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= 0002.0252.p (232 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... 339 1e-94 gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspir... 323 7e-90 gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [... 137 6e-34 gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 117 6e-28 gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709... 103 9e-24 >gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 250 Score = 339 bits (869), Expect = 1e-94, Method: Compositional matrix adjust. Identities = 164/228 (71%), Positives = 188/228 (82%) Query: 1 MTSREAARLLGVSITTAQMWMESGMLASWKTPGGHRRTRLSSVMTLLGHREVKQPEPTAG 60 MTSREAAR+LGVSITTAQMWME+GMLASWKTPGGHRRTRLSSVM+LLGH KQ P A Sbjct: 19 MTSREAARMLGVSITTAQMWMETGMLASWKTPGGHRRTRLSSVMSLLGHNGAKQSGPAAV 78 Query: 61 HAGPQIEVPYPVSPNEPERARFVEQTMEDTHSEARFHRLTWLASELLDVPIALVTFLTTE 120 + P S +E +A + Q T +EARFHRLTWLASELL+VPIALVTF T E Sbjct: 79 QPAAVAQTPEAASTDEARQAPLMAQAKTGTQAEARFHRLTWLASELLEVPIALVTFQTAE 138 Query: 121 LQIFRAAHGLNITSTPRSWAFCNYAVMQEDIFTVSDATKDARFVNNPMVTGAPFIRFYAG 180 LQIF AAHGLNI +TPRSWAFCNYA M ED+FTV+DA+KDARF NNPMVT APFIRFYA Sbjct: 139 LQIFHAAHGLNIAATPRSWAFCNYADMDEDVFTVADASKDARFANNPMVTSAPFIRFYAA 198 Query: 181 IRLMYQGRAFGSLCVIDTEPRILRAHERQALEELAALATDILSLQLLE 228 + LMYQG+AFGSLC+IDTE R+LR+ ER+AL+ELAALATD+++LQL+E Sbjct: 199 VPLMYQGKAFGSLCIIDTEARLLRSQERRALQELAALATDMMALQLME 246 >gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 236 Score = 323 bits (828), Expect = 7e-90, Method: Compositional matrix adjust. Identities = 156/232 (67%), Positives = 189/232 (81%), Gaps = 7/232 (3%) Query: 1 MTSREAARLLGVSITTAQMWMESGMLASWKTPGGHRRTRLSSVMTLLGHREVKQPEPTAG 60 MTSREAAR+LGVSITTAQ+WMESGMLASWKTPGGHRRTR SSVM+L+GH+EV P G Sbjct: 8 MTSREAARMLGVSITTAQIWMESGMLASWKTPGGHRRTRRSSVMSLIGHQEV----PAVG 63 Query: 61 HA-GPQ-IE-VPYPVSPNEPERARFVEQTMEDTHSEARFHRLTWLASELLDVPIALVTFL 117 GP+ +E + YP E +RA FVE+ +E + + RF RLTWLASELLD PI+L+TFL Sbjct: 64 EEDGPEELEALAYPAGAEEGDRAAFVERIIERSAPDTRFDRLTWLASELLDAPISLITFL 123 Query: 118 TTELQIFRAAHGLNITSTPRSWAFCNYAVMQEDIFTVSDATKDARFVNNPMVTGAPFIRF 177 T+ELQIF++AHGL++ TPR+WAFCNY + E +F VSD D RF+NNP+VT PF RF Sbjct: 124 TSELQIFKSAHGLSLNETPRAWAFCNYTIAHEGVFAVSDTQTDMRFMNNPLVTSTPFFRF 183 Query: 178 YAGIRLMYQGRAFGSLCVIDTEPRILRAHERQALEELAALATDILSLQLLEA 229 YAG+RLMY+G+AFGSLCVIDTEPRILR+HE+QALEELA LA+DIL L +LE+ Sbjct: 184 YAGVRLMYEGKAFGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILES 235 >gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 137 bits (346), Expect = 6e-34, Method: Compositional matrix adjust. Identities = 69/138 (50%), Positives = 93/138 (67%), Gaps = 1/138 (0%) Query: 92 SEARFHRLTWLASELLDVPIALVTFLTTELQIFRAAHGLNITSTPRSWAFCNYAVMQEDI 151 SE RF RL WLASELLDVP++L+ + +E I+ GL++ T R AF + ++ E + Sbjct: 3 SEERFRRLNWLASELLDVPMSLIGLVASETVIWHGPVGLHVEETTRPCAFVEHTLLHEGV 62 Query: 152 FTVSDATKDARFVNNPMVTGAPFIRFYAGIRL-MYQGRAFGSLCVIDTEPRILRAHERQA 210 F V DA+KD RF ++ +VTGAPF+R +AG+RL + G FG+LCV+DTEPRI RA E + Sbjct: 63 FLVPDASKDPRFSDHSLVTGAPFVRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIRT 122 Query: 211 LEELAALATDILSLQLLE 228 E LA +A DI L L E Sbjct: 123 FEGLAQIAEDIYRLFLFE 140 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 117 bits (294), Expect = 6e-28, Method: Compositional matrix adjust. Identities = 63/131 (48%), Positives = 83/131 (63%), Gaps = 2/131 (1%) Query: 89 DTHSEARFHRLTWLASELLDVPIALVTFLTTELQIFRAAHGL-NITSTPRSWAFCNYAVM 147 DT E RF RLT LA L DVP+A+VT + Q F++ GL + T T R +FC +A++ Sbjct: 24 DTPREERFDRLTRLARRLFDVPMAVVTMIDVNRQWFKSCVGLGDATETSREVSFCAHAIL 83 Query: 148 QEDIFTVSDATKDARFVNNPMVTGAPFIRFYAGIRLMYQ-GRAFGSLCVIDTEPRILRAH 206 E++ V DAT D RF NP VTG PFIRFYAG + + G G+LC++DT PR A Sbjct: 84 HEEMTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDAD 143 Query: 207 ERQALEELAAL 217 ER L++LAA+ Sbjct: 144 ERALLKDLAAM 154 >gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709 [Herbaspirillum seropedicae SmR1] Length = 598 Score = 103 bits (258), Expect = 9e-24, Method: Compositional matrix adjust. Identities = 57/136 (41%), Positives = 83/136 (61%), Gaps = 2/136 (1%) Query: 89 DTHSEARFHRLTWLASELLDVPIALVTFLTTELQIFRAAHGLNITSTPRSWAFCNYAVMQ 148 DT + ++T LA + DV IALV + Q F++ GL ++ TPR+ +FCN+A+ Sbjct: 32 DTPPDKLCDQVTQLACSMFDVEIALVALVDEHRQWFKSRVGLEVSETPRADSFCNHAIQT 91 Query: 149 EDIFTVSDATKDARFVNNPMVTGAPFIRFYAGIRLMY-QGRAFGSLCVIDTEPR-ILRAH 206 V+DA +DARF + +VTGAPFIRFYAG L+ QG + G+LC+ID+ PR A Sbjct: 92 RHGMVVTDALQDARFSRHALVTGAPFIRFYAGAPLVTPQGLSLGTLCIIDSRPRPDFGAS 151 Query: 207 ERQALEELAALATDIL 222 + L +LAA+ + L Sbjct: 152 QFAQLNQLAAIVMERL 167 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 0.132 0.395 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: 679,560 Number of extensions: 25742 Number of successful extensions: 89 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 83 Number of HSP's successfully gapped: 7 Length of query: 232 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 150 Effective length of database: 1,231,600 Effective search space: 184740000 Effective search space used: 184740000 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)