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= 0002.0501.p (333 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 443 e-126 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 107 1e-24 gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodies... 103 2e-23 gi|300312318|ref|YP_003776410.1| diguanylate cyclase with PAS/PA... 103 3e-23 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 101 8e-23 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 443 bits (1139), Expect = e-126, Method: Compositional matrix adjust. Identities = 224/344 (65%), Positives = 264/344 (76%), Gaps = 18/344 (5%) Query: 1 MNSAVDTQALMEENQQLHAELQDLLEQARINQQIMQRHQAFDLRLIGSSEFRDLIETVSL 60 M SA+D++AL+ +N+QL AELQDLL+QA INQ I++RHQAFDL+LIG+SEFR+LIE + Sbjct: 1 MRSAIDSEALIADNEQLRAELQDLLQQAHINQSIIERHQAFDLKLIGASEFRELIEVMLT 60 Query: 61 LMPNTFNLEIVTLSLVDYAFDVRRILHDLQIGLDEYPNLLFRAE------DGPALPLEKP 114 +MP F+LE VTLSL+D + ++RIL DLQIG++E+P LLF + D EKP Sbjct: 61 VMPGVFSLETVTLSLIDGDYAIQRILRDLQIGINEFPKLLFLKQALAFPDDDLTRADEKP 120 Query: 115 TLGPYQDDVHQSLFPTYRPASVAILPLTRHQTLIGYLALGSAHEGRFTGNLATDFIERLA 174 LGPY +H LFP Y P SVA+LPL R L+GYLALGSA+ RFT +LATDFIERLA Sbjct: 121 RLGPYVAALHGPLFPHYEPVSVAVLPLVRQHRLLGYLALGSAYGERFTRSLATDFIERLA 180 Query: 175 SVVAICLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEIGRAQRDRSALSCLFIDID 234 ++ A+CLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEE+ R+QRDRSALSCLFIDID Sbjct: 181 TIAAVCLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDID 240 Query: 235 HFKRVNDKFGHQSGDDVLREVATRIKKELRLSDSLGRYGGEEFIVLLTQATLHDAERIAE 294 HFKRVND+FGHQSGDDVLREVA RIKKELRLSD+LGR+GGEEF+VLLT AT DA RIAE Sbjct: 241 HFKRVNDQFGHQSGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAE 300 Query: 295 RIRASVAX----------PTKRCKSPSPSA--PPHKHRPTAACR 326 RIRA V P K S +A PP + RP A + Sbjct: 301 RIRAGVCSRGVMIEGSRDPLKITASIGAAALTPPDRSRPAAEVK 344 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 107 bits (267), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 51/111 (45%), Positives = 75/111 (67%) Query: 187 NERLKHIGLTDPLTGVNNRRYIEQRMQEEIGRAQRDRSALSCLFIDIDHFKRVNDKFGHQ 246 NE+L + +TD LTG+ NR +++ + EI RA R LS + +DIDHFK VND FGH Sbjct: 156 NEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDHFKEVNDNFGHS 215 Query: 247 SGDDVLREVATRIKKELRLSDSLGRYGGEEFIVLLTQATLHDAERIAERIR 297 +GD VL +A ++ +R SD GR+GGEEF+++L + + DA R+AE++R Sbjct: 216 TGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLR 266 >gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodiesterase A protein [Herbaspirillum seropedicae SmR1] Length = 1002 Score = 103 bits (257), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 54/147 (36%), Positives = 87/147 (59%), Gaps = 1/147 (0%) Query: 169 FIERLASVVAICLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEIGRAQRDRSALSC 228 +E + A+ +E R+ + D LTG+ NR + + + I A+R+ S ++ Sbjct: 533 LVEAGLHLCALAIEREDARARIHQLAFYDSLTGLPNRSLLLVQAGQAIAAAERNCSTVAV 592 Query: 229 LFIDIDHFKRVNDKFGHQSGDDVLREVATRIKKELRLSDSLGRYGGEEFIVLLTQATLHD 288 +FID+D FK+VND GHQ+GD++LR VATR++ + R SD +GR G+EF+V+LTQ Sbjct: 593 MFIDLDRFKQVNDSLGHQAGDELLRTVATRLQSQARRSDIVGRLSGDEFVVVLTQYDTQH 652 Query: 289 AERIAERIRASVAXPTKRCKSP-SPSA 314 + +RI+ +A P +P +PSA Sbjct: 653 LTEVVKRIQERLAMPCHINGTPLNPSA 679 >gi|300312318|ref|YP_003776410.1| diguanylate cyclase with PAS/PAC sensor protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 70/173 (40%), Positives = 89/173 (51%), Gaps = 21/173 (12%) Query: 123 VHQSLFPTYRPASVAILPLTRHQTL----------IGYLALGSAHEGRFTGN--LATDFI 170 +H P Y A A+L H TL + +L G + R L FI Sbjct: 366 IHPDDMPLYEAAREAVLGGAAHWTLEFRVLPPGQGVRWLR-GQSRPRRLDDGTTLWHGFI 424 Query: 171 ERLASVVAICLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEIGRAQRDRSA-LSCL 229 ++ AI LE L+ LTD LT + NRRY QR+QEE R QR +A + L Sbjct: 425 SDISQSKAIELE-------LQEFALTDYLTQLPNRRYFMQRLQEEYSRIQRSVTAGAAVL 477 Query: 230 FIDIDHFKRVNDKFGHQSGDDVLREVATRIKKELRLSDSLGRYGGEEFIVLLT 282 D+DHFKR+ND GH GD VLR AT +K +LR SD+ GR GGEEF ++LT Sbjct: 478 MCDLDHFKRINDSLGHAVGDLVLRHFATVLKSQLRRSDTAGRLGGEEFAIILT 530 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 101 bits (252), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 50/106 (47%), Positives = 72/106 (67%) Query: 196 TDPLTGVNNRRYIEQRMQEEIGRAQRDRSALSCLFIDIDHFKRVNDKFGHQSGDDVLREV 255 TD LTGV NRR Q+++ A+R L+ + DIDHFK++ND +GHQ+GD +LR V Sbjct: 415 TDFLTGVLNRRAFFTHGQQQMTVAKRYGRELAVVLFDIDHFKQINDSYGHQAGDAILRGV 474 Query: 256 ATRIKKELRLSDSLGRYGGEEFIVLLTQATLHDAERIAERIRASVA 301 A + + LR D L RYGGEEFI+LL +++L A +E++RA++A Sbjct: 475 AQSVSQLLRKVDVLARYGGEEFIILLPESSLLQAAAASEKLRAALA 520 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 0.137 0.393 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: 979,425 Number of extensions: 40248 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 156 Number of HSP's successfully gapped: 39 Length of query: 333 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 247 Effective length of database: 1,212,660 Effective search space: 299527020 Effective search space used: 299527020 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: 131 (55.1 bits)