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= 0001.3323.p (445 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport resp... 791 0.0 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 285 6e-78 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 282 3e-77 gi|300314016|ref|YP_003778108.1| two component transcription reg... 270 2e-73 gi|300313916|ref|YP_003778008.1| two component response regulato... 249 3e-67 >gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 445 Score = 791 bits (2042), Expect = 0.0, Method: Compositional matrix adjust. Identities = 394/445 (88%), Positives = 411/445 (92%) Query: 1 MDTPAAAPSAILIEDEQAVRRATAQALELEGFTVTACASAEEALPLLTRDFPGVLVTDVR 60 MD P A SA+LIEDEQ VRRATAQALEL GF VTAC SAEEALPL+TRDF GV+V+DVR Sbjct: 1 MDKPGGAASALLIEDEQTVRRATAQALELGGFAVTACGSAEEALPLITRDFAGVVVSDVR 60 Query: 61 LPGWSGLQVLAHVVAIDADLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFGSDSLLEIAL 120 LPG SGL VLA VVAID DLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPF SD+LLEIAL Sbjct: 61 LPGLSGLDVLARVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIAL 120 Query: 121 RAQEKRSLVLENRRLREAWAQDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGS 180 RAQEKR+LVLENRRLREAWA DPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTG+ Sbjct: 121 RAQEKRNLVLENRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGT 180 Query: 181 GKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHEAGAFTGAQKRRIGKLEYAHG 240 GKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHE GAFTGAQKRRIGKLEYA+G Sbjct: 181 GKEVVARQLHAASGRKGPFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANG 240 Query: 241 GTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKVDLLKLAGQGQF 300 GTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASK DLLKLA +GQF Sbjct: 241 GTLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQF 300 Query: 301 REDLYYRIGVVAIDLPALHQRSSDIPLLLAHFCQAAAVRYRREVPPWTAAQMQQWQQREW 360 REDLYYRIGVVAIDLPAL+QR DI LLLAHFCQAAAVRYRRE P W+AAQMQQWQQR+W Sbjct: 301 REDLYYRIGVVAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDW 360 Query: 361 PGNVRELRNFADRWVLGVEQMAGTGLPVGAQPALPLPEQVEQFEAGLIAAALKDSEGSVA 420 PGNVRELRNFADRWVLGVEQMA + + LPEQVEQFEAGLIAAALKDSEGSVA Sbjct: 361 PGNVRELRNFADRWVLGVEQMAASAVSSAVPVLSSLPEQVEQFEAGLIAAALKDSEGSVA 420 Query: 421 LAAERLGIPRKTLYDKIRKYQLAGT 445 +AAERLGIP+KTLYDKIRKYQLAG+ Sbjct: 421 VAAERLGIPKKTLYDKIRKYQLAGS 445 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 285 bits (729), Expect = 6e-78, Method: Compositional matrix adjust. Identities = 156/365 (42%), Positives = 230/365 (63%), Gaps = 8/365 (2%) Query: 12 LIEDEQAVRRATAQALELEGFTVTACASAEEALPLLTRDFPGVLVTDVRLPGWSGLQVLA 71 +++D++++R +AL E + +SA +A+ L P VLV+D+R+PG SGL++L Sbjct: 6 IVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASGLELLQ 65 Query: 72 HVVAIDADLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFGSDSLLEIALRAQEKRSLVLE 131 V A +PVI++T D+ AV A + GA++++ KPF D +E+ RA ++ L Sbjct: 66 TVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES---LR 122 Query: 132 NRRLREAWAQDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGSGKEVVARQLHA 191 + + AQ PE+ +GQ+PA++ V I L ++V VLI G++GSGKE+VAR LH Sbjct: 123 ETDIEQGAAQTPEI---LGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHK 179 Query: 192 ASGRKG-PFVALNCGALPETVFESEIFGHEAGAFTGAQKRRIGKLEYAHGGTLFLDEIES 250 S R PFVALN A+P+ + ESE+FGHE GAFTGAQ R G+ E A GGTLFLDEI Sbjct: 180 HSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGD 239 Query: 251 MPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKVDLLKLAGQGQFREDLYYRIGV 310 MPL LQ +LLRVL + R+GG++S+ + RV+AA+ +L + +G FREDLY+R+ V Sbjct: 240 MPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNV 299 Query: 311 VAIDLPALHQRSSDIPLLLAHFCQAAAVRYRREVPPWTAAQMQQWQQREWPGNVRELRNF 370 + + LP+L +RS DIP+L +F +A + E + MQ Q E+PGNVR+L N Sbjct: 300 IRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 Query: 371 ADRWV 375 + W+ Sbjct: 360 CN-WI 363 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 282 bits (722), Expect = 3e-77, Method: Compositional matrix adjust. Identities = 170/447 (38%), Positives = 255/447 (57%), Gaps = 15/447 (3%) Query: 8 PSAILIEDEQAVRRATAQALELEGFTVTACASAEEALPLLTRDFPGVLVTDVRLP----- 62 P +++ED+ +++ +L+ + V E AL ++ R P V+ D+ LP Sbjct: 6 PKLLIVEDDPGLQKQLRWSLD--AYEVLVAGDRESALAMVRRHEPAVVTMDLGLPPDPDG 63 Query: 63 GWSGLQVLAHVVAIDADLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFGSDSLLEIALRA 122 G L V+A+ D VI++TG+ D AV+A+ GAYDF +KP ++L + RA Sbjct: 64 ASEGFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPCIDETLRLVVQRA 123 Query: 123 QEKRSLVLENRRLREAWAQDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGSGK 182 +L EN+R+++A L L+ + + V I + P+ V++ G +G+GK Sbjct: 124 FYLHALQRENQRMQQAGGHTA-LGGLITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGK 182 Query: 183 EVVARQLHAASGRKGP-FVALNCGALPETVFESEIFGHEAGAFTGAQKRRIGKLEYAHGG 241 EV+AR LH S R G F+A+NC A+PE + ESE+FG+E GAFTGA K+ IGK+E AHGG Sbjct: 183 EVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIGKVELAHGG 242 Query: 242 TLFLDEIESMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKVDLLKLAGQGQFR 301 T FLDE+ +P+ LQ KLLR LQER +ER+GG+ + +D RV+ A+ +L +L G FR Sbjct: 243 TFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTASGGFR 302 Query: 302 EDLYYRIGVVAIDLPALHQRSSDIPLLLAHFCQAAAVRYRREVPPWTAAQMQQWQQREWP 361 EDLYYR+ + I +PAL +R D LL HF Q + R + + ++ EWP Sbjct: 303 EDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWP 362 Query: 362 GNVRELRNFADRWVLGVEQMAGT----GLPVGAQPALPLP-EQV-EQFEAGLIAAALKDS 415 GNVRE+ N R V+ + T GL V + A PL QV ++ E + AL Sbjct: 363 GNVREMENCVMRAVIMADGQQITAEDLGLSVEGREAEPLNLRQVRDEAERKAVVKALTRM 422 Query: 416 EGSVALAAERLGIPRKTLYDKIRKYQL 442 +G++ AAE LG+ R TLYD + ++++ Sbjct: 423 DGNILKAAELLGVSRPTLYDLMSRHEI 449 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 270 bits (689), Expect = 2e-73, Method: Compositional matrix adjust. Identities = 165/426 (38%), Positives = 238/426 (55%), Gaps = 28/426 (6%) Query: 31 GFTVTACASAEEALPLLTRDFPGVLVTDVRLPGWSGLQVLAHVVAIDADLPVIVVTGHGD 90 G+ + A SAE AL L P +++TDVRLPG GL + A + + LPVI++T HG Sbjct: 34 GYRILAVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPALPVILLTAHGT 93 Query: 91 VGMAVEAMRAGAYDFVEKPFGSDSLLEIALRAQEKRSLVLENRRLREAWAQDPELPPLVG 150 + AV+A GA+ ++ KPF LL+ AQ ++W D ++ Sbjct: 94 IPDAVDATTQGAFAYLTKPFDGHVLLDKV--AQALSLAAPAPLSPDQSWRAD-----ILS 146 Query: 151 QSPAIERVRTLIRSLGPADVDVLINGQTGSGKEVVARQLHAASGR-KGPFVALNCGALPE 209 +S + + R + +D +LI G +G+GKE++AR +H AS R + PF+A+NCGA+PE Sbjct: 147 RSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAIPE 206 Query: 210 TVFESEIFGHEAGAFTGAQKRRIGKLEYAHGGTLFLDEIESMPLALQVKLLRVLQERRLE 269 + ESE+FGH GAFTGA + R G + AHGGTLFLDEI MPL LQVKLLRVLQE+ + Sbjct: 207 QLLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVR 266 Query: 270 RLGGNESVAIDCRVVAASKVDLLKLAGQGQFREDLYYRIGVVAIDLPALHQRSSDIPLLL 329 ++G N++ +D R+++A+ DL +GQFREDLYYR+ VV + LPAL +R DI LL Sbjct: 267 QVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLA 326 Query: 330 AHFCQAAAVRYRREVPPWTAAQMQQWQQREWPGNVRELRNFADRWVLGVEQMAGTG---- 385 HF + A +Y + + + ++ WPGNVR+L N VEQ+ Sbjct: 327 NHFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNV-------VEQVCALSTAPL 379 Query: 386 LPVG-AQPALPLP--------EQVEQFEAGLIAAALKDSEGSVALAAERLGIPRKTLYDK 436 +P Q AL P E ++FE + LK ++G+V+ AA R Y Sbjct: 380 IPASLVQRALRTPTLDLLRYAEAKQKFERDYLIRLLKLTDGNVSDAARLADRNRTEFYRL 439 Query: 437 IRKYQL 442 ++K L Sbjct: 440 LQKNGL 445 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 249 bits (636), Expect = 3e-67, Method: Compositional matrix adjust. Identities = 165/447 (36%), Positives = 235/447 (52%), Gaps = 27/447 (6%) Query: 11 ILIEDEQAVRRATAQALELEGFTVTACASAEEALPLLTRDFPGVLVTDVRLPGWSGLQVL 70 ++++D+ A R + A+ + G V S L LL + D+R+P GL L Sbjct: 5 LIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDGLAFL 64 Query: 71 AHVVAIDADLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFGSDSLLEIALRAQEKRSLVL 130 AI A +P I++T + +EA+R GA+D + KP +L+E +R+L Sbjct: 65 QRAPAIAA-IPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETL-----ERALRQ 118 Query: 131 ENRRLREAWAQDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGSGKEVVARQLH 190 A E LVG+S A+ +V I +D VL+ G+TG+GKE+VAR LH Sbjct: 119 GASTPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALH 178 Query: 191 AASGRKG-PFVALNCGALPETVFESEIFGHEAGAFTGAQKRRIGKLEYAHGGTLFLDEIE 249 R PFVA+NC A+P + ESE+FGH GAF+GA R+G+ + A GGTLFLDEI Sbjct: 179 RNGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIG 238 Query: 250 SMPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKVDLLKLAGQGQFREDLYYRIG 309 M LA Q K+LRVLQER L +GGN+SV +D RV+AA+ DL QG+FREDL+YR+ Sbjct: 239 DMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQ 298 Query: 310 VVAIDLPALHQRSSDIPLLLAHFCQAAAVRYRREVPPWTAAQMQQWQQREWPGNVRELRN 369 V+ I +PAL +R DI + HF + + + P A + Q WPGNVRELRN Sbjct: 299 VLTIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAAA---RLLLQHAWPGNVRELRN 355 Query: 370 FADRWVLGVEQMAGTGLPVGAQPAL-----------------PLPEQVEQFEAGLIAAAL 412 +R + + +G PL + + E +I AL Sbjct: 356 TMERAAVMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEVERVMIERAL 415 Query: 413 KDSEGSVALAAERLGIPRKTLYDKIRK 439 + + G+ A AA RLGI R+ LY ++ + Sbjct: 416 QGAAGNRAEAARRLGISRQQLYRRLEE 442 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 0.320 0.136 0.396 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: 1,478,810 Number of extensions: 67543 Number of successful extensions: 391 Number of sequences better than 1.0e-08: 23 Number of HSP's gapped: 382 Number of HSP's successfully gapped: 23 Length of query: 445 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 357 Effective length of database: 1,203,190 Effective search space: 429538830 Effective search space used: 429538830 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: 132 (55.5 bits)