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= 0229.0067.p (217 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312012|ref|YP_003776104.1| phosphodiesterase transmembrane... 242 2e-65 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 86 2e-18 gi|300312093|ref|YP_003776185.1| hypothetical protein Hsero_2782... 81 5e-17 gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [... 74 1e-14 gi|300311453|ref|YP_003775545.1| signal transduction containing ... 74 1e-14 >gi|300312012|ref|YP_003776104.1| phosphodiesterase transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 797 Score = 242 bits (617), Expect = 2e-65, Method: Compositional matrix adjust. Identities = 135/217 (62%), Positives = 156/217 (71%), Gaps = 3/217 (1%) Query: 2 KTREXLLVLAKGRNNQSAVAVLQRSISEAVAPYRRLQLILLSISIIGVIMAIFASAFVAR 61 + R LL LA+ N Q AVAVLQRS+SEAV PY+RLQLILLSI+++GV+ A ASA +AR Sbjct: 242 QYRARLLPLAQASNGQQAVAVLQRSVSEAVEPYQRLQLILLSITVLGVLGAAVASAVLAR 301 Query: 62 RITRPLRALADIAKRLGTGDYRARIDIKGGDEIGKLADAFESMRSGIANRELEIRRLAYW 121 RIT PLR LAD+AKRLG GDY + I+ DEIG+L +AFE+MR IA+REL+I RLAY Sbjct: 302 RITSPLRDLADVAKRLGEGDYSEGLFIRRQDEIGRLGNAFETMRLEIASRELKISRLAYQ 361 Query: 122 DPLTDLPNRVQFATLLNTAI-ERAKTTGGQCHILMMDLDRFQHVNDVLGHSFGDSLLRQV 180 D LT LPNRVQFA LL AI E A+T G C+ILMMDLDRFQ VNDVLGHSFGD LLRQV Sbjct: 362 DQLTGLPNRVQFADLLRDAIAEAARTPGAACYILMMDLDRFQQVNDVLGHSFGDDLLRQV 421 Query: 181 GRRLEQQLERENDKVARLG--XFVAGLPQAPAGGRTE 215 RL QL K++RLG F LP G E Sbjct: 422 ALRLSAQLLHPGAKLSRLGGDEFAILLPGVDQEGAVE 458 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 86.3 bits (212), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 58/179 (32%), Positives = 87/179 (48%), Gaps = 22/179 (12%) Query: 41 LLSISIIGVIMAIFASAFVARRITRPLRALADIAKRLGTGDYRARIDIKGGDEIGKLADA 100 +++I ++ +++ SA ++R I+ PL+ L K G+GD R++ G DEI L+ Sbjct: 306 IIAIGLVCFAVSLLLSALISRSISVPLQRLVAAMKEAGSGDTTVRVEQHGNDEIAVLSRK 365 Query: 101 FESMRSGI--------------------ANRELEIRRLAYWDPLTDLPNRVQFATLLNTA 140 F M + ANR+LE L+ D LT + NR +F L Sbjct: 366 FNEMAGKLQQNREVLEEQVRLRTRELERANRKLEA--LSATDGLTGVANRRRFDEALANE 423 Query: 141 IERAKTTGGQCHILMMDLDRFQHVNDVLGHSFGDSLLRQVGRRLEQQLERENDKVARLG 199 + RA +G +LM+D+D F+ ND GH GD LR V R L++ R D VAR G Sbjct: 424 MRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYG 482 >gi|300312093|ref|YP_003776185.1| hypothetical protein Hsero_2782 [Herbaspirillum seropedicae SmR1] Length = 601 Score = 81.3 bits (199), Expect = 5e-17, Method: Compositional matrix adjust. Identities = 48/136 (35%), Positives = 78/136 (57%), Gaps = 2/136 (1%) Query: 65 RPLRALADIAKRLGTGDYR-ARIDIKGGDEIGKLADAFESMRSGIANRELEIRRLAYWDP 123 RPLR A +A R+ G+ + + + DE+G+L AF + + + + E++ A+ D Sbjct: 355 RPLRRAAALADRMTRGELPLSPLPVDRRDEVGQLTMAFNGLLARLKLHQAELQHQAHHDV 414 Query: 124 LTDLPNRVQFATLLNTAIERAKTTGGQCHILMMDLDRFQHVNDVLGHSFGDSLLRQVGRR 183 LT LPNR+ A + A+ A +L +DLD F+ +ND LGH GD +L+++ RR Sbjct: 415 LTGLPNRMMLAERMQAALTHACRERNGVGLLFLDLDGFKPINDTLGHKAGDQVLQEITRR 474 Query: 184 LEQQLERENDKVARLG 199 L +Q+ R D +AR+G Sbjct: 475 L-RQVARHGDTLARVG 489 >gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 1036 Score = 73.9 bits (180), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 44/102 (43%), Positives = 61/102 (59%), Gaps = 4/102 (3%) Query: 101 FESMRSGIANREL---EIRRLAYWDPLTDLPNRVQFATLLNTAIERAKTTGGQCHILMMD 157 + S I++R+L IR LA++D LT LPNR L AI + T +L +D Sbjct: 578 YVSTHHDISDRKLAEERIRELAFFDALTRLPNRTLLLDRLKQAIALSLRTKTCAALLFID 637 Query: 158 LDRFQHVNDVLGHSFGDSLLRQVGRRLEQQLERENDKVARLG 199 LD F+ +ND +GH GD+LL+QV +RL + REND VAR+G Sbjct: 638 LDHFKTLNDTIGHEKGDTLLKQVAQRLLANV-RENDTVARVG 678 >gi|300311453|ref|YP_003775545.1| signal transduction containing PAS/GGDEF/EAL domains protein [Herbaspirillum seropedicae SmR1] Length = 683 Score = 73.6 bits (179), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 46/106 (43%), Positives = 59/106 (55%), Gaps = 6/106 (5%) Query: 94 IGKLADAFESMRSGIANRELEIRRLAYWDPLTDLPNRVQFATLLNTAIERAKTTGGQCHI 153 IG L D E N E I LAY+D LT LPNR ++ A+E A+ + Sbjct: 224 IGYLNDITER-----KNAEKLIHHLAYYDALTGLPNRTLLTRTVDQALEEARHENLHGCV 278 Query: 154 LMMDLDRFQHVNDVLGHSFGDSLLRQVGRRLEQQLERENDKVARLG 199 + +DL+RF+ +ND LGH GD LL +V RL + L RE D VARLG Sbjct: 279 MFIDLNRFKPINDTLGHVAGDMLLVEVAMRLRRAL-REQDVVARLG 323 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 0.324 0.139 0.389 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: 619,803 Number of extensions: 24158 Number of successful extensions: 202 Number of sequences better than 1.0e-08: 26 Number of HSP's gapped: 205 Number of HSP's successfully gapped: 26 Length of query: 217 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 136 Effective length of database: 1,236,335 Effective search space: 168141560 Effective search space used: 168141560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 128 (53.9 bits)