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= 0029.0221.p (221 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspir... 450 e-128 gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspir... 268 4e-73 gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [... 137 5e-34 gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 101 6e-23 gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709... 99 3e-22 >gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 236 Score = 450 bits (1157), Expect = e-128, Method: Compositional matrix adjust. Identities = 218/221 (98%), Positives = 218/221 (98%) Query: 1 MLGVSITTAQIWMESGMLVSWKTPGGHRRTRRSSVMSLIGHQEVPAVGEEDGPEELEALA 60 MLGVSITTAQIWMESGML SWKTPGGHRRTRRSSVMSLIGHQEVPAVGEEDGPEELEALA Sbjct: 16 MLGVSITTAQIWMESGMLASWKTPGGHRRTRRSSVMSLIGHQEVPAVGEEDGPEELEALA 75 Query: 61 YPAGAEEGDRAAFVERIIERSQPDTRFDRLTWLASELLDAPISLITFLTSELQIFKSAHG 120 YPAGAEEGDRAAFVERIIERS PDTRFDRLTWLASELLDAPISLITFLTSELQIFKSAHG Sbjct: 76 YPAGAEEGDRAAFVERIIERSAPDTRFDRLTWLASELLDAPISLITFLTSELQIFKSAHG 135 Query: 121 LSLNETPRAWAFCNYTIAHEGVFAVSDTQTDMRFMNNPLVTSAPFFRFYAGVRLMYEGKA 180 LSLNETPRAWAFCNYTIAHEGVFAVSDTQTDMRFMNNPLVTS PFFRFYAGVRLMYEGKA Sbjct: 136 LSLNETPRAWAFCNYTIAHEGVFAVSDTQTDMRFMNNPLVTSTPFFRFYAGVRLMYEGKA 195 Query: 181 FGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILESR 221 FGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILESR Sbjct: 196 FGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILESR 236 >gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 250 Score = 268 bits (684), Expect = 4e-73, Method: Compositional matrix adjust. Identities = 130/220 (59%), Positives = 161/220 (73%), Gaps = 1/220 (0%) Query: 1 MLGVSITTAQIWMESGMLVSWKTPGGHRRTRRSSVMSLIGHQEVPAVGEEDGPEELEALA 60 MLGVSITTAQ+WME+GML SWKTPGGHRRTR SSVMSL+GH G A Sbjct: 27 MLGVSITTAQMWMETGMLASWKTPGGHRRTRLSSVMSLLGHNGAKQSGPAAVQPAAVAQT 86 Query: 61 YPAGA-EEGDRAAFVERIIERSQPDTRFDRLTWLASELLDAPISLITFLTSELQIFKSAH 119 A + +E +A + + +Q + RF RLTWLASELL+ PI+L+TF T+ELQIF +AH Sbjct: 87 PEAASTDEARQAPLMAQAKTGTQAEARFHRLTWLASELLEVPIALVTFQTAELQIFHAAH 146 Query: 120 GLSLNETPRAWAFCNYTIAHEGVFAVSDTQTDMRFMNNPLVTSAPFFRFYAGVRLMYEGK 179 GL++ TPR+WAFCNY E VF V+D D RF NNP+VTSAPF RFYA V LMY+GK Sbjct: 147 GLNIAATPRSWAFCNYADMDEDVFTVADASKDARFANNPMVTSAPFIRFYAAVPLMYQGK 206 Query: 180 AFGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILE 219 AFGSLC+IDTE R+LRS E++AL+ELA LA+D++ L ++E Sbjct: 207 AFGSLCIIDTEARLLRSQERRALQELAALATDMMALQLME 246 >gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 137 bits (346), Expect = 5e-34, Method: Compositional matrix adjust. Identities = 72/139 (51%), Positives = 90/139 (64%), Gaps = 1/139 (0%) Query: 82 QPDTRFDRLTWLASELLDAPISLITFLTSELQIFKSAHGLSLNETPRAWAFCNYTIAHEG 141 Q + RF RL WLASELLD P+SLI + SE I+ GL + ET R AF +T+ HEG Sbjct: 2 QSEERFRRLNWLASELLDVPMSLIGLVASETVIWHGPVGLHVEETTRPCAFVEHTLLHEG 61 Query: 142 VFAVSDTQTDMRFMNNPLVTSAPFFRFYAGVRL-MYEGKAFGSLCVIDTEPRILRSHEQQ 200 VF V D D RF ++ LVT APF R +AG+RL + G FG+LCV+DTEPRI R+ E + Sbjct: 62 VFLVPDASKDPRFSDHSLVTGAPFVRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIR 121 Query: 201 ALEELAMLASDILRLHILE 219 E LA +A DI RL + E Sbjct: 122 TFEGLAQIAEDIYRLFLFE 140 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 101 bits (251), Expect = 6e-23, Method: Compositional matrix adjust. Identities = 55/125 (44%), Positives = 72/125 (57%), Gaps = 2/125 (1%) Query: 86 RFDRLTWLASELLDAPISLITFLTSELQIFKSAHGL-SLNETPRAWAFCNYTIAHEGVFA 144 RFDRLT LA L D P++++T + Q FKS GL ET R +FC + I HE + Sbjct: 30 RFDRLTRLARRLFDVPMAVVTMIDVNRQWFKSCVGLGDATETSREVSFCAHAILHEEMTI 89 Query: 145 VSDTQTDMRFMNNPLVTSAPFFRFYAGVRLMYE-GKAFGSLCVIDTEPRILRSHEQQALE 203 V D D RF NP VT PF RFYAG + E G G+LC++DT PR + E+ L+ Sbjct: 90 VPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERALLK 149 Query: 204 ELAML 208 +LA + Sbjct: 150 DLAAM 154 >gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709 [Herbaspirillum seropedicae SmR1] Length = 598 Score = 99.0 bits (245), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 49/111 (44%), Positives = 67/111 (60%), Gaps = 1/111 (0%) Query: 83 PDTRFDRLTWLASELLDAPISLITFLTSELQIFKSAHGLSLNETPRAWAFCNYTIAHEGV 142 PD D++T LA + D I+L+ + Q FKS GL ++ETPRA +FCN+ I Sbjct: 35 PDKLCDQVTQLACSMFDVEIALVALVDEHRQWFKSRVGLEVSETPRADSFCNHAIQTRHG 94 Query: 143 FAVSDTQTDMRFMNNPLVTSAPFFRFYAGVRLMY-EGKAFGSLCVIDTEPR 192 V+D D RF + LVT APF RFYAG L+ +G + G+LC+ID+ PR Sbjct: 95 MVVTDALQDARFSRHALVTGAPFIRFYAGAPLVTPQGLSLGTLCIIDSRPR 145 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 0.321 0.134 0.397 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: 715,688 Number of extensions: 28668 Number of successful extensions: 77 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 72 Number of HSP's successfully gapped: 6 Length of query: 221 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 139 Effective length of database: 1,231,600 Effective search space: 171192400 Effective search space used: 171192400 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)