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= 0001.1261.p (348 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310777|ref|YP_003774869.1| GGDEF family protein [Herbaspir... 651 0.0 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 99 5e-22 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 99 5e-22 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 97 1e-21 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 97 2e-21 >gi|300310777|ref|YP_003774869.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 651 bits (1680), Expect = 0.0, Method: Compositional matrix adjust. Identities = 309/352 (87%), Positives = 331/352 (94%), Gaps = 4/352 (1%) Query: 1 MKQPLLKHLVEITAHREHSRLAISVISALYQLTEVQSIRMLDIFTLRDEYFVQEKMVIRD 60 MK+PLLKHLVEITAHREHSRLAISV+SALYQLT+V++IRM+DIFT+RDE++VQEKMVIRD Sbjct: 1 MKKPLLKHLVEITAHREHSRLAISVVSALYQLTDVKTIRMMDIFTMRDEHYVQEKMVIRD 60 Query: 61 GTVHTIAELTSDDPKEPLAAYPAMLACIRNHLNEYQETTDSGEHLLWLPVWLHGKMNSCL 120 GT+HTI E T+DDPKE L+AYPAM+ACIRNHLNEY E T G H+LWLPVWLHGKMNSCL Sbjct: 61 GTLHTIDEHTADDPKELLSAYPAMVACIRNHLNEYLEATPDGLHVLWLPVWLHGKMNSCL 120 Query: 121 EIRSQSAFTPAMMDVIHGIFHVYCNYQSLLDYSERDALTGLFNRKTFDEQFTRYAFAIAP 180 EIRSQ F P MMDVIHGIFHV+CNYQSLLDYSERDALTGLFNRKTFDEQFTRYAFAIAP Sbjct: 121 EIRSQQPFAPQMMDVIHGIFHVFCNYQSLLDYSERDALTGLFNRKTFDEQFTRYAFAIAP 180 Query: 181 HEAHSLEENERRHED----HGEPKGHWLGVVDIDHFKQVNDRYGHLYGDEVLILVANILR 236 HEAHS+E++ERRH+ EPKGHWL VVDIDHFKQVNDRYGHLYGDEVLILVANILR Sbjct: 181 HEAHSMEQDERRHDSAEAQDDEPKGHWLAVVDIDHFKQVNDRYGHLYGDEVLILVANILR 240 Query: 237 ASFRAHDRIFRFGGEEFVILLRSTTLSDARKIFDRFRQNVQEYDFPQVGKVTVSLGFVGI 296 ASFR+HDRIFRFGGEEFVILLRSTTLSDARKIFDRFRQNVQEYDFPQVGKVTVSLGFVGI Sbjct: 241 ASFRSHDRIFRFGGEEFVILLRSTTLSDARKIFDRFRQNVQEYDFPQVGKVTVSLGFVGI 300 Query: 297 ARETPVVILGHADQALYHAKKSGRNRICYYQELVNAGVLRSGITTNDTVEFF 348 ARETPVVILGHADQALYHAKK+GRNRICYYQELVN+GVLRSGI TNDTVEFF Sbjct: 301 ARETPVVILGHADQALYHAKKTGRNRICYYQELVNSGVLRSGIATNDTVEFF 352 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 99.0 bits (245), Expect = 5e-22, Method: Compositional matrix adjust. Identities = 69/193 (35%), Positives = 88/193 (45%), Gaps = 26/193 (13%) Query: 147 QSLLDYSERDALTGLFNRKTFDEQFTRYAFAIAPHEAHSLEENERRHEDHGEPKGHWLGV 206 + L S D LTG+ NR++FDE +LE+ RR HG P L Sbjct: 191 EQLRSLSLTDGLTGIANRRSFDE---------------TLEQEWRRSMRHGTPL--MLAF 233 Query: 207 VDIDHFKQVNDRYGHLYGDEVLILVANILRASF-RAHDRIFRFGGEEFVILLRSTTLSDA 265 +D+D FK ND YGHL GD VL VA LR S R D + R+GGEEF I+ T Sbjct: 234 IDVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAG 293 Query: 266 RKIFDRFRQNVQEYDFPQ----VGKVTVSLGFVGIARETPVV----ILGHADQALYHAKK 317 + R V +G++T+S G P +L AD ALY AK Sbjct: 294 ADMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGAGLDGLLQAADAALYRAKM 353 Query: 318 SGRNRICYYQELV 330 GRNR+ EL+ Sbjct: 354 EGRNRVVLATELI 366 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 99.0 bits (245), Expect = 5e-22, Method: Compositional matrix adjust. Identities = 66/181 (36%), Positives = 90/181 (49%), Gaps = 30/181 (16%) Query: 156 DALTGLFNRKTFDEQFTRYAFAIAPHEAHSLEENERRHEDHGEPKGHWLGVVDIDHFKQV 215 D LTG+ NR+ +++ EE R D + +DIDHFK+V Sbjct: 203 DPLTGVNNRRYIEQRMQ--------------EEVARSQRDRSALSCLF---IDIDHFKRV 245 Query: 216 NDRYGHLYGDEVLILVANILRASFRAHDRIFRFGGEEFVILLRSTTLSDARKIFDRFRQN 275 ND++GH GD+VL VA ++ R D + RFGGEEFV+LL T DA +I +R R Sbjct: 246 NDQFGHQSGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAG 305 Query: 276 VQEYDFPQVG-----KVTVSLGFVGI--------ARETPVVILGHADQALYHAKKSGRNR 322 V G K+T S+G + A E +L ADQALY AK++GRNR Sbjct: 306 VCSRGVMIEGSRDPLKITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNR 365 Query: 323 I 323 + Sbjct: 366 V 366 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 97.4 bits (241), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 64/180 (35%), Positives = 94/180 (52%), Gaps = 25/180 (13%) Query: 153 SERDALTGLFNRKTFDEQFTRYAFAIAPHEAHSLEENERRHEDHGEPKGHWLGVVDIDHF 212 S D LTG+ NR+ FDE +L RR G+ L ++D+D+F Sbjct: 402 SATDGLTGVANRRRFDE---------------ALANEMRRAVRSGQSLA--LLMLDVDYF 444 Query: 213 KQVNDRYGHLYGDEVLILVANIL-RASFRAHDRIFRFGGEEFVILLRSTTLSDARKIFDR 271 K+ NDRYGHL GDE L +VA +L ++S RA D + R+GGEEF +++ + A + + Sbjct: 445 KKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAEN 504 Query: 272 FRQNVQEYDFPQV----GKVTVSLGFVGIARE---TPVVILGHADQALYHAKKSGRNRIC 324 Q + E P G ++ S+G + + P ++ ADQALYHAK GRNR+ Sbjct: 505 ICQAIFELKLPHADSPFGYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNRVV 564 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 97.4 bits (241), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 66/169 (39%), Positives = 93/169 (55%), Gaps = 18/169 (10%) Query: 156 DALTGLFNRKTFDEQFTRYAFAIAPHEAHSLEENERRHEDHGEPKGHWLGVVDIDHFKQV 215 D LTGL NR DE L+ R + +G K L ++DIDHFK+V Sbjct: 166 DKLTGLANRMKLDE---------------VLDNEINRADRYG--KNLSLILLDIDHFKEV 208 Query: 216 NDRYGHLYGDEVLILVANILRASFRAHDRIFRFGGEEFVILLRSTTLSDARKIFDRFRQN 275 ND +GH GD VL+ +A ILRA+ R+ D R+GGEEF+++L + DA ++ ++ R Sbjct: 209 NDNFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLRLL 268 Query: 276 VQEYDFPQVGKVTVSLGFVGI-ARETPVVILGHADQALYHAKKSGRNRI 323 ++ Y+F VG+ T S G A +L AD ALY AK +GRNR+ Sbjct: 269 IENYNFVPVGRRTCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRV 317 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 0.324 0.138 0.415 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: 1,067,997 Number of extensions: 42804 Number of successful extensions: 225 Number of sequences better than 1.0e-08: 38 Number of HSP's gapped: 166 Number of HSP's successfully gapped: 38 Length of query: 348 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 262 Effective length of database: 1,212,660 Effective search space: 317716920 Effective search space used: 317716920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 131 (55.1 bits)