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= 0025.0053.p (823 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313423|ref|YP_003777515.1| SAM-dependent methyltransferase... 486 e-138 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 468 e-133 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 109 1e-24 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 108 2e-24 gi|300313030|ref|YP_003777122.1| two component response regulato... 106 7e-24 >gi|300313423|ref|YP_003777515.1| SAM-dependent methyltransferase [Herbaspirillum seropedicae SmR1] Length = 299 Score = 486 bits (1250), Expect = e-138, Method: Compositional matrix adjust. Identities = 235/269 (87%), Positives = 250/269 (92%), Gaps = 1/269 (0%) Query: 7 EIRPGQSIELLKELHILTRDGKLNQDSRRKLKQVYHLYQFIEPLLQEIRNAHPDVSVVDH 66 EIRPGQSIELLKELHILTRDGKLNQDSRRKLKQVYHLYQFIEPLLQE+ HPDVS+VDH Sbjct: 28 EIRPGQSIELLKELHILTRDGKLNQDSRRKLKQVYHLYQFIEPLLQEVLEQHPDVSLVDH 87 Query: 67 GAGKSYLGFILYDLFFKALEGNSRIYGIETREELVQKSTELAKRLGFPGMSFLNLSVADS 126 GAGKSYLGFILYDLFFK L G IYGIETREELV+KS ELA RLGF GMSFLNLSVADS Sbjct: 88 GAGKSYLGFILYDLFFKGLPGAPHIYGIETREELVRKSEELASRLGFGGMSFLNLSVADS 147 Query: 127 IVSPALPEQIDVVTALHACDTATDDAIHFALKKHAQFIVLVPCCQAEVASVLNRNKGASL 186 I SP+LPE+IDVVTALHACDTATDDAIHFAL K A+FIVLVPCCQAEVASVLNRNKG SL Sbjct: 148 ISSPSLPEKIDVVTALHACDTATDDAIHFALAKEARFIVLVPCCQAEVASVLNRNKGKSL 207 Query: 187 GRTSLTELWRHPLHTREFGSQVTNVLRCLQLEAHGYQVSVTELVGWEHSMKNELIIARYK 246 SLTE+WRHPLHTREFGSQVTNVLRCLQLEAHGY+VSVTELVGWEHSMKNELIIA+Y+ Sbjct: 208 A-NSLTEIWRHPLHTREFGSQVTNVLRCLQLEAHGYKVSVTELVGWEHSMKNELIIAQYR 266 Query: 247 DLPRKRPTERLQDVLQSLGLEEMGERFFA 275 DLPR+RP ERLQ+VL++LGLEEMG+RFFA Sbjct: 267 DLPRRRPAERLQEVLRTLGLEEMGQRFFA 295 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 468 bits (1204), Expect = e-133, Method: Compositional matrix adjust. Identities = 232/344 (67%), Positives = 278/344 (80%), Gaps = 9/344 (2%) Query: 304 MNSAVDTQALLEENQQLHAELQDLLEQARINQQIMQRHQAFDLRLIGSSEFRDLIETASL 363 M SA+D++AL+ +N+QL AELQDLL+QA INQ I++RHQAFDL+LIG+SEFR+LIE Sbjct: 1 MRSAIDSEALIADNEQLRAELQDLLQQAHINQSIIERHQAFDLKLIGASEFRELIEVMLT 60 Query: 364 LMPNTFNLEIVTLALVDYAFDVRRILHDLQIGLDEYPNLLFLAENGPALPL-------EK 416 +MP F+LE VTL+L+D + ++RIL DLQIG++E+P LLFL + A P EK Sbjct: 61 VMPGVFSLETVTLSLIDGDYAIQRILRDLQIGINEFPKLLFL-KQALAFPDDDLTRADEK 119 Query: 417 PTLGPYQHELHQSLFPTYRPASVAILPLTRHQKLIGYLALGSAHEGRFTGNLATDFIERL 476 P LGPY LH LFP Y P SVA+LPL R +L+GYLALGSA+ RFT +LATDFIERL Sbjct: 120 PRLGPYVAALHGPLFPHYEPVSVAVLPLVRQHRLLGYLALGSAYGERFTRSLATDFIERL 179 Query: 477 ASVVAICLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEIGRAQRERSALSCLFIDI 536 A++ A+CLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEE+ R+QR+RSALSCLFIDI Sbjct: 180 ATIAAVCLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDI 239 Query: 537 DHFKRVNDKFGHQSGDDVLREVATRIKKELRLSDSLGRYGGEEFIVLLTQATLRDAERIA 596 DHFKRVND+FGHQSGDDVLREVA RIKKELRLSD+LGR+GGEEF+VLLT AT DA RIA Sbjct: 240 DHFKRVNDQFGHQSGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIA 299 Query: 597 ERIRASVAQQAIEIAGADEALQVTVSIGAASQTPPDPRXEPAGQ 640 ERIRA V + + I G+ + L++T SIGAA+ TPPD R PA + Sbjct: 300 ERIRAGVCSRGVMIEGSRDPLKITASIGAAALTPPD-RSRPAAE 342 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 109 bits (272), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 58/130 (44%), Positives = 84/130 (64%), Gaps = 1/130 (0%) Query: 499 TDPLTGVNNRRYIEQRMQEEIGRAQRERSALSCLFIDIDHFKRVNDKFGHQSGDDVLREV 558 TD LTGV NRR Q+++ A+R L+ + DIDHFK++ND +GHQ+GD +LR V Sbjct: 415 TDFLTGVLNRRAFFTHGQQQMTVAKRYGRELAVVLFDIDHFKQINDSYGHQAGDAILRGV 474 Query: 559 ATRIKKELRLSDSLGRYGGEEFIVLLTQATLRDAERIAERIRASVAQQAIEIAGADEALQ 618 A + + LR D L RYGGEEFI+LL +++L A +E++RA++A EI G ++ Sbjct: 475 AQSVSQLLRKVDVLARYGGEEFIILLPESSLLQAAAASEKLRAALAAGEFEIDGGRR-IR 533 Query: 619 VTVSIGAASQ 628 VT S G A++ Sbjct: 534 VTASFGVAAE 543 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 108 bits (269), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 51/111 (45%), Positives = 75/111 (67%) Query: 490 NERLKHIGLTDPLTGVNNRRYIEQRMQEEIGRAQRERSALSCLFIDIDHFKRVNDKFGHQ 549 NE+L + +TD LTG+ NR +++ + EI RA R LS + +DIDHFK VND FGH Sbjct: 156 NEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDHFKEVNDNFGHS 215 Query: 550 SGDDVLREVATRIKKELRLSDSLGRYGGEEFIVLLTQATLRDAERIAERIR 600 +GD VL +A ++ +R SD GR+GGEEF+++L + + DA R+AE++R Sbjct: 216 TGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLR 266 >gi|300313030|ref|YP_003777122.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 320 Score = 106 bits (265), Expect = 7e-24, Method: Compositional matrix adjust. Identities = 59/146 (40%), Positives = 82/146 (56%), Gaps = 1/146 (0%) Query: 495 HIGLTDPLTGVNNRRYIEQRMQEEIGRAQRERSALSCLFIDIDHFKRVNDKFGHQSGDDV 554 +I +TD LTG+ NRR + + E+ +R A+S L IDIDHFK+ ND +GHQ+GD Sbjct: 143 NIAVTDSLTGLFNRRKFDSELAEKWELCKRSGQAMSLLLIDIDHFKQYNDHYGHQAGDHC 202 Query: 555 LREVATRIKKEL-RLSDSLGRYGGEEFIVLLTQATLRDAERIAERIRASVAQQAIEIAGA 613 L EVA I+ R D + RYGGEEF +L A R A+ + SVA+ + A + Sbjct: 203 LAEVAHTIRSNFHRSYDCVARYGGEEFACILPMTGREQAIRQAQEVCHSVARLHLPHARS 262 Query: 614 DEALQVTVSIGAASQTPPDPRXEPAG 639 D + V++SIG A+ PD P Sbjct: 263 DTSAWVSLSIGVATMIAPDHNASPVA 288 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 0.136 0.401 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: 2,594,942 Number of extensions: 111731 Number of successful extensions: 378 Number of sequences better than 1.0e-08: 40 Number of HSP's gapped: 358 Number of HSP's successfully gapped: 40 Length of query: 823 Length of database: 1,619,870 Length adjustment: 93 Effective length of query: 730 Effective length of database: 1,179,515 Effective search space: 861045950 Effective search space used: 861045950 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: 135 (56.6 bits)