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= 0001.4604.p (573 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 937 0.0 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 189 5e-49 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 169 5e-43 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 169 8e-43 gi|300312843|ref|YP_003776935.1| response regulator containing a... 154 2e-38 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 937 bits (2422), Expect = 0.0, Method: Compositional matrix adjust. Identities = 477/573 (83%), Positives = 516/573 (90%) Query: 1 MPARFDFLWLGFLRKIEIRYRLITSFILVSLVPLVISGLLAYRETTRATQDKVRTYSVQV 60 M R DFL FLR+I I YRLI++FILVSL+PL+ISGLLAY ET+RATQDKVR YSVQV Sbjct: 1 MRKRLDFLSRHFLRRIAIGYRLISAFILVSLLPLLISGLLAYGETSRATQDKVRAYSVQV 60 Query: 61 AKQIAQNLMLRMERIEDTSEELALSDKLQRLLGDYYSGSEAASATARSAVARVLLDTYGS 120 +QI+QNL+LRME+IEDTSE LALS+K+QRLL DYYSG ASA AR++ ARVLLDTYG+ Sbjct: 61 VQQISQNLLLRMEKIEDTSEALALSEKMQRLLADYYSGDADASAAARNSAARVLLDTYGA 120 Query: 121 LPDVNQKYLLDRKRQVIDPQIFAPLASSIGRVAEEAPDLSGRAWWTLYNGGHGQKSVAML 180 L VNQKYLLDR RQVIDPQIFAPLASSIGRVAEEAP+L+GR WWTLY+ GHGQKS+AML Sbjct: 121 LTYVNQKYLLDRDRQVIDPQIFAPLASSIGRVAEEAPELTGRGWWTLYHAGHGQKSLAML 180 Query: 181 REIRFTGNNRPAGILFVGVRPSYFFSIFEGVDLGYDSSIFIVDASDGTVVVQSRESNAST 240 RE+RFT NNRPAG+LFVGV PSYFF IF G DLGY +SI IVDASDG VVVQSRES+AS Sbjct: 181 REVRFTANNRPAGVLFVGVHPSYFFDIFRGADLGYGASISIVDASDGAVVVQSRESSASQ 240 Query: 241 VDPALLEGITASLTQRRSSDFIAYTRADKTRYYAAIAQLPHTSWWVVSATPSDKLNADTR 300 DPALL GIT SL Q R SDFIAY ADKT YYAAIA+LPHTSWWV S TPSD+LNADTR Sbjct: 241 ADPALLGGITESLAQGRDSDFIAYVGADKTPYYAAIARLPHTSWWVASITPSDRLNADTR 300 Query: 301 SVRDKIIAIGLLCFAASLLLSALIARSISLPLQRLVGAMREAGSGDTTVRVEQAGDDEIT 360 SVRDKIIAIGL+CFA SLLLSALI+RSIS+PLQRLV AM+EAGSGDTTVRVEQ G+DEI Sbjct: 301 SVRDKIIAIGLVCFAVSLLLSALISRSISVPLQRLVAAMKEAGSGDTTVRVEQHGNDEIA 360 Query: 361 VLSRKFNEMAGKLQQHKEELEQQVALRTRELERANRKLEALSATDGLTGVANRRRFDEAL 420 VLSRKFNEMAGKLQQ++E LE+QV LRTRELERANRKLEALSATDGLTGVANRRRFDEAL Sbjct: 361 VLSRKFNEMAGKLQQNREVLEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFDEAL 420 Query: 421 VNELRRSVRSGHALALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVAR 480 NE+RR+VRSG +LALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVAR Sbjct: 421 ANEMRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVAR 480 Query: 481 YGGEEFSVIIAESDTAHALQQAENICQAIFELKLPHADSPFGYITASIGVASLLPDEHTS 540 YGGEEFSVIIAE DT ALQQAENICQAIFELKLPHADSPFGYI+ASIGVA LLPDEHT+ Sbjct: 481 YGGEEFSVIIAECDTTQALQQAENICQAIFELKLPHADSPFGYISASIGVAVLLPDEHTA 540 Query: 541 AEQMLRIADQALYHAKYQGRNRVVLGSDATQDL 573 EQM+RIADQALYHAKYQGRNRVVLGSDATQ L Sbjct: 541 PEQMVRIADQALYHAKYQGRNRVVLGSDATQGL 573 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 189 bits (480), Expect = 5e-49, Method: Compositional matrix adjust. Identities = 116/269 (43%), Positives = 153/269 (56%), Gaps = 26/269 (9%) Query: 326 RSISLPLQRLVGAMREA--GSGDTTVRVEQAGD--DEITVLSRKFNEMAGKLQQHK---- 377 R + P+ RL +RE +T + G E+ L+ N M KL +H Sbjct: 96 RWLGQPITRLADFVRELDLNQMETPRSIHLPGRRRHELHFLADAINLMLAKLHRHTIHNH 155 Query: 378 ---EELEQQ--------------VALRTRELERANRKLEALSATDGLTGVANRRRFDEAL 420 +ELEQ+ +A RTR+L +AN +L +LS TDGLTG+ANRR FDE L Sbjct: 156 ALYKELEQEKQSLSALNRSLELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETL 215 Query: 421 VNELRRSVRSGHALALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVAR 480 E RRS+R G L L +DVD+FK YND YGHLAGD LR VA+ L++S R D VAR Sbjct: 216 EQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVAR 275 Query: 481 YGGEEFSVIIAESDTAHALQQAENICQAIFELKLPHADSPFGYITASIGVASLLPDEHTS 540 YGGEEF++I A++D +C A+ L + HA S G IT S GVAS P + + Sbjct: 276 YGGEEFAIIAADTDGQAGADMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGA 335 Query: 541 A-EQMLRIADQALYHAKYQGRNRVVLGSD 568 + +L+ AD ALY AK +GRNRVVL ++ Sbjct: 336 GLDGLLQAADAALYRAKMEGRNRVVLATE 364 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 169 bits (429), Expect = 5e-43, Method: Compositional matrix adjust. Identities = 95/209 (45%), Positives = 129/209 (61%), Gaps = 10/209 (4%) Query: 366 FNEMAGKLQQH-KEELEQQVALRTRELERANRKLEALSATDGLTGVANRRRFDEALVNEL 424 F +AG L + EL ++VA A ++LE L+ TDGLTG+ NRR DEAL+ Sbjct: 298 FTALAGVLLMLVRRELLKRVA--------AEKQLEDLARTDGLTGLLNRRSLDEALLAVW 349 Query: 425 RRSVRSGHA-LALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGG 483 +RS RS A + L +DVDYFK+YND YGH GD L+ VA VL++ +R DL RYGG Sbjct: 350 QRSQRSPTAGFSTLFIDVDYFKRYNDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGG 409 Query: 484 EEFSVIIAESDTAHALQQAENICQAIFELKLPHADSPFGYITASIGVASLLPDEHTSAEQ 543 EEF V++ ++D AL+ A+ +C+AI+ +PH+ SP G I+ SIGVA++ H E Sbjct: 410 EEFVVLLEQTDEHGALRMAQQLCEAIYNRGIPHSGSPLGVISVSIGVATMNRAPHQRMED 469 Query: 544 MLRIADQALYHAKYQGRNRVVLGSDATQD 572 +L AD ALY AK +GRNRV + D Sbjct: 470 VLNAADHALYIAKREGRNRVCVAHPGQND 498 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 169 bits (427), Expect = 8e-43, Method: Compositional matrix adjust. Identities = 87/179 (48%), Positives = 123/179 (68%), Gaps = 5/179 (2%) Query: 389 RELERANRKLEALSATDGLTGVANRRRFDEALVNELRRSVRSGHALALLMLDVDYFKKYN 448 ++L+++N +L+ L+ TDGLTG+ANRR FD+ L E RR+ R G LALL++DVD+FK YN Sbjct: 161 QQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYN 220 Query: 449 DRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAES--DTAHALQQAENIC 506 D YGH+AGD LR VA L S +R DL AR+GGEEF++I+ + D AHA+ A+ +C Sbjct: 221 DNYGHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAI--AQKVC 278 Query: 507 QAIFELKLPHADSPF-GYITASIGVASLLPDEHTSAEQMLRIADQALYHAKYQGRNRVV 564 + L++PH S ++T S+G A+L+P E +++ AD+ LY AK QGRNRVV Sbjct: 279 HLVESLQVPHEGSSVSAWLTVSVGAATLVPQEQQELRELIEAADRRLYLAKQQGRNRVV 337 >gi|300312843|ref|YP_003776935.1| response regulator containing a CheY-like receiver and a GGDEF domains protein [Herbaspirillum seropedicae SmR1] Length = 525 Score = 154 bits (390), Expect = 2e-38, Method: Compositional matrix adjust. Identities = 93/180 (51%), Positives = 122/180 (67%), Gaps = 2/180 (1%) Query: 390 ELERANRKLEALSATDGLTGVANRRRFDEALVNELRRSVRSGHALALLMLDVDYFKKYND 449 EL+ AN +LE L+ DGLTG+ANRR D L E +R+ RSG ALAL+M+DVD+FK+YND Sbjct: 335 ELQMANHRLEMLAHQDGLTGLANRRHLDTMLETEFKRAERSGAALALIMIDVDFFKQYND 394 Query: 450 RYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAESDTAHALQQAENICQAI 509 YGH AGDECLR VA VL++ RR DL ARYGGEE ++++ +D A AE + I Sbjct: 395 LYGHQAGDECLRRVAGVLKERQRRPGDLAARYGGEEMAMLLPGTDAEGACAVAEKLRAGI 454 Query: 510 FELKLPHADSPFGYITASIGVAS--LLPDEHTSAEQMLRIADQALYHAKYQGRNRVVLGS 567 L+LPH +P G +T S+GV + LLP S + +L AD ALY AK++GRN+V L + Sbjct: 455 QALELPHRGNPVGVVTVSVGVCALELLPSAARSVQALLGAADAALYEAKHEGRNQVRLAA 514 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 0.134 0.374 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: 1,555,960 Number of extensions: 59396 Number of successful extensions: 342 Number of sequences better than 1.0e-08: 40 Number of HSP's gapped: 279 Number of HSP's successfully gapped: 40 Length of query: 573 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 483 Effective length of database: 1,193,720 Effective search space: 576566760 Effective search space used: 576566760 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: 133 (55.8 bits)