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= 0001.3641.p (320 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313025|ref|YP_003777117.1| chemotaxis signal transduction ... 601 e-173 gi|300311277|ref|YP_003775369.1| chemotaxis signal transduction ... 419 e-118 gi|300312287|ref|YP_003776379.1| chemotaxis cheY protein [Herbas... 57 2e-09 gi|300311026|ref|YP_003775118.1| chemotaxis response regulator r... 56 4e-09 gi|300311339|ref|YP_003775431.1| CheY chemotaxis protein [Herbas... 55 8e-09 >gi|300313025|ref|YP_003777117.1| chemotaxis signal transduction protein [Herbaspirillum seropedicae SmR1] Length = 320 Score = 601 bits (1550), Expect = e-173, Method: Compositional matrix adjust. Identities = 291/320 (90%), Positives = 308/320 (96%) Query: 1 MDAFQKEIDERTNLTSSNKFELLLFRLGTPDGSTDKPGELYGINVFKIREIVPMMDITAA 60 MD+FQKEIDERTNLTS+NKFELLLFRLGTPDGSTDKPGELYGINVFKIREIVPMMDITAA Sbjct: 1 MDSFQKEIDERTNLTSTNKFELLLFRLGTPDGSTDKPGELYGINVFKIREIVPMMDITAA 60 Query: 61 AGMRSPMLGMVNIRGQVMSVVDLPAVAGCKPGNGMNILLITEFARHTQAFAVESVEEIVR 120 AGMRSPM+GMVNIRGQVMSVVDLPAVAGCK G+G NILLITEFARHTQAFAVESVEEIVR Sbjct: 61 AGMRSPMMGMVNIRGQVMSVVDLPAVAGCKAGHGNNILLITEFARHTQAFAVESVEEIVR 120 Query: 121 LDWSQVLPADSNASGSVVTSIARLDSAQDGGRLVQVLDVEQILNMVSPVKEQLQSPPPGS 180 LDWSQVLPADS++ GS+VTSIARLDS DGGRLVQVLDVE ILN+VSPVKEQ+Q PPG+ Sbjct: 121 LDWSQVLPADSHSPGSLVTSIARLDSEVDGGRLVQVLDVEHILNLVSPVKEQMQPAPPGA 180 Query: 181 TELKLKPGSVVLAADDSRMARALIEQCLKDLNLPYMMTTDGLQAWKKLQELARQAEQEGK 240 ELKLKPG+VVLAADDSRMARALIEQCLKDLNLP++M TDGLQAWKKLQ+L++ A QEGK Sbjct: 181 AELKLKPGAVVLAADDSRMARALIEQCLKDLNLPFIMETDGLQAWKKLQQLSQAAAQEGK 240 Query: 241 PLTDKVAMVLTDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGANG 300 PLTDKVAMVLTDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGANG Sbjct: 241 PLTDKVAMVLTDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGANG 300 Query: 301 YVAKFSPPELAAMLRKVLPP 320 YVAKFSPPELAAMLR+VLPP Sbjct: 301 YVAKFSPPELAAMLRQVLPP 320 >gi|300311277|ref|YP_003775369.1| chemotaxis signal transduction protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 419 bits (1077), Expect = e-118, Method: Compositional matrix adjust. Identities = 206/320 (64%), Positives = 254/320 (79%), Gaps = 5/320 (1%) Query: 1 MDAFQKEIDERTNLTSSNKFELLLFRLGT-PDGSTDKPGELYGINVFKIREIVPMMDITA 59 MD FQKEIDERTNLT+SNKFELLLFRLGT P G + EL+GINVFKIREIVPM +T Sbjct: 1 MDNFQKEIDERTNLTASNKFELLLFRLGTDPHG---ERSELFGINVFKIREIVPMPPVTK 57 Query: 60 AAGMRSPMLGMVNIRGQVMSVVDLPAVAGCKPGNGMNILLITEFARHTQAFAVESVEEIV 119 AAG +SPMLGMVNIRGQ++SV+DLPAV GC P G+NILL+TE+AR TQAFAVESV+EIV Sbjct: 58 AAGTQSPMLGMVNIRGQIISVIDLPAVVGCVPKTGLNILLVTEYARSTQAFAVESVDEIV 117 Query: 120 RLDWSQVLPADSNASGSVVTSIARLDSAQDGGRLVQVLDVEQILNMVSPVKEQLQSPP-P 178 RL+WSQVL A++++ G+ VTSIARLD+ +D RL QVLDVEQIL+ + P L+ Sbjct: 118 RLEWSQVLSAETSSGGAFVTSIARLDADKDTSRLAQVLDVEQILHEIMPTDRDLKMESLE 177 Query: 179 GSTELKLKPGSVVLAADDSRMARALIEQCLKDLNLPYMMTTDGLQAWKKLQELARQAEQE 238 S ++PG+V +AADDS++AR+LIEQ L+ + +PY M G +AW+K+Q+LAR+A E Sbjct: 178 KSASHGIRPGTVAIAADDSKVARSLIEQGLRAMEIPYEMHVTGKEAWEKIQKLAREARAE 237 Query: 239 GKPLTDKVAMVLTDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGA 298 G+P++DK++ VLTDLEMPEMDGFTLTR IK D K +PV+IHSSL+GSANEDHVRSVG Sbjct: 238 GRPISDKISFVLTDLEMPEMDGFTLTRNIKREDYLKSIPVIIHSSLSGSANEDHVRSVGG 297 Query: 299 NGYVAKFSPPELAAMLRKVL 318 + YVAKF ELAA + VL Sbjct: 298 DAYVAKFEANELAATIYGVL 317 >gi|300312287|ref|YP_003776379.1| chemotaxis cheY protein [Herbaspirillum seropedicae SmR1] Length = 121 Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 37/129 (28%), Positives = 62/129 (48%), Gaps = 14/129 (10%) Query: 191 VLAADDSRMARALIEQCLKDLNLPYMMTTDGLQAWKKLQELARQAEQEGKPLTDKVAMVL 250 +LA DDS R ++ LK DG+ A +K + + +VL Sbjct: 5 ILAVDDSGSLRQMVVFSLKAAGYNVTEAVDGVDALEKAK-------------SQTFDLVL 51 Query: 251 TDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGANGYVAK-FSPPE 309 TD MP MDG TL R ++ Y ++P+++ ++ + ++ GANG++ K F P Sbjct: 52 TDQNMPRMDGLTLIRSLRELTSYARVPILMLTTEFSDEMKAKGKAAGANGWLVKPFDPQR 111 Query: 310 LAAMLRKVL 318 L ++RKV+ Sbjct: 112 LTEVVRKVI 120 >gi|300311026|ref|YP_003775118.1| chemotaxis response regulator receiver domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 134 Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 43/131 (32%), Positives = 63/131 (48%), Gaps = 17/131 (12%) Query: 192 LAADDSRMARALIEQCLKDLNLPYMMTTD---GLQAWKKLQELARQAEQEGKPLTDKVAM 248 L DD R +I LK+L Y+ TD G AWK L+ A ++ Sbjct: 8 LVVDDFSTMRRIIIGLLKELE--YLKVTDADDGTSAWKILESGALP-----------ISF 54 Query: 249 VLTDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGANGYVAK-FSP 307 V+TD MP MDG L +KI+ + + K+LPV++ S+ N GA+GY+ K F+ Sbjct: 55 VITDWNMPGMDGLGLLKKIRETPRLKRLPVLMVSAEAKKENIVLAAETGADGYIVKPFNA 114 Query: 308 PELAAMLRKVL 318 L + K+L Sbjct: 115 ATLDDKISKIL 125 >gi|300311339|ref|YP_003775431.1| CheY chemotaxis protein [Herbaspirillum seropedicae SmR1] Length = 131 Score = 55.1 bits (131), Expect = 8e-09, Method: Compositional matrix adjust. Identities = 39/134 (29%), Positives = 62/134 (46%), Gaps = 15/134 (11%) Query: 187 PGSVVLAADDSRMARALIEQCLKDLNLPYM-MTTDGLQAWKKLQELARQAEQEGKPLTDK 245 P + L DD R ++ LK+L + DG+QA +KL+ +D+ Sbjct: 4 PNTKFLVVDDFSTMRRIVRNLLKELGYTNVDEAEDGVQALQKLR-------------SDQ 50 Query: 246 VAMVLTDLEMPEMDGFTLTRKIKASDQYKQLPVVIHSSLTGSANEDHVRSVGANGYVAK- 304 V++D MP MDG T+ ++I+ +LPV++ ++ N GANGYV K Sbjct: 51 FDFVVSDWNMPNMDGLTMLQEIRKDPALSKLPVLMVTAEAKKENIVAAAQAGANGYVVKP 110 Query: 305 FSPPELAAMLRKVL 318 F+ L L K+ Sbjct: 111 FTAATLDEKLGKIF 124 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 0.316 0.132 0.371 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: 978,393 Number of extensions: 39937 Number of successful extensions: 188 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 192 Number of HSP's successfully gapped: 7 Length of query: 320 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 235 Effective length of database: 1,217,395 Effective search space: 286087825 Effective search space used: 286087825 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 130 (54.7 bits)