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= 0088.0026.p (179 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 104 5e-24 gi|300310696|ref|YP_003774788.1| hypothetical protein Hsero_1364... 85 4e-18 gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709... 68 4e-13 gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspir... 61 5e-11 gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [... 57 6e-10 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 104 bits (259), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 54/138 (39%), Positives = 82/138 (59%), Gaps = 12/138 (8%) Query: 1 MKMPDMSPHDFYQVNASHAFGLLASSAEMRFERLTRLAKRLFNVPVAFVSLVEAHRPWPL 60 M++ ++ ++ +++A H+ +L + E RF+RLTRLA+RLF+VP+A V++++ +R W Sbjct: 1 MRIAELPANEAARIDALHSLRILDTPREERFDRLTRLARRLFDVPMAVVTMIDVNRQWFK 60 Query: 61 QKHDDGR------------HAFAAADLLVVQDTVLDQRFEGNPLRMGESRVRFYAGCPIR 108 G HA ++ +V D LD RF GNP GE +RFYAGCPI+ Sbjct: 61 SCVGLGDATETSREVSFCAHAILHEEMTIVPDATLDPRFSGNPQVTGEPFIRFYAGCPIK 120 Query: 109 VGNGDQLGTLCLIDDQPR 126 +G LGTLCL+D PR Sbjct: 121 SESGFTLGTLCLVDTVPR 138 >gi|300310696|ref|YP_003774788.1| hypothetical protein Hsero_1364 [Herbaspirillum seropedicae SmR1] Length = 606 Score = 84.7 bits (208), Expect = 4e-18, Method: Compositional matrix adjust. Identities = 50/119 (42%), Positives = 64/119 (53%), Gaps = 11/119 (9%) Query: 19 AFGLLASSAEMRFERLTRLAKRLFNVPVAFVSLVEAHRPW-----PLQKHDDGR------ 67 A+ LL + + + +T LA RLF+V +A VSLV HR W L R Sbjct: 31 AYCLLDTQPDPLCDMITELATRLFDVEIALVSLVAEHRQWFKSRRGLDAPGTPRSQSFCA 90 Query: 68 HAFAAADLLVVQDTVLDQRFEGNPLRMGESRVRFYAGCPIRVGNGDQLGTLCLIDDQPR 126 HA A +V+ D D+RF GNPL +GE +RFYAG +R +G LGTLCLI PR Sbjct: 91 HAIVQAQTMVIPDARQDERFAGNPLVLGEPGIRFYAGAALRTADGVALGTLCLIGKSPR 149 >gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709 [Herbaspirillum seropedicae SmR1] Length = 598 Score = 68.2 bits (165), Expect = 4e-13, Method: Compositional matrix adjust. Identities = 42/120 (35%), Positives = 63/120 (52%), Gaps = 11/120 (9%) Query: 18 HAFGLLASSAEMRFERLTRLAKRLFNVPVAFVSLVEAHRPW-----PLQKHDDGR----- 67 H + L + + +++T+LA +F+V +A V+LV+ HR W L+ + R Sbjct: 26 HGYCALDTPPDKLCDQVTQLACSMFDVEIALVALVDEHRQWFKSRVGLEVSETPRADSFC 85 Query: 68 -HAFAAADLLVVQDTVLDQRFEGNPLRMGESRVRFYAGCPIRVGNGDQLGTLCLIDDQPR 126 HA +VV D + D RF + L G +RFYAG P+ G LGTLC+ID +PR Sbjct: 86 NHAIQTRHGMVVTDALQDARFSRHALVTGAPFIRFYAGAPLVTPQGLSLGTLCIIDSRPR 145 >gi|300311039|ref|YP_003775131.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 250 Score = 61.2 bits (147), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 38/118 (32%), Positives = 50/118 (42%), Gaps = 22/118 (18%) Query: 25 SSAEMRFERLTRLAKRLFNVPVAFVSLVEAH----------------RPWPLQKHDDGRH 68 + AE RF RLT LA L VP+A V+ A R W + D Sbjct: 108 TQAEARFHRLTWLASELLEVPIALVTFQTAELQIFHAAHGLNIAATPRSWAFCNYADMDE 167 Query: 69 AFAAADLLVVQDTVLDQRFEGNPLRMGESRVRFYAGCPIRVGNGDQLGTLCLIDDQPR 126 D+ V D D RF NP+ +RFYA P+ + G G+LC+ID + R Sbjct: 168 -----DVFTVADASKDARFANNPMVTSAPFIRFYAAVPL-MYQGKAFGSLCIIDTEAR 219 >gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 57.4 bits (137), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 37/111 (33%), Positives = 53/111 (47%), Gaps = 11/111 (9%) Query: 27 AEMRFERLTRLAKRLFNVPVAFVSLVEA-----HRPWPLQKHDDGR------HAFAAADL 75 +E RF RL LA L +VP++ + LV + H P L + R H + Sbjct: 3 SEERFRRLNWLASELLDVPMSLIGLVASETVIWHGPVGLHVEETTRPCAFVEHTLLHEGV 62 Query: 76 LVVQDTVLDQRFEGNPLRMGESRVRFYAGCPIRVGNGDQLGTLCLIDDQPR 126 +V D D RF + L G VR +AG +R+ NG G LC++D +PR Sbjct: 63 FLVPDASKDPRFSDHSLVTGAPFVRCFAGMRLRLNNGVVFGALCVMDTEPR 113 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 0.325 0.134 0.422 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: 488,161 Number of extensions: 16801 Number of successful extensions: 67 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 61 Number of HSP's successfully gapped: 6 Length of query: 179 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 100 Effective length of database: 1,245,805 Effective search space: 124580500 Effective search space used: 124580500 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 (21.6 bits) S2: 127 (53.5 bits)