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= 0001.1429.p (214 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312431|ref|YP_003776523.1| two component LuxR family trans... 114 8e-27 gi|300310869|ref|YP_003774961.1| response regulator for colanic ... 109 2e-25 gi|300311885|ref|YP_003775977.1| LuxR family two component respo... 91 1e-19 gi|300312077|ref|YP_003776169.1| response regulator containing a... 89 3e-19 gi|300310532|ref|YP_003774624.1| virulence regulator protein [He... 76 2e-15 >gi|300312431|ref|YP_003776523.1| two component LuxR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 114 bits (284), Expect = 8e-27, Method: Compositional matrix adjust. Identities = 81/237 (34%), Positives = 123/237 (51%), Gaps = 28/237 (11%) Query: 3 IRVAIADDYPVVLRGIEAILAPCPDITLAFSAESITQLMACLEQAAVDVLLCDYAFDDDP 62 +R+A+ DD+ VV G+ A LA PD+ + S + +LM L + D+LL DY+ + Sbjct: 47 MRIALLDDHAVVRYGLAARLAEEPDLEVVGSFATSKELMTALRASPADLLLIDYSLGSN- 105 Query: 63 QADGIDLLKRLRRHHPAVKVIFLSAHAQPHIISSALELGAVGFIGKSRSDFVNLPQAIYC 122 DG++L++ LR P K++ SAH P ++ A++ GA GF+GKS+ + L QAI Sbjct: 106 DIDGLNLIRALRVRFPRSKILVTSAHNNPATVALAMKAGARGFVGKSQ-ELGELVQAIRT 164 Query: 123 VQNGQVYLPQSLSSALLGNL---------------YRVHTRQ----------SGLGQLSE 157 V G+ YL +++ L L R R+ S + LS Sbjct: 165 VSVGREYLNAAMARELTAMLASDSPTPAPEGGPPQVRPPRRKRNSPPSSDSLSEMPSLSP 224 Query: 158 RELTVARMICQGMSIGTIAERLKRSPKTISNQKVAAMKKLGVSNDVELSRV-FQTLD 213 RE V R G+S+ IA++ RS KTIS QK +A +KLGV +D EL ++ +Q D Sbjct: 225 REREVLRCCLDGLSVTAIADKFARSVKTISGQKQSAFRKLGVRSDNELFKIEYQIKD 281 >gi|300310869|ref|YP_003774961.1| response regulator for colanic capsule biosynthesis protein [Herbaspirillum seropedicae SmR1] Length = 221 Score = 109 bits (272), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 11/210 (5%) Query: 2 MIRVAIADDYPVVLRGIEAILAPCPDITLAFSAESITQLMACLEQAAVDVLLCDYAF--D 59 ++ VAIADD+P+VL + LA P+I + ++ L+ L++ ++++ D+A + Sbjct: 6 VLHVAIADDHPIVLGALRNELARLPEIRIDLEVDTGEDLINALKRTPCEIVITDFAMPNE 65 Query: 60 DDPQADGIDLLKRLRRHHPAVKVIFLSAHAQPHIISSALELGAVGFIGKSRSDFVNLPQA 119 + ++DG L+KR++ HP+ K+I +A +I +G I K R L A Sbjct: 66 ESDESDGFALVKRIKAEHPSTKLIVYTAMNNGAVIRRLYRMGVFAVINK-REKPDELINA 124 Query: 120 IYCVQNG-QVYLPQSLSSALLGNLYRVHTRQSGLG---QLSERELTVARMICQGMSIGTI 175 Q+ Q+Y P SL G L + G +L++ EL V R+ +G S+G I Sbjct: 125 CLATQSSKQLYFPVSLR----GELEMSWAQGDGFAATRELTQSELEVVRLFVEGQSLGEI 180 Query: 176 AERLKRSPKTISNQKVAAMKKLGVSNDVEL 205 RL R+P TIS K AM+KLG+S+D EL Sbjct: 181 CVRLSRTPSTISTHKNNAMRKLGLSSDAEL 210 >gi|300311885|ref|YP_003775977.1| LuxR family two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 216 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 57/202 (28%), Positives = 106/202 (52%), Gaps = 5/202 (2%) Query: 1 MMIRVAIADDYPVVLRGIEAILAPCPDITLAFSAESITQLMACLEQAAVDVLLCDYAFDD 60 M+ R+ +ADD+ +V GI+A+L P + + A +++ + Q D++L D A Sbjct: 1 MLTRIMLADDHALVRSGIKALLTAMPGVEVVGEASDGAEVIEMIPQLKPDLVLLDIAMKG 60 Query: 61 DPQADGIDLLKRLRRHHPAVKVIFLSAHAQPHIISSALELGAVGFIGKSRSDFVNLPQAI 120 +G++ L+RLR +P ++ + LS + + AL GA G++ K S L +A+ Sbjct: 61 ---MNGLEALRRLRGEYPTIRFLMLSMYGSEEYVMQALNAGANGYLFKD-SAATELEKAL 116 Query: 121 YCVQNGQVYLPQSLSSALLGN-LYRVHTRQSGLGQLSERELTVARMICQGMSIGTIAERL 179 Y V++G+ YL +S L N + RV + + L+ R+ + ++I +G + IA +L Sbjct: 117 YEVKHGRQYLDSHISREALDNYMKRVAQNGTPVEVLTPRQREILQLIAEGNNTKEIAYQL 176 Query: 180 KRSPKTISNQKVAAMKKLGVSN 201 S KTI + M++L + + Sbjct: 177 NVSAKTIETHRAQLMERLDIRD 198 >gi|300312077|ref|YP_003776169.1| response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 217 Score = 88.6 bits (218), Expect = 3e-19, Method: Compositional matrix adjust. Identities = 66/205 (32%), Positives = 105/205 (51%), Gaps = 7/205 (3%) Query: 3 IRVAIADDYPVVLRGIEAILAPCPDITLAFSAESITQLMACLEQAAVDVLLCDYAFDDDP 62 I+V IADD+ +V G+ I A DI +A +A + + + + DVLL D P Sbjct: 9 IKVLIADDHAIVREGLRQICAGSKDIMVAGNAANGLEAIKLAREGNGDVLLLDIVL---P 65 Query: 63 QADGIDLLKRLRRHHPAVKVIFLSAHAQPHIISSALELGAVGFIGKSRSDFVNLPQAIYC 122 +GID+LK++R+ P + V+ LS H + AL+ GA GF+ K + L AI Sbjct: 66 DRNGIDILKQIRKEQPELPVLILSIHREDQYAIRALKAGAAGFLNKQAAP-AELLAAIRQ 124 Query: 123 VQNGQVYLPQSLSSALLGNLYRVHTRQSGLGQ-LSERELTVARMICQGMSIGTIAERLKR 181 +G+ Y+ SL+ L + H ++ L + LS+RE MI G ++ IA L Sbjct: 125 AASGRKYVSPSLAQELANQIGFDH--ETPLHETLSDREYQTMVMIASGKTVSDIAAELTL 182 Query: 182 SPKTISNQKVAAMKKLGVSNDVELS 206 S KTIS + + K+ + ++ EL+ Sbjct: 183 SVKTISMYRSRVLSKMKMRHNAELT 207 >gi|300310532|ref|YP_003774624.1| virulence regulator protein [Herbaspirillum seropedicae SmR1] Length = 209 Score = 75.9 bits (185), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 50/206 (24%), Positives = 99/206 (48%), Gaps = 10/206 (4%) Query: 2 MIRVAIADDYPVVLRGIEAILAPCPDITLAFSAESITQLMACLEQAAVDVLLCDYAFDDD 61 M ++ + DD+ VV G+ ++ P + + A + + + + D++L D A Sbjct: 1 MTKILVVDDHAVVRAGVHHFISEIPSMEIGGEASTAEEAIRLVRTQDWDIVLLDIAM--- 57 Query: 62 PQADGIDLLKRLRRHHPAVKVIFLSAHAQPHIISSALELGAVGFIGKS--RSDFVNLPQA 119 P G+++LK+++R P + V+ LS H + L GA G++ K ++ VN A Sbjct: 58 PDKSGVEVLKQIKREKPELPVLMLSMHPESRYAVQVLRSGASGYVQKEALATELVN---A 114 Query: 120 IYCVQNGQVYLPQSLSSALLGNLYRVHTRQSGLGQLSERELTVARMICQGMSIGTIAERL 179 I + G Y+ ++ L V + + LS+RE + + QG + IA+ L Sbjct: 115 INTILRGHKYISYGVAELLTSE--PVDSEKPLHETLSQREYEIFYKLGQGQGVTQIADEL 172 Query: 180 KRSPKTISNQKVAAMKKLGVSNDVEL 205 S KT+S + ++K+ ++N+ ++ Sbjct: 173 CLSVKTVSTYRSRVLQKMSMTNNADI 198 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 0.323 0.136 0.387 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: 610,859 Number of extensions: 23556 Number of successful extensions: 118 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 115 Number of HSP's successfully gapped: 6 Length of query: 214 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 133 Effective length of database: 1,236,335 Effective search space: 164432555 Effective search space used: 164432555 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 (22.0 bits) S2: 128 (53.9 bits)