAHERQALEELAVMATDIL 240 F NNPMVTS P+IRFYA + LM+QGKAFGSLC+IDTE R+LR+ ER+AL+ELA +ATD++ Sbjct: 181 FANNPMVTSAPFIRFYAAVPLMYQGKAFGSLCIIDTEARLLRSQERRALQELAALATDMM 240 Query: 241 SLQILE 246 +LQ++E Sbjct: 241 ALQLME 246 >gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 236 Score = 333 bits (855), Expect = 6e-93, Method: Compositional matrix adjust. Identities = 160/240 (66%), Positives = 192/240 (80%), Gaps = 7/240 (2%) Query: 12 MPPSDPAMTSREAAKMLGVSITTAQMWMESGMLASWKTPGGHRRTRLSSVMTLLGHREVK 71 M DP MTSREAA+MLGVSITTAQ+WMESGMLASWKTPGGHRRTR SSVM+L+GH+EV Sbjct: 1 MSIVDPVMTSREAARMLGVSITTAQIWMESGMLASWKTPGGHRRTRRSSVMSLIGHQEV- 59 Query: 72 QPEPTAGPSAPPIEV---PYPVSQNEPERARFVEQIMEDVHCEARFQRLTWLASELLDVP 128 P G P E+ YP E +RA FVE+I+E + RF RLTWLASELLD P Sbjct: 60 ---PAVGEEDGPEELEALAYPAGAEEGDRAAFVERIIERSAPDTRFDRLTWLASELLDAP 116 Query: 129 IALVTFLTSELQIFRAAHGLNISSTPRSWAFCNYAVMQEDIFTVPDATRDARFVNNPMVT 188 I+L+TFLTSELQIF++AHGL+++ TPR+WAFCNY + E +F V D D RF+NNP+VT Sbjct: 117 ISLITFLTSELQIFKSAHGLSLNETPRAWAFCNYTIAHEGVFAVSDTQTDMRFMNNPLVT 176 Query: 189 SDPYIRFYAGIRLMHQGKAFGSLCVIDTEPRILRAHERQALEELAVMATDILSLQILETR 248 S P+ RFYAG+RLM++GKAFGSLCVIDTEPRILR+HE+QALEELA++A+DIL L ILE+R Sbjct: 177 STPFFRFYAGVRLMYEGKAFGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILESR 236 >gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 134 bits (336), Expect = 9e-33, Method: Compositional matrix adjust. Identities = 65/137 (47%), Positives = 93/137 (67%), Gaps = 1/137 (0%) Query: 111 EARFQRLTWLASELLDVPIALVTFLTSELQIFRAAHGLNISSTPRSWAFCNYAVMQEDIF 170 E RF+RL WLASELLDVP++L+ + SE I+ GL++ T R AF + ++ E +F Sbjct: 4 EERFRRLNWLASELLDVPMSLIGLVASETVIWHGPVGLHVEETTRPCAFVEHTLLHEGVF 63 Query: 171 TVPDATRDARFVNNPMVTSDPYIRFYAGIRL-MHQGKAFGSLCVIDTEPRILRAHERQAL 229 VPDA++D RF ++ +VT P++R +AG+RL ++ G FG+LCV+DTEPRI RA E + Sbjct: 64 LVPDASKDPRFSDHSLVTGAPFVRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIRTF 123 Query: 230 EELAVMATDILSLQILE 246 E LA +A DI L + E Sbjct: 124 EGLAQIAEDIYRLFLFE 140 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 113 bits (283), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 59/127 (46%), Positives = 81/127 (63%), Gaps = 2/127 (1%) Query: 111 EARFQRLTWLASELLDVPIALVTFLTSELQIFRAAHGL-NISSTPRSWAFCNYAVMQEDI 169 E RF RLT LA L DVP+A+VT + Q F++ GL + + T R +FC +A++ E++ Sbjct: 28 EERFDRLTRLARRLFDVPMAVVTMIDVNRQWFKSCVGLGDATETSREVSFCAHAILHEEM 87 Query: 170 FTVPDATRDARFVNNPMVTSDPYIRFYAGIRLMHQ-GKAFGSLCVIDTEPRILRAHERQA 228 VPDAT D RF NP VT +P+IRFYAG + + G G+LC++DT PR A ER Sbjct: 88 TIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERAL 147 Query: 229 LEELAVM 235 L++LA M Sbjct: 148 LKDLAAM 154 >gi|300310696|ref|YP_003774788.1| hypothetical protein Hsero_1364 [Herbaspirillum seropedicae SmR1] Length = 606 Score = 97.1 bits (240), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 47/104 (45%), Positives = 64/104 (61%), Gaps = 1/104 (0%) Query: 117 LTWLASELLDVPIALVTFLTSELQIFRAAHGLNISSTPRSWAFCNYAVMQEDIFTVPDAT 176 +T LA+ L DV IALV+ + Q F++ GL+ TPRS +FC +A++Q +PDA Sbjct: 46 ITELATRLFDVEIALVSLVAEHRQWFKSRRGLDAPGTPRSQSFCAHAIVQAQTMVIPDAR 105 Query: 177 RDARFVNNPMVTSDPYIRFYAGIRL-MHQGKAFGSLCVIDTEPR 219 +D RF NP+V +P IRFYAG L G A G+LC+I PR Sbjct: 106 QDERFAGNPLVLGEPGIRFYAGAALRTADGVALGTLCLIGKSPR 149 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.320 0.132 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 734,508 Number of extensions: 28363 Number of successful extensions: 106 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 100 Number of HSP's successfully gapped: 7 Length of query: 250 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 167 Effective length of database: 1,226,865 Effective search space: 204886455 Effective search space used: 204886455 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: 129 (54.3 bits)