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= 0001.3287.p (340 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 514 e-147 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 136 2e-33 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 133 2e-32 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 132 4e-32 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 127 1e-30 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 514 bits (1324), Expect = e-147, Method: Compositional matrix adjust. Identities = 257/334 (76%), Positives = 282/334 (84%) Query: 1 MKRDLEERHRQSQAEKSGVSHLPRLLRAALDSLDSQIALIDRAGVIRYVNKTWCEFGKEN 60 MKRDLEERHRQSQAEKS PRLLRA LDSLDSQIALIDRAGVI YVNKTWCEFG EN Sbjct: 1 MKRDLEERHRQSQAEKSVGRQFPRLLRATLDSLDSQIALIDRAGVIHYVNKTWCEFGIEN 60 Query: 61 GIPPQYSWIGTNYLAVCRSASKSSEEDGQQVYAGIRSVLESRAPSFQYEYPCHSPNQQRW 120 GIP YSWIG NYL VCRSA + DG++VY GIRSV+ES AP FQYEYPCHSPN+QRW Sbjct: 61 GIPAGYSWIGVNYLVVCRSAGDRGDGDGREVYEGIRSVVESGAPFFQYEYPCHSPNEQRW 120 Query: 121 FIMRIAPVLEMESFFVISHSVITGRKLAEQRIEHLNEKLALLAVTDKLTGLANRMKLDET 180 F+MRIAPVL E FFVISH VITGRKLAEQR+E LNEKLALLAVTDKLTGLANRMKLDE Sbjct: 121 FMMRIAPVLGAEDFFVISHVVITGRKLAEQRVERLNEKLALLAVTDKLTGLANRMKLDEV 180 Query: 181 LDSEIARAHRYGTKLSLILLDVDHFKEVNDKFGHSAGDAVLVSIAEILRTNVRATDIVGR 240 LD+EI RA RYG LSLILLD+DHFKEVND FGHS GDAVLV IAEILR NVR++D+ GR Sbjct: 181 LDNEINRADRYGKNLSLILLDIDHFKEVNDNFGHSTGDAVLVRIAEILRANVRSSDLAGR 240 Query: 241 WGGEEFLLILPQCDIEASSRMAEKLRLIVERHSFALIDKRTCSFGVAAYQFGHDGTTLLS 300 WGGEEFLLILP+CD+E ++RMAEKLRL++E ++F + +RTCSFGVAAYQ GHD TTLL+ Sbjct: 241 WGGEEFLLILPECDMEDAARMAEKLRLLIENYNFVPVGRRTCSFGVAAYQAGHDRTTLLT 300 Query: 301 LADSALYRAKKNGRNRVEIAIEPEPSVNSRDRKI 334 LAD ALYRAK GRNRVEIA E +V+ RD I Sbjct: 301 LADLALYRAKNTGRNRVEIAANLESAVSHRDCNI 334 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 136 bits (343), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 80/175 (45%), Positives = 107/175 (61%), Gaps = 8/175 (4%) Query: 156 NEKLALLAVTDKLTGLANRMKLDETLDSEIARAHRYGTKLSLILLDVDHFKEVNDKFGHS 215 NE+L L++TD LTG+ANR DETL+ E R+ R+GT L L +DVD FK ND +GH Sbjct: 190 NEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHL 249 Query: 216 AGDAVLVSIAEILRTNV-RATDIVGRWGGEEFLLILPQCDIEASS----RMAEKLRLIVE 270 AGDAVL +A+ LR ++ R D V R+GGEEF +I D +A + RM + + + Sbjct: 250 AGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRMCDAVHALAI 309 Query: 271 RHSFALIDKRTCSFGVAAYQFGHDGT---TLLSLADSALYRAKKNGRNRVEIAIE 322 H+ + + + T S GVA+ G G LL AD+ALYRAK GRNRV +A E Sbjct: 310 AHAGSAMGRITISAGVASCNPGQPGAGLDGLLQAADAALYRAKMEGRNRVVLATE 364 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 133 bits (334), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 73/184 (39%), Positives = 109/184 (59%), Gaps = 6/184 (3%) Query: 148 AEQRIEHLNEKL---ALLAVTDKLTGLANRMKLDETLDSEIARAHRYGTKLSLILLDVDH 204 AE+RI+ L ++L L D+LTG NR +DE+LD EI A R T L + LLD+D Sbjct: 346 AEERIQTLEQQLLQMGELVREDQLTGSLNRRGMDESLDREITNALRRDTPLCVALLDLDD 405 Query: 205 FKEVNDKFGHSAGDAVLVSIAEILRTNVRATDIVGRWGGEEFLLILPQCDIEASSRMAEK 264 FK +ND GH+ GD VLV + +++R +R D++ R+GGEEFL+++P+ + + ++ + Sbjct: 406 FKRINDTHGHATGDEVLVHMVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDAVQIITR 465 Query: 265 LRLIVERHSFALIDKR---TCSFGVAAYQFGHDGTTLLSLADSALYRAKKNGRNRVEIAI 321 ++ + + F +R T S GVA Y G LL AD ALY+AK G+NR+ A Sbjct: 466 VQRELTKRIFMHESQRLLITFSAGVAVYHPGESQADLLKRADVALYKAKNAGKNRIVFAD 525 Query: 322 EPEP 325 P P Sbjct: 526 PPAP 529 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 132 bits (332), Expect = 4e-32, Method: Compositional matrix adjust. Identities = 76/193 (39%), Positives = 113/193 (58%), Gaps = 5/193 (2%) Query: 131 MESFFVISHSVITGRKLAEQRIEHLNEKLALLAVTDKLTGLANRMKLDETLDSEIARAHR 190 M + V+ + LA +R E L +L + TD LTG+ NR ++ A R Sbjct: 382 MRALKVLRQRMRERNSLARER-EALITQLQTSSNTDFLTGVLNRRAFFTHGQQQMTVAKR 440 Query: 191 YGTKLSLILLDVDHFKEVNDKFGHSAGDAVLVSIAEILRTNVRATDIVGRWGGEEFLLIL 250 YG +L+++L D+DHFK++ND +GH AGDA+L +A+ + +R D++ R+GGEEF+++L Sbjct: 441 YGRELAVVLFDIDHFKQINDSYGHQAGDAILRGVAQSVSQLLRKVDVLARYGGEEFIILL 500 Query: 251 PQCDIEASSRMAEKLRLIVERHSFALIDKR----TCSFGVAAYQFGHDGTTLLSLADSAL 306 P+ + ++ +EKLR + F + R T SFGVAA G L+ AD AL Sbjct: 501 PESSLLQAAAASEKLRAALAAGEFEIDGGRRIRVTASFGVAAENGGPGLEHLIKQADIAL 560 Query: 307 YRAKKNGRNRVEI 319 YRAKK GRNRVE+ Sbjct: 561 YRAKKLGRNRVEL 573 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 127 bits (318), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 76/180 (42%), Positives = 112/180 (62%), Gaps = 9/180 (5%) Query: 146 KLAEQRIEHLNEKLALLAVTDKLTGLANRMKLDETLDSEIARAHRYGTKLSLILLDVDHF 205 +L + +E N KL L+ TD LTG+ANR + DE L +E+ RA R G L+L++LDVD+F Sbjct: 385 RLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDYF 444 Query: 206 KEVNDKFGHSAGDAVLVSIAEIL-RTNVRATDIVGRWGGEEFLLILPQCDIEASSRMAEK 264 K+ ND++GH AGD L +A +L +++ RATD+V R+GGEEF +I+ +CD + + AE Sbjct: 445 KKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAEN 504 Query: 265 L-RLIVE---RHSFALIDKRTCSFGVAAYQFGHDGTT---LLSLADSALYRAKKNGRNRV 317 + + I E H+ + + S GVA + T ++ +AD ALY AK GRNRV Sbjct: 505 ICQAIFELKLPHADSPFGYISASIGVAVL-LPDEHTAPEQMVRIADQALYHAKYQGRNRV 563 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 0.134 0.387 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: 992,021 Number of extensions: 39055 Number of successful extensions: 192 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 145 Number of HSP's successfully gapped: 39 Length of query: 340 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 254 Effective length of database: 1,212,660 Effective search space: 308015640 Effective search space used: 308015640 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 (21.8 bits) S2: 131 (55.1 bits)