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= 0013.0029.p (402 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309962|ref|YP_003774054.1| response regulator [Herbaspiril... 160 1e-40 gi|300312012|ref|YP_003776104.1| phosphodiesterase transmembrane... 130 1e-31 gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protei... 127 1e-30 gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709... 127 1e-30 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 126 3e-30 >gi|300309962|ref|YP_003774054.1| response regulator [Herbaspirillum seropedicae SmR1] Length = 420 Score = 160 bits (406), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 110/392 (28%), Positives = 197/392 (50%), Gaps = 36/392 (9%) Query: 1 LQKIFAVEKLRELGCVNVVEAADGMEAMERLSERRIDL--IFCDIGMPNMDGSQFVLAQD 58 +Q+ +V+ L++LG + EA +G EA++ L ++ + D+ MP MDG + + Sbjct: 21 VQRQHSVQLLQQLGADLIYEAGNGNEALDLLGLLKLPPSLMVVDLEMPGMDGIELI---- 76 Query: 59 RSVQSAGKELPMLVWMSVHAEDVRESHLQLA-----YSAGFPFVDAISKPLTLPTLQSIL 113 + +Q G ++P++V S RE+ L L+ ++ G + + KPL L++ L Sbjct: 77 QQLQQKGIDVPLIVASS------RETSLLLSVETMIHALGMNLIGVLQKPLNQHQLRAAL 130 Query: 114 AT----ALTMMNAIKPAPAKGGKTISATADGAIGDDDILRAICDTSEFEVWYQPQISLKT 169 + P P+ + A +G + ++QP++ ++T Sbjct: 131 ESFRPHGTEHQPDHDPQPSMCEHDLGAAIEGG--------------QVLPYFQPKVDVQT 176 Query: 170 KAIIGADAMVRWSHPKFSYLAPEQFMTLIERQGLGLMLFYRTVNHVLKTQQKLEHIGCSL 229 + G +A+ RW HP+ ++P++F+ L E+ GL L ++ + G ++ Sbjct: 177 GILKGVEALARWIHPERGMVSPDRFIPLAEQCGLIHPLTLAMMDQAMGQAAIWHSRGLAI 236 Query: 230 PICIKASASTLEIPEIADYLHERSQRYGISSHLVTVGISEEEPSQHALKLAASLNRLRLR 289 + + S LE P+ + E ++ + + V + I+E H L RLRL+ Sbjct: 237 KVAVNLSPLLLEKPDFLHRILELVDKHALPAEHVVLEITESSVVAHKGNSLGMLARLRLK 296 Query: 290 GFGLSIDDFGSGISTMKLLSQMPFTEIRIDRHFVRQFLRQPQCRVIVESIIGIAKRLQLA 349 GFGLSIDD+G+G S+M+ L+++PFTE++IDR FV + RVI++S + +A+RL+L Sbjct: 297 GFGLSIDDYGTGFSSMQQLARIPFTELKIDRSFVHGAHDRKNLRVILQSALDMAQRLELV 356 Query: 350 VIAEGIENARQMEVLAAMGCGRGQGF-IAAPM 380 +AEG+E +L GC GQG+ I PM Sbjct: 357 TVAEGVETMEDWRLLQDFGCSLGQGYLIGKPM 388 >gi|300312012|ref|YP_003776104.1| phosphodiesterase transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 797 Score = 130 bits (328), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 74/240 (30%), Positives = 122/240 (50%), Gaps = 1/240 (0%) Query: 149 RAICDTSEFEVWYQPQISLKTKAIIGADAMVRWSHPKFSYLAPEQFMTLIERQGLGLMLF 208 R + EF ++ QP++ L + ++GA+A+VRW HP+ ++ P+ F+ E G ML Sbjct: 539 RRALERDEFMLYLQPKLELCSGQVVGAEALVRWIHPEKGFIGPDNFIPFAETTGFIRMLT 598 Query: 209 YRTVNHVLKTQQKLEHIGCSLPICIKASASTLEIPEIADYLHERSQRYGISSHLVTVGIS 268 + V + ++L+ G L + S L E+ QR+ + + + I+ Sbjct: 599 LWMMEQVARLSEQLQQQGVQLKFSVNLSTRDLLDQELPTAFAAILQRHRLQPAALCLEIT 658 Query: 269 EEEPSQHALKLAASLNRLRLRGFGLSIDDFGSGISTMKLLSQMPFTEIRIDRHFVRQFLR 328 E + +L RL GF LSIDDFG+G S++ L ++P E++ID+ FV + + Sbjct: 659 ESAIMDDPARAQNTLERLSNMGFALSIDDFGTGYSSLAYLKRLPVDELKIDKSFVMKMAQ 718 Query: 329 QPQCRVIVESIIGIAKRLQLAVIAEGIENARQMEVLAAMGCGRGQG-FIAAPMRQDDFLS 387 IV S + + L L V+AEG+E+ +L MGC +GQG F+ PM FL+ Sbjct: 719 DQDDAKIVRSTVDLGHNLGLRVVAEGVESEEVWFLLRQMGCDQGQGYFMGKPMPVQHFLA 778 >gi|300312606|ref|YP_003776698.1| EAL domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 695 Score = 127 bits (320), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 70/240 (29%), Positives = 126/240 (52%), Gaps = 2/240 (0%) Query: 149 RAICDTSEFEVWYQPQISLKTKAIIGADAMVRWSHPKFSYLAPEQFMTLIERQGLGLMLF 208 R + +F + YQP+ SL ++GA+A++RW HP +AP+QF+ L ER GL L + Sbjct: 445 RVALERGQFRLVYQPKFSLPAGPVLGAEALLRWEHPVHGLVAPDQFIGLAERSGLILPIG 504 Query: 209 YRTVNHVLKTQQKLEHIG-CSLPICIKASASTLEIPEIADYLHERSQRYGISSHLVTVGI 267 ++ + ++ +G + + SA P + + + +R+ + +T+ + Sbjct: 505 AWVLDEACRQMREWFALGYVDWTMSVNLSALQFADPHLLEVVRTTLERHQLPPPCLTLEV 564 Query: 268 SEEEPSQHALKLAASLNRLRLRGFGLSIDDFGSGISTMKLLSQMPFTEIRIDRHFVRQFL 327 +E +L ++ G +SIDDFG+G S++ L ++P E++IDR FVR+ Sbjct: 565 TESTAMHDTEASLQTLRQIADLGVEISIDDFGTGYSSLLYLKRLPANELKIDRGFVRELR 624 Query: 328 RQPQCRVIVESIIGIAKRLQLAVIAEGIENARQMEVLAAMGCGRGQGFIAA-PMRQDDFL 386 + + IV +I+ + + L L ++AEG+E Q + L A GC QG++ PM + FL Sbjct: 625 QDGEDAAIVSAIVALGRTLNLRIVAEGVETVEQQDFLTAAGCDALQGYLMGRPMTPELFL 684 >gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709 [Herbaspirillum seropedicae SmR1] Length = 598 Score = 127 bits (319), Expect = 1e-30, Method: Compositional matrix adjust. Identities = 68/232 (29%), Positives = 123/232 (53%), Gaps = 1/232 (0%) Query: 150 AICDTSEFEVWYQPQISLKTKAIIGADAMVRWSHPKFSYLAPEQFMTLIERQGLGLMLFY 209 A+ E + +QP++ L+ A +G +A++RW HP + P+ F+ L E+ G + Sbjct: 354 ALTTPDELVLHFQPKVRLRDGACVGVEALIRWHHPIHGNIPPDVFIPLAEKTGQIRQVTA 413 Query: 210 RTVNHVLKTQQKLEHIGCSLPICIKASASTLEIPEIADYLHERSQRYGISSHLVTVGISE 269 + V+ + G +LP+ ASA + E+ + L ++ + + + L+ + +E Sbjct: 414 WVLRQVVAQVARWLKSGRALPVAFNASARDFDSDELRELLAQQLKLHKVPPALIEIEFTE 473 Query: 270 EEPSQHALKLAASLNRLRLRGFGLSIDDFGSGISTMKLLSQMPFTEIRIDRHFVRQFLRQ 329 + H ++ + LR G ++IDDFG+G S + L +P ++IDR F+ + L Sbjct: 474 HAMANHPQQVRQRVQALRELGVKVAIDDFGAGFSNLSYLKNIPADTMKIDRSFIHRLLDD 533 Query: 330 PQCRVIVESIIGIAKRLQLAVIAEGIENARQMEVLAAMGCGRGQGF-IAAPM 380 ++IV SI+ +A L +V+AEG+E+ R +L +GC GQG+ IA PM Sbjct: 534 EADQLIVPSILHLAHNLGFSVVAEGLESERTATLLRHLGCDYGQGYAIARPM 585 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 126 bits (317), Expect = 3e-30, Method: Compositional matrix adjust. Identities = 72/235 (30%), Positives = 125/235 (53%), Gaps = 3/235 (1%) Query: 148 LRAICDTSEFEVWYQPQISLKTKAIIGADAMVRWSHPKFSYLAPEQFMTLIERQGLGLML 207 LR D EF+++YQP++SL+ +IGA+A++RW P+ + P++F+ E GL + + Sbjct: 446 LRRALDQDEFKLYYQPKLSLQDGRLIGAEALIRWESPQQGMVPPDRFIPFAEEAGLIVPI 505 Query: 208 FYRTVNHVLKTQQKLEHIGCS-LPICIKASASTLEIPEIADYLHERSQRYGISSHLVTVG 266 + + Q + G +P+ + S L + D++ + G+++ + + Sbjct: 506 GEWVLRTACRQNQAWQQAGLPPIPVAVNLSPRQLN-QSLPDFVAGVLAQSGLAASWLELE 564 Query: 267 ISEEEPSQHALKLAASLNRLRLRGFGLSIDDFGSGISTMKLLSQMPFTEIRIDRHFVRQF 326 I+E + A K A+L+ L+ G +S+DDFG+G S++ L + P ++ID+ FVR Sbjct: 565 ITENVVMKDAEKSVATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDKSFVRDI 624 Query: 327 LRQPQCRVIVESIIGIAKRLQLAVIAEGIENARQMEVLAAMGCGRGQG-FIAAPM 380 +R IV++II +A L L VIAEG+E+ Q L C QG + PM Sbjct: 625 VRDADSAAIVKAIISLAHILNLRVIAEGVEDEEQHAFLKENACDEVQGYYFGKPM 679 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 0.322 0.136 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: 1,137,418 Number of extensions: 44350 Number of successful extensions: 218 Number of sequences better than 1.0e-08: 18 Number of HSP's gapped: 198 Number of HSP's successfully gapped: 18 Length of query: 402 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 315 Effective length of database: 1,207,925 Effective search space: 380496375 Effective search space used: 380496375 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: 132 (55.5 bits)