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= 0005.0168.p (190 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 318 1e-88 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 122 1e-29 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 113 9e-27 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 109 1e-25 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 109 2e-25 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 318 bits (816), Expect = 1e-88, Method: Compositional matrix adjust. Identities = 153/190 (80%), Positives = 170/190 (89%) Query: 1 MINARQEMQKAEARITALESQLVHMGELVREDQLTGSLNRRGMDESLEREIMNADRLGAP 60 M +ARQE++KAE RI LE QL+ MGELVREDQLTGSLNRRGMDESL+REI NA R P Sbjct: 336 MEDARQEVEKAEERIQTLEQQLLQMGELVREDQLTGSLNRRGMDESLDREITNALRRDTP 395 Query: 61 LCIALLDLDDFKRINDTHGHATGDEVLVHLVNVVKETLRKLDVIARFGGEEFLVLLPETE 120 LC+ALLDLDDFKRINDTHGHATGDEVLVH+V V++ETLRKLDVIARFGGEEFLVL+PET Sbjct: 396 LCVALLDLDDFKRINDTHGHATGDEVLVHMVQVIRETLRKLDVIARFGGEEFLVLMPETA 455 Query: 121 PAEAMQIITRVQRELTKRIFMHNTQRLLITFSAGVAYRAQGETQADLIKRADVALYKAKN 180 P +A+QIITRVQRELTKRIFMH +QRLLITFSAGVA GE+QADL+KRADVALYKAKN Sbjct: 456 PQDAVQIITRVQRELTKRIFMHESQRLLITFSAGVAVYHPGESQADLLKRADVALYKAKN 515 Query: 181 AGKNRVILAD 190 AGKNR++ AD Sbjct: 516 AGKNRIVFAD 525 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 122 bits (307), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 70/183 (38%), Positives = 106/183 (57%), Gaps = 1/183 (0%) Query: 5 RQEMQKAEARITALESQLVHMGELVREDQLTGSLNRRGMDESLEREIMNADRLGAPLCIA 64 RQ M++ + E+ + + D LTG LNRR ++++ A R G L + Sbjct: 389 RQRMRERNSLAREREALITQLQTSSNTDFLTGVLNRRAFFTHGQQQMTVAKRYGRELAVV 448 Query: 65 LLDLDDFKRINDTHGHATGDEVLVHLVNVVKETLRKLDVIARFGGEEFLVLLPETEPAEA 124 L D+D FK+IND++GH GD +L + V + LRK+DV+AR+GGEEF++LLPE+ +A Sbjct: 449 LFDIDHFKQINDSYGHQAGDAILRGVAQSVSQLLRKVDVLARYGGEEFIILLPESSLLQA 508 Query: 125 MQIITRVQRELTKRIF-MHNTQRLLITFSAGVAYRAQGETQADLIKRADVALYKAKNAGK 183 +++ L F + +R+ +T S GVA G LIK+AD+ALY+AK G+ Sbjct: 509 AAASEKLRAALAAGEFEIDGGRRIRVTASFGVAAENGGPGLEHLIKQADIALYRAKKLGR 568 Query: 184 NRV 186 NRV Sbjct: 569 NRV 571 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 113 bits (283), Expect = 9e-27, Method: Compositional matrix adjust. Identities = 73/179 (40%), Positives = 107/179 (59%), Gaps = 6/179 (3%) Query: 11 AEARITALESQLVHMGELVREDQLTGSLNRRGMDESLEREIMNADRLGAPLCIALLDLDD 70 AE R+ L +L L D+LTG NR +DE L+ EI ADR G L + LLD+D Sbjct: 148 AEQRVERLNEKLAL---LAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDH 204 Query: 71 FKRINDTHGHATGDEVLVHLVNVVKETLRKLDVIARFGGEEFLVLLPETEPAEAMQIITR 130 FK +ND GH+TGD VLV + +++ +R D+ R+GGEEFL++LPE + +A ++ + Sbjct: 205 FKEVNDNFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEK 264 Query: 131 VQRELTKRIFMHNTQRLLITFSAGVAYRAQGETQADLIKRADVALYKAKNAGKNRVILA 189 ++ + F+ +R T S GVA G + L+ AD+ALY+AKN G+NRV +A Sbjct: 265 LRLLIENYNFVPVGRR---TCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRVEIA 320 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 109 bits (272), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 63/163 (38%), Positives = 95/163 (58%), Gaps = 5/163 (3%) Query: 32 DQLTGSLNRRGMDESLEREIMNADRLGAPLCIALLDLDDFKRINDTHGHATGDEVLVHLV 91 D LTG NRR DE+LE+E + R G PL +A +D+D FK ND +GH GD VL + Sbjct: 200 DGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHLAGDAVLRQVA 259 Query: 92 NVVKETLRKL-DVIARFGGEEFLVLLPETEPAEAMQIITRVQRELTKRIFMHNTQRL-LI 149 +++++ ++ D +AR+GGEEF ++ +T+ ++ R+ + H + I Sbjct: 260 QTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRMCDAVHALAIAHAGSAMGRI 319 Query: 150 TFSAGVAYRAQGETQA---DLIKRADVALYKAKNAGKNRVILA 189 T SAGVA G+ A L++ AD ALY+AK G+NRV+LA Sbjct: 320 TISAGVASCNPGQPGAGLDGLLQAADAALYRAKMEGRNRVVLA 362 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 109 bits (272), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 66/167 (39%), Positives = 95/167 (56%), Gaps = 9/167 (5%) Query: 32 DQLTGSLNRRGMDESLEREIMNADRLGAPLCIALLDLDDFKRINDTHGHATGDEVLVHLV 91 D LTG NRR +++ ++ E+ + R + L +D+D FKR+ND GH +GD+VL + Sbjct: 203 DPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQSGDDVLREVA 262 Query: 92 NVVKETLRKLDVIARFGGEEFLVLLPETEPAEAMQIITRVQRELTKRIFMHNTQR--LLI 149 +K+ LR D + RFGGEEF+VLL +A +I R++ + R M R L I Sbjct: 263 ARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAGVCSRGVMIEGSRDPLKI 322 Query: 150 TFSAGVA-------YRAQGETQADLIKRADVALYKAKNAGKNRVILA 189 T S G A R E + ++K AD ALY+AK AG+NRV+LA Sbjct: 323 TASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRVMLA 369 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 0.135 0.367 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: 533,344 Number of extensions: 21144 Number of successful extensions: 138 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 89 Number of HSP's successfully gapped: 39 Length of query: 190 Length of database: 1,619,870 Length adjustment: 80 Effective length of query: 110 Effective length of database: 1,241,070 Effective search space: 136517700 Effective search space used: 136517700 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: 128 (53.9 bits)