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= 0001.3692.p (738 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313074|ref|YP_003777166.1| GGDEF domain-containing protein... 1197 0.0 gi|300311453|ref|YP_003775545.1| signal transduction containing ... 147 3e-36 gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspi... 145 8e-36 gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [... 144 4e-35 gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protei... 142 7e-35 >gi|300313074|ref|YP_003777166.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 738 Score = 1197 bits (3097), Expect = 0.0, Method: Compositional matrix adjust. Identities = 608/736 (82%), Positives = 666/736 (90%), Gaps = 3/736 (0%) Query: 5 RFTGEPSCIQPYCSI---LSQLNNNKAPSPPNLSSLITLGVVITVLITTVSVLLLVDQFT 61 RFTGEPSCIQPYC QLN KAPSPPNLSSLITLGVV+TVL+TTVSVL+LVDQFT Sbjct: 2 RFTGEPSCIQPYCCSSYQAYQLNKKKAPSPPNLSSLITLGVVVTVLVTTVSVLILVDQFT 61 Query: 62 RGYARSESETRMKQLAWQMQDALERGMSEREIDLRQLVSRPSIRNGHDLSLIRRILDELQ 121 RGYARSE ETR+KQLAWQMQDALERGM+EREID+R LVSRPSIR D + IR +L+ELQ Sbjct: 62 RGYARSEVETRLKQLAWQMQDALERGMAEREIDIRLLVSRPSIRQAQDPAHIRAVLEELQ 121 Query: 122 ASVPHYAWIGLARPDGSIMVASQGWLEGASVAERPWFQEGRKGPYAGDYHPAVLLSHQLP 181 +VPHYAWIG+ARPDG+++ A++G LEG SVAERPWFQ+G++ YA DYHPAVLL +LP Sbjct: 122 RNVPHYAWIGMARPDGTVLAATKGLLEGMSVAERPWFQQGQQTEYAADYHPAVLLEKKLP 181 Query: 182 PQSNPWRFVDLSAPVHDLQGRFIGVLGMHLSWSWARDIAGKLLAPTSNRYDVEVIIVRSD 241 PQS+PWRFVDLS PV ++QG+ IGV+GMHLSW WAR+IA KLL PTS+RYDV+V+IVRSD Sbjct: 182 PQSDPWRFVDLSMPVLNMQGQMIGVMGMHLSWGWAREIASKLLNPTSSRYDVDVLIVRSD 241 Query: 242 GTVILGPKSMEESKIDTASWRASLKATNGGSMIETWPDGQRYVSGYARTGSTGGMKLQWS 301 GTVILGPK MEE+KIDTAS+RA+ ++ GGS+IETWPDG+RYV+GYARTG G MKL+W+ Sbjct: 242 GTVILGPKDMEETKIDTASFRAAQHSSAGGSLIETWPDGRRYVTGYARTGQGGEMKLKWT 301 Query: 302 VIVRQPEVVALAAFRDLERRVILVGALSCVALVILAFVLTRRLVAPINALSAALEQRAAG 361 VIVRQPE VAL AFRDLERRVI+VGAL+ LV+LAF+LTRRLVAPINALSAALEQRAAG Sbjct: 302 VIVRQPETVALEAFRDLERRVIVVGALAGAVLVLLAFMLTRRLVAPINALSAALEQRAAG 361 Query: 362 QAEVAIPQVNSYREIQLLSSTLVNMVEREERYLSEVRSLNESLEQRVAERTSRLHETATA 421 EV IP V S RE+QLLSS L MVEREERYL E+RSLNESLE+RV ERTSRLHETATA Sbjct: 362 LQEVEIPLVTSVRELQLLSSALGTMVEREERYLREMRSLNESLEERVVERTSRLHETATA 421 Query: 422 LQQALDQQQDNQLQLEETAAELRAILENAQDAFIAADEHGRVVEWNRQAELLLGWPRDQA 481 LQQALDQQQ NQ+QLEE+AAELRAILENAQDAFIAADEHG +VEWNRQAELLLGWPRD Sbjct: 422 LQQALDQQQTNQIQLEESAAELRAILENAQDAFIAADEHGHIVEWNRQAELLLGWPRDTV 481 Query: 482 MGRDMAELIIPPDLRAAHNRGMAQFLKDGTSVVINNRIELQALHHDGHELPVEITVGHVK 541 MGR MAELIIP D+RAAHN GMAQFLKDGTSVVINNRIELQALH DGHELPVEITVGHVK Sbjct: 482 MGRSMAELIIPSDMRAAHNHGMAQFLKDGTSVVINNRIELQALHRDGHELPVEITVGHVK 541 Query: 542 RQSGHLFIAFLHDITERLAFRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRADQLL 601 RQSGHLFIAFLHDITERLAFRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRA QLL Sbjct: 542 RQSGHLFIAFLHDITERLAFRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRAHQLL 601 Query: 602 SLFFMDIDGFKGVNDRYGHEAGDELLVEFARRLQRSVRDVDTVARLAGDEFVVILENLQS 661 +LFFMD+DGFKG+NDRYGHEAGDELLVEFARRLQ SVRDVDTVARLAGDEFVVILENLQS Sbjct: 602 ALFFMDLDGFKGINDRYGHEAGDELLVEFARRLQASVRDVDTVARLAGDEFVVILENLQS 661 Query: 662 QEDAVMVAEKILATIREPFELTHSTVHISSSIGVAVYQPNLDGEVGPEELLSMADKAMYT 721 Q+DA+MVAEKIL IREPFELTHSTVHISSSIGVAVYQP+LDGE+GPEELLSMADKAMY Sbjct: 662 QQDAIMVAEKILHAIREPFELTHSTVHISSSIGVAVYQPDLDGEIGPEELLSMADKAMYA 721 Query: 722 AKRLGKNRVELGRPTD 737 AKRLGKNR+ELGR D Sbjct: 722 AKRLGKNRIELGRVGD 737 >gi|300311453|ref|YP_003775545.1| signal transduction containing PAS/GGDEF/EAL domains protein [Herbaspirillum seropedicae SmR1] Length = 683 Score = 147 bits (371), Expect = 3e-36, Method: Compositional matrix adjust. Identities = 102/297 (34%), Positives = 154/297 (51%), Gaps = 16/297 (5%) Query: 435 QLEETAAELRAILENAQDAFIAADEHGRVVEWNRQAELLLGWPRDQAMGRDMAELIIPPD 494 Q+E + IL ++ I D G + WNR AE L G+ +A+GR++ L D Sbjct: 116 QIEAKLEQQAQILNQMHESVITMDPAGFITSWNRGAEQLFGYSAMEAIGRNVLFLYENED 175 Query: 495 LR-AAHNRGMAQFLKDGTSVVINNRIELQALHHDGHELPVEITVGHVKRQSGHL--FIAF 551 + H+ FL+ G +E++ G +++ ++ Q+GH I + Sbjct: 176 EEDSLHDL----FLEHG-----GREMEVRRRKKSGEVFWASLSLSVMRDQNGHPIGLIGY 226 Query: 552 LHDITERLAFRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRADQLLSLFFMDIDGF 611 L+DITER + LA D LT LPNR + + + + AR + + F+D++ F Sbjct: 227 LNDITERKNAEKLIHHLAYYDALTGLPNRTLLTRTVDQALEEARHENLHGCVMFIDLNRF 286 Query: 612 KGVNDRYGHEAGDELLVEFARRLQRSVRDVDTVARLAGDEFVVILENLQSQEDAVMVAEK 671 K +ND GH AGD LLVE A RL+R++R+ D VARL DEF V L + A VA+K Sbjct: 287 KPINDTLGHVAGDMLLVEVAMRLRRALREQDVVARLGADEFAVALFGIDKDSPAY-VAQK 345 Query: 672 ILATIREPFELTHSTVHISSSIGVAVYQPNLDGEVGPEELLSMADKAMYTAKRLGKN 728 +LA +PF + + + +SIGV++Y N E LL +AD AMY AK+ G+N Sbjct: 346 LLALFDDPFFIDGHELRVGASIGVSLYPEN---ATDTETLLRLADIAMYRAKQGGEN 399 >gi|300310189|ref|YP_003774281.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 706 Score = 145 bits (367), Expect = 8e-36, Method: Compositional matrix adjust. Identities = 75/174 (43%), Positives = 109/174 (62%), Gaps = 3/174 (1%) Query: 563 DQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRADQLLSLFFMDIDGFKGVNDRYGHEA 622 D++ A DVLT LPNR +DR+ + ARR + ++ FMD+DGFK +ND GH Sbjct: 256 DKLLHFATHDVLTGLPNRALLADRIQHAVEVARRNGKTFAVLFMDLDGFKAINDSLGHAV 315 Query: 623 GDELLVEFARRLQRSVRDVDTVARLAGDEFVVILENLQSQEDAVMVAEKILATIREPFEL 682 GD LLV A+R+++ +R D VAR+ GDEFVV++ NL S + ++E ILA +R+ F++ Sbjct: 316 GDGLLVAVAQRIRQCLRGEDMVARIGGDEFVVVVGNLSSPDVVEQLSENILAALRQDFQI 375 Query: 683 THSTVHISSSIGVAVYQPNLDGEVGPEELLSMADKAMYTAKRLGKNRVELGRPT 736 +T+ ++SSIG+AVY PN V + L+ AD AMY AK+ G+N P Sbjct: 376 DDATLRVTSSIGIAVY-PNSGDSV--DALMKNADAAMYEAKQSGRNTYRFFEPA 426 >gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 1036 Score = 144 bits (362), Expect = 4e-35, Method: Compositional matrix adjust. Identities = 98/310 (31%), Positives = 161/310 (51%), Gaps = 21/310 (6%) Query: 437 EETAAELR--AILENAQDAFIAADEHGRVVEWNRQAELLLGWPRDQAMGRDMAELIIPPD 494 ++ AELR A+ ++++ + D + +++ N+ + G+ ++ +G+ P+ Sbjct: 468 KQIEAELRISAVAFDSREGMLITDANSKILRVNKAFTEITGYSAEEIVGKH-------PN 520 Query: 495 LRAAHNRGMAQF--LKDGTSVVINNRIELQALHHDGHELPVEITVGHVKRQSGHL--FIA 550 L + G A F +++ + E+ +G P +T+ VK + + +++ Sbjct: 521 LLRSDRHGPAFFQEMRESIRRFGKWQGEIWDRRKNGEVYPEWLTISAVKNKDQQVTHYVS 580 Query: 551 FLHDITERLAFRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRADQLLSLFFMDIDG 610 HDI++R +++RELA D LT LPNR DRL + + + R +L F+D+D Sbjct: 581 THHDISDRKLAEERIRELAFFDALTRLPNRTLLLDRLKQAIALSLRTKTCAALLFIDLDH 640 Query: 611 FKGVNDRYGHEAGDELLVEFARRLQRSVRDVDTVARLAGDEFVVILENLQS--QEDAVM- 667 FK +ND GHE GD LL + A+RL +VR+ DTVAR+ GDEFVV+LE L QE A Sbjct: 641 FKTLNDTIGHEKGDTLLKQVAQRLLANVRENDTVARVGGDEFVVVLEGLNELQQEAATQT 700 Query: 668 --VAEKILATIREPFELTHSTVHISSSIGVAVYQPNLDGEVGPEELLSMADKAMYTAKRL 725 + EKIL + ++L ++SIG V+ L +EL+ AD AMY AK Sbjct: 701 RAIGEKILTALGSTYQLDDVEYRTTASIGATVF---LGRAASVDELMKQADLAMYKAKET 757 Query: 726 GKNRVELGRP 735 G+N + P Sbjct: 758 GRNALRFFDP 767 >gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 142 bits (359), Expect = 7e-35, Method: Compositional matrix adjust. Identities = 78/177 (44%), Positives = 109/177 (61%), Gaps = 4/177 (2%) Query: 560 AFRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRADQLLSLFFMDIDGFKGVNDRYG 619 A +++ ++ L D LT LPNR DRL + + +A R +L FMD+DGFK +ND G Sbjct: 257 AANEELTQMVLHDQLTRLPNRTLLEDRLNQAINKAAREQGHFALMFMDLDGFKAINDSLG 316 Query: 620 HEAGDELLVEFARRLQRSVRDVDTVARLAGDEFVVILENLQSQEDAVMVAEKILATIREP 679 H GD LLVE A+RL S R DTVARL GDEF VIL +L + EDA+ VAEK++ + +P Sbjct: 317 HHVGDRLLVEVAQRLTSSSRANDTVARLGGDEF-VILVDLNTPEDAMGVAEKLVEAVNQP 375 Query: 680 FELTHSTVHISSSIGVAVYQPNLDGEVGPEELLSMADKAMYTAKRLGKNRVELGRPT 736 F++ + +S+S+G+A+Y DG +L+ AD AMY KR G+N P+ Sbjct: 376 FKVDQHELRVSASVGIAIYPE--DGAT-RHDLVINADAAMYHTKRSGRNGYHFFEPS 429 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 0.319 0.134 0.388 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: 2,180,812 Number of extensions: 90473 Number of successful extensions: 446 Number of sequences better than 1.0e-08: 40 Number of HSP's gapped: 391 Number of HSP's successfully gapped: 40 Length of query: 738 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 646 Effective length of database: 1,184,250 Effective search space: 765025500 Effective search space used: 765025500 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: 134 (56.2 bits)