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= 0001.3099.p (235 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312430|ref|YP_003776522.1| sensor histidine kinase [Herbas... 289 2e-79 gi|300313023|ref|YP_003777115.1| hypothetical protein Hsero_3729... 73 2e-14 gi|300313029|ref|YP_003777121.1| two component hybrid sensor his... 70 1e-13 gi|300310566|ref|YP_003774658.1| Hpt sensor hybrid histidine kin... 65 4e-12 gi|300312688|ref|YP_003776780.1| response regulator consisting o... 56 2e-09 >gi|300312430|ref|YP_003776522.1| sensor histidine kinase [Herbaspirillum seropedicae SmR1] Length = 233 Score = 289 bits (739), Expect = 2e-79, Method: Compositional matrix adjust. Identities = 156/228 (68%), Positives = 180/228 (78%) Query: 3 MKDSGPRVLLVDDSATIRYAMQNRLQMLGCQVDCVADGGSALAAIQAQSYGMVLLDCFLP 62 M S PRVLLVDDSATIRYAMQNRLQ LGCQV ADG +ALAAI+AQ G+VLLDCFLP Sbjct: 1 MNRSEPRVLLVDDSATIRYAMQNRLQSLGCQVQVAADGAAALAAIRAQPQGLVLLDCFLP 60 Query: 63 DMPGPEVARQVRLLEQHDSTRSYTPLIGISAEADATHVQRCLDSGMDGTLDKPLQTVAIR 122 D+PG EVARQVR LEQ D R YTPLIGISAEADA HV+ CLD GMDG LDKP+QT +R Sbjct: 61 DLPGHEVARQVRALEQEDPQRPYTPLIGISAEADAAHVRLCLDGGMDGMLDKPVQTADLR 120 Query: 123 RLLALWCDHESGEDGAPATAEEEHSQDLARLFIQTAQSDLQALQQASVMGDAARLGQLTH 182 ++L+LWCDHE G++GA EE+++DLARLF+ T+Q DL ALQQA GD A +G+L H Sbjct: 121 KMLSLWCDHECGDEGAALPPREEYARDLARLFLSTSQHDLAALQQAHRAGDQATMGKLAH 180 Query: 183 RMKGAALTMGRAEIVALLECVEEALRADTDERQAIGLLLQSLSSALQA 230 RMKGAALTM R+EIVALLEC+EEA++ D D + AI LLL SL L A Sbjct: 181 RMKGAALTMQRSEIVALLECLEEAMQDDYDTQDAISLLLSSLEKVLAA 228 >gi|300313023|ref|YP_003777115.1| hypothetical protein Hsero_3729 [Herbaspirillum seropedicae SmR1] Length = 765 Score = 73.2 bits (178), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 42/125 (33%), Positives = 68/125 (54%), Gaps = 5/125 (4%) Query: 6 SGPRVLLVDDSATIRYAMQNRLQMLGCQVDCVADGGSALAAIQAQSYGMVLLDCFLPDMP 65 +G R+L+ +D+ R ++ L GC + V +G A+ AI+ Y +VL+DC +P M Sbjct: 640 AGARILMAEDTEINRQLLRILLARKGCILQEVENGLQAVEAIRTGHYDLVLMDCMMPIMD 699 Query: 66 GPEVARQVRLLEQHDSTRSY--TPLIGISAEADATHVQRCLDSGMDGTLDKPLQTVAIRR 123 G + ++R H++ R TP+I ++A A QRCLD+GMD L KP V + + Sbjct: 700 GYQATAEIR---AHEAARGLPRTPIIALTASAIEGDRQRCLDAGMDDYLSKPFTQVGLMQ 756 Query: 124 LLALW 128 + W Sbjct: 757 TVEKW 761 >gi|300313029|ref|YP_003777121.1| two component hybrid sensor histidine kinase/response regulator protein [Herbaspirillum seropedicae SmR1] Length = 1524 Score = 70.5 bits (171), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 55/167 (32%), Positives = 84/167 (50%), Gaps = 11/167 (6%) Query: 7 GPRVLLVDDSATIRYAMQNRLQMLGCQVDCVADG--GSALAAIQAQSYGMVLLDCFLPDM 64 G ++LLV+D+ R L + G QV C G G A+A A+ + +VL+D +P M Sbjct: 1171 GVQILLVEDNPVNRQVASELLALSGAQVTCADSGSMGVAMACDPARHFDLVLMDLQMPGM 1230 Query: 65 PGPEVARQVRLLEQHDSTRSYTPLIGISAEADATHVQRCLDSGMDGTLDKPLQTVAIRRL 124 G E R++R Q++ P++ ++A A QRC+++GM G + KP+ I L Sbjct: 1231 DGIEATRRIR--GQYELRG--LPILAMTANASPEDKQRCIEAGMAGHIAKPID---IATL 1283 Query: 125 LALWCDHESGEDGAPATAEEEHSQDLA--RLFIQTAQSDLQALQQAS 169 + + H E P A + QDLA RL ++ S L QQAS Sbjct: 1284 IPVLLAHLHHERPVPEAAPQAVPQDLADDRLSVEDYSSILHRFQQAS 1330 >gi|300310566|ref|YP_003774658.1| Hpt sensor hybrid histidine kinase [Herbaspirillum seropedicae SmR1] Length = 723 Score = 65.5 bits (158), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 40/124 (32%), Positives = 68/124 (54%), Gaps = 4/124 (3%) Query: 6 SGPR-VLLVDDSATIRYAMQNRLQMLGCQVDCVADGGSALAAIQAQSYGMVLLDCFLPDM 64 SG R +LLV+D+ + +L +G D A+G AL + Y +VL+DC +P + Sbjct: 473 SGQRDILLVEDNVMNQKVAVYQLNAMGYAADIAANGLEALERLARHRYALVLMDCQMPLL 532 Query: 65 PGPEVARQVRLLEQHDSTRSYTPLIGISAEADATHVQRCLDSGMDGTLDKPLQTVAIRRL 124 G E R++R ++ ++T ++ ++A A A +RCL++GMD L KPL + + Sbjct: 533 DGYETTRRIRRMQ---GELAHTTIVAMTANAMAGDRERCLEAGMDDYLTKPLLRSQLSAM 589 Query: 125 LALW 128 LA + Sbjct: 590 LAHY 593 >gi|300312688|ref|YP_003776780.1| response regulator consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 222 Score = 56.2 bits (134), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 36/118 (30%), Positives = 64/118 (54%), Gaps = 9/118 (7%) Query: 9 RVLLVDDSATIRYAMQNRLQMLGCQVDCVADGGSALAAIQAQSYGMVLLDCFLPDMPGPE 68 ++LL++D+ + + ++ L+ +VD ADG A ++ ++Y +VLLD LP + G Sbjct: 2 KLLLIEDNPQLAHWLEQILKEHKFKVDIAADGEIADQVLRDENYDVVLLDLMLPKLHGKN 61 Query: 69 VARQVRLLEQHDSTRSYTPLIGISAEADATHVQRCLDSGMDGTLDKPLQTVAIRRLLA 126 V R++R E+H+ P++ ++A CL +G D L KP + IR L+A Sbjct: 62 VLRRLR--ERHNG----VPVMILTASGSIDEKVECLGAGADDYLVKPFE---IRELVA 110 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 0.319 0.131 0.369 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: 645,929 Number of extensions: 24959 Number of successful extensions: 183 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 193 Number of HSP's successfully gapped: 7 Length of query: 235 Length of database: 1,619,870 Length adjustment: 82 Effective length of query: 153 Effective length of database: 1,231,600 Effective search space: 188434800 Effective search space used: 188434800 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: 129 (54.3 bits)