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= 0002.0386.p (557 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309853|ref|YP_003773945.1| two-component response regulato... 193 3e-50 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 188 1e-48 gi|300312843|ref|YP_003776935.1| response regulator containing a... 166 4e-42 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 157 2e-39 gi|300310865|ref|YP_003774957.1| response regulator containing a... 154 1e-38 >gi|300309853|ref|YP_003773945.1| two-component response regulator with GGDEF domain [Herbaspirillum seropedicae SmR1] Length = 277 Score = 193 bits (491), Expect = 3e-50, Method: Compositional matrix adjust. Identities = 97/205 (47%), Positives = 138/205 (67%) Query: 349 LGSAFNSLMRERKDAEMDLDQARVNLESMNKALERLALEDDLTGLANRRQFDLSLQEEFS 408 L + +L +ER + D ARV+LE M K L R+ LED LTGLANRRQF+ L EEF+ Sbjct: 66 LEANLQALQQERVQLVEERDDARVHLEEMEKTLARVGLEDALTGLANRRQFERGLLEEFN 125 Query: 409 RAMRNGVSLALVMIDVDHFKQYNDIYGHLAGDQCLRKVGRVIKAQQTRPGDLMARYGGEE 468 RA R +SLA++MID+D F +YND YG +AGD+ LR+VG I+ RP DL++R+G +E Sbjct: 126 RAARTSLSLAVIMIDIDLFDEYNDSYGRMAGDKVLRRVGSAIRDTNVRPEDLLSRFGAQE 185 Query: 469 VGILLPGADEAGAMAVAERIRLAVRQLGLLHEGNDAGIVTISAGVSAFVPIRDIDAADKL 528 + +LLPG+ GA+ VAERIR ++ L + H + G VTIS G+S+ P R +D + + Sbjct: 186 IAVLLPGSRLEGALIVAERIRKSIELLDIPHSASPTGRVTISIGISSVAPQRQVDEPETV 245 Query: 529 MRAADKALYLAKAQGRDRICSSSEL 553 +R A+++L LAK+ GRD I + +L Sbjct: 246 LREAEESLALAKSAGRDCIRTVEDL 270 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 188 bits (477), Expect = 1e-48, Method: Compositional matrix adjust. Identities = 124/350 (35%), Positives = 195/350 (55%), Gaps = 13/350 (3%) Query: 214 IVDHVDKARILQHVDHVGGKS-----GGTEQALAGFEGS--MEGLSRSNQPALFSFKRMK 266 IVD D A ++Q + ++ GG ++LA S + + P + R+ Sbjct: 221 IVDASDGAVVVQSRESSASQADPALLGGITESLAQGRDSDFIAYVGADKTPYYAAIARLP 280 Query: 267 TVDWIIGSIYLREEAFVPVRDMQNKALLVSLSLAALAGWLAWLIMSRLIDPLLRLHGHIQ 326 W + SI + R +++K + + L A++ L+ LI + PL RL ++ Sbjct: 281 HTSWWVASITPSDRLNADTRSVRDKIIAIGLVCFAVSLLLSALISRSISVPLQRLVAAMK 340 Query: 327 KIRTSKTYDEVPLSYRDDEIGDLGSAFNSLM-RERKDAEMDLDQARV---NLESMNKALE 382 + + T V + +DEI L FN + + +++ E+ +Q R+ LE N+ LE Sbjct: 341 EAGSGDTTVRVE-QHGNDEIAVLSRKFNEMAGKLQQNREVLEEQVRLRTRELERANRKLE 399 Query: 383 RLALEDDLTGLANRRQFDLSLQEEFSRAMRNGVSLALVMIDVDHFKQYNDIYGHLAGDQC 442 L+ D LTG+ANRR+FD +L E RA+R+G SLAL+M+DVD+FK+YND YGHLAGD+C Sbjct: 400 ALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDEC 459 Query: 443 LRKVGRVIKAQQTRPGDLMARYGGEEVGILLPGADEAGAMAVAERIRLAVRQLGLLHEGN 502 LR V RV++ R DL+ARYGGEE +++ D A+ AE I A+ +L L H + Sbjct: 460 LRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAENICQAIFELKLPHADS 519 Query: 503 DAGIVTISAGVSAFVPIRDIDAADKLMRAADKALYLAKAQGRDRICSSSE 552 G ++ S GV+ +P + A ++++R AD+ALY AK QGR+R+ S+ Sbjct: 520 PFGYISASIGVAVLLP-DEHTAPEQMVRIADQALYHAKYQGRNRVVLGSD 568 >gi|300312843|ref|YP_003776935.1| response regulator containing a CheY-like receiver and a GGDEF domains protein [Herbaspirillum seropedicae SmR1] Length = 525 Score = 166 bits (420), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 81/134 (60%), Positives = 98/134 (73%) Query: 369 QARVNLESMNKALERLALEDDLTGLANRRQFDLSLQEEFSRAMRNGVSLALVMIDVDHFK 428 QA L+ N LE LA +D LTGLANRR D L+ EF RA R+G +LAL+MIDVD FK Sbjct: 331 QAMGELQMANHRLEMLAHQDGLTGLANRRHLDTMLETEFKRAERSGAALALIMIDVDFFK 390 Query: 429 QYNDIYGHLAGDQCLRKVGRVIKAQQTRPGDLMARYGGEEVGILLPGADEAGAMAVAERI 488 QYND+YGH AGD+CLR+V V+K +Q RPGDL ARYGGEE+ +LLPG D GA AVAE++ Sbjct: 391 QYNDLYGHQAGDECLRRVAGVLKERQRRPGDLAARYGGEEMAMLLPGTDAEGACAVAEKL 450 Query: 489 RLAVRQLGLLHEGN 502 R ++ L L H GN Sbjct: 451 RAGIQALELPHRGN 464 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 157 bits (398), Expect = 2e-39, Method: Compositional matrix adjust. Identities = 87/203 (42%), Positives = 122/203 (60%) Query: 354 NSLMRERKDAEMDLDQARVNLESMNKALERLALEDDLTGLANRRQFDLSLQEEFSRAMRN 413 SL + E+ + + +L N+ L L+L D LTG+ANRR FD +L++E+ R+MR+ Sbjct: 166 QSLSALNRSLELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRH 225 Query: 414 GVSLALVMIDVDHFKQYNDIYGHLAGDQCLRKVGRVIKAQQTRPGDLMARYGGEEVGILL 473 G L L IDVD FK YND YGHLAGD LR+V + ++ R GD +ARYGGEE I+ Sbjct: 226 GTPLMLAFIDVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIA 285 Query: 474 PGADEAGAMAVAERIRLAVRQLGLLHEGNDAGIVTISAGVSAFVPIRDIDAADKLMRAAD 533 D + R+ AV L + H G+ G +TISAGV++ P + D L++AAD Sbjct: 286 ADTDGQAGADMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGAGLDGLLQAAD 345 Query: 534 KALYLAKAQGRDRICSSSELSTS 556 ALY AK +GR+R+ ++EL S Sbjct: 346 AALYRAKMEGRNRVVLATELIVS 368 >gi|300310865|ref|YP_003774957.1| response regulator containing a CheY-like receiver domain and a GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 554 Score = 154 bits (390), Expect = 1e-38, Method: Compositional matrix adjust. Identities = 89/192 (46%), Positives = 119/192 (61%), Gaps = 1/192 (0%) Query: 356 LMRERKDAEMDLDQARVNLESMNKALERLALEDDLTGLANRRQFDLSLQEEFSRAMRNGV 415 L+ R+ AE AR LES+ + LE + +D LT + NRR FD +L E +R R G Sbjct: 324 LVAGRERAEAQAIAARQELESLYRTLEAQSQKDGLTDVFNRRYFDAALAAELARLNRTGE 383 Query: 416 SLALVMIDVDHFKQYNDIYGHLAGDQCLRKVGRVIKAQQTRPGDLMARYGGEEVGILLPG 475 SL+L+MIDVDHFKQ+ND YGH AGD CLR+V I R GD++ARYGGEE ++LP Sbjct: 384 SLSLMMIDVDHFKQFNDTYGHAAGDVCLRQVAAAISTVARRQGDIVARYGGEEFAVILPN 443 Query: 476 ADEAGAMAVAERIRLAVRQLGLLHEGNDAGIVTISAGVSAFVPIRD-IDAADKLMRAADK 534 A +A R+ AVR L + HE + G+VTIS GV++ + + +L+ +AD Sbjct: 444 CHPGSAQGLAHRVVQAVRGLEIAHERSPMGVVTISVGVASLASGKSLLIEPRELIDSADG 503 Query: 535 ALYLAKAQGRDR 546 ALY AK +GRDR Sbjct: 504 ALYRAKEEGRDR 515 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 0.135 0.379 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: 1,507,903 Number of extensions: 60985 Number of successful extensions: 298 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 237 Number of HSP's successfully gapped: 39 Length of query: 557 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 467 Effective length of database: 1,193,720 Effective search space: 557467240 Effective search space used: 557467240 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: 133 (55.8 bits)