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= 0001.3095.p (499 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 939 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 301 8e-83 gi|300314016|ref|YP_003778108.1| two component transcription reg... 293 2e-80 gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport resp... 276 3e-75 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 259 5e-70 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 939 bits (2427), Expect = 0.0, Method: Compositional matrix adjust. Identities = 480/502 (95%), Positives = 486/502 (96%), Gaps = 5/502 (0%) Query: 1 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDAMAALQNGTPQVLVSDIRMPGASG 60 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDA+AALQNGTPQVLVSDIRMPGASG Sbjct: 1 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASG 60 Query: 61 LELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES 120 LELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES Sbjct: 61 LELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES 120 Query: 121 LRETDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKH 180 LRETDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKH Sbjct: 121 LRETDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKH 180 Query: 181 SPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDM 240 SPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDM Sbjct: 181 SPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDM 240 Query: 241 PLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVI 300 PLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVI Sbjct: 241 PLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVI 300 Query: 301 RLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLC 360 RLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLC Sbjct: 301 RLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLC 360 Query: 361 NWITVMAPGQTVEIKDLPQDLVEERVHAPQPAQIVAAPASASALAAPLAYAEAAPGA--- 417 NWITVMAPGQTVEIKDLPQDLVEERVHAPQPAQ VAAPASA+AL AY E APG Sbjct: 361 NWITVMAPGQTVEIKDLPQDLVEERVHAPQPAQTVAAPASAAALPT--AYTEPAPGVASA 418 Query: 418 TTAEAGSSSWISLLETEAAQMLASEQPEVMDILGRQFEAALIKIALKHTHGRKNDAAVRL 477 + A +SWI+LLETEAAQMLASEQPEVMDILGRQFEAALIK+ALKHTHGRKNDAAVRL Sbjct: 419 SADGAAGASWITLLETEAAQMLASEQPEVMDILGRQFEAALIKVALKHTHGRKNDAAVRL 478 Query: 478 GIGRNTITRKIQELGIGGAEDD 499 GIGRNTITRKIQELGIGGAEDD Sbjct: 479 GIGRNTITRKIQELGIGGAEDD 500 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 301 bits (771), Expect = 8e-83, Method: Compositional matrix adjust. Identities = 168/379 (44%), Positives = 241/379 (63%), Gaps = 7/379 (1%) Query: 1 MKPIWIVDDDESIRWVLEKALARENLATQSFSSARDAMAALQNGTPQVLVSDIRMPGASG 60 M I IVDDD + R L + ++ S + L + D+RMP G Sbjct: 1 MARILIVDDDAAFRGSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMPDEDG 60 Query: 61 LELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES 120 L LQ A IP I++TA++ D+ + A + GAF++L KP VE + RAL + Sbjct: 61 LAFLQRAPAI-AAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERALRQG 119 Query: 121 LRETDIEQGAAQT-PEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHK 179 A + +++G++ AM+ VF+ IGR + S+ TVL+ GE+G+GKELVARALH+ Sbjct: 120 ASTPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHR 179 Query: 180 HSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGD 239 + RA++PFVA+N AAIP +L+ESELFGH +GAF+GA + R GRF++A+GGTLFLDEIGD Sbjct: 180 NGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGD 239 Query: 240 MPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNV 299 M L Q ++LRVL + VGG+QS++ +VRVIAATH++L+ + +G FREDL++RL V Sbjct: 240 MELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQV 299 Query: 300 IRLRLPSLRERSEDIPILARYFLAQSARQLGVEA-KRLSPQAMQFLSQLEFPGNVRQLEN 358 + + +P+LRER DI +A +FL RQLG +A KR+SP A + L Q +PGNVR+L N Sbjct: 300 LTIMVPALRERPGDILTIAEHFL----RQLGGDAPKRISPAAARLLLQHAWPGNVRELRN 355 Query: 359 LCNWITVMAPGQTVEIKDL 377 VM+ G +E +D+ Sbjct: 356 TMERAAVMSHGLCIEAEDI 374 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 293 bits (751), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 160/370 (43%), Positives = 230/370 (62%), Gaps = 26/370 (7%) Query: 30 SFSSARDAMAALQNGTPQVLVSDIRMPGASGLELLQTVKAKHPGIPVIIITAFSDLDSAV 89 + SA A+A L P ++++D+R+PG GL L +++++P +PVI++TA + AV Sbjct: 39 AVESAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPALPVILLTAHGTIPDAV 98 Query: 90 SAFQGGAFEYLAKPFDVDKAVELIRRAL----------DESLRETDIEQGAAQTPEILGQ 139 A GAF YL KPFD ++ + +AL D+S R DI + + E+L + Sbjct: 99 DATTQGAFAYLTKPFDGHVLLDKVAQALSLAAPAPLSPDQSWR-ADILSRSQRVAELLAE 157 Query: 140 APAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALNTAAIPKD 199 A + + S+ ++LI G+SG+GKEL+ARA+H+ S RA QPF+A+N AIP+ Sbjct: 158 ARLV----------AASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAIPEQ 207 Query: 200 LLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYR 259 LLESELFGH +GAFTGA R G F+ A GGTLFLDEIGDMPL LQ +LLRVL + + Sbjct: 208 LLESELFGHVKGAFTGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVRQ 267 Query: 260 VGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSEDIPILAR 319 VG +Q+ + +VR+I+ATH++LE +REG FREDLY+RLNV+ L LP+L ER EDI +LA Sbjct: 268 VGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLAN 327 Query: 320 YFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLCNWITVMAPGQTVEIKDLPQ 379 +FL A + +P A++ LS +PGNVRQL N+ + ++ + P Sbjct: 328 HFLKTIAAKYPKRLTGFAPDALEILSLAHWPGNVRQLYNVVEQVCALSTAPLI-----PA 382 Query: 380 DLVEERVHAP 389 LV+ + P Sbjct: 383 SLVQRALRTP 392 >gi|300312654|ref|YP_003776746.1| C4-dicarboxylate transport response regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 445 Score = 276 bits (706), Expect = 3e-75, Method: Compositional matrix adjust. Identities = 152/365 (41%), Positives = 227/365 (62%), Gaps = 8/365 (2%) Query: 6 IVDDDESIRWVLEKALARENLATQSFSSARDAMAALQNGTPQVLVSDIRMPGASGLELLQ 65 +++D++++R +AL A + SA +A+ + V+VSD+R+PG SGL++L Sbjct: 12 LIEDEQTVRRATAQALELGGFAVTACGSAEEALPLITRDFAGVVVSDVRLPGLSGLDVLA 71 Query: 66 TVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALDES---LR 122 V A +PVI++T D+ AV A + GA++++ KPF D +E+ RA ++ L Sbjct: 72 RVVAIDHDLPVIVVTGHGDVGMAVEAMRAGAYDFVEKPFSSDTLLEIALRAQEKRNLVLE 131 Query: 123 ETDIEQGAAQTPEI---LGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHK 179 + + A PE+ +GQ+PA++ V I L ++V VLI G++G+GKE+VAR LH Sbjct: 132 NRRLREAWAHDPELPPLVGQSPAIERVRTLIRSLGPADVDVLINGQTGTGKEVVARQLHA 191 Query: 180 HSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGD 239 S R PFVALN A+P+ + ESE+FGHE GAFTGAQ R G+ E A GGTLFLDEI Sbjct: 192 ASGRKG-PFVALNCGALPETVFESEIFGHEPGAFTGAQKRRIGKLEYANGGTLFLDEIES 250 Query: 240 MPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNV 299 MPL LQ +LLRVL + R+GG++S+ + RV+AA+ +L + EG FREDLY+R+ V Sbjct: 251 MPLALQVKLLRVLQERRLERLGGNESVAIDCRVVAASKADLLKLAAEGQFREDLYYRIGV 310 Query: 300 IRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 + + LP+L +R EDI +L +F +A + E+ S MQ Q ++PGNVR+L N Sbjct: 311 VAIDLPALNQRREDIALLLAHFCQAAAVRYRRESPAWSAAQMQQWQQRDWPGNVRELRNF 370 Query: 360 CN-WI 363 + W+ Sbjct: 371 ADRWV 375 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 259 bits (661), Expect = 5e-70, Method: Compositional matrix adjust. Identities = 161/392 (41%), Positives = 237/392 (60%), Gaps = 23/392 (5%) Query: 2 KP-IWIVDDD----ESIRWVLEKALARENLATQSFSSARDAMAALQNGTPQVLVSDIRMP 56 KP + IV+DD + +RW L+ A E L SA +A ++ P V+ D+ +P Sbjct: 5 KPKLLIVEDDPGLQKQLRWSLD---AYEVLVAGDRESA---LAMVRRHEPAVVTMDLGLP 58 Query: 57 ----GAS-GLELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVE 111 GAS G LQ V A P VI++T D AV A GA+++ KP +D+ + Sbjct: 59 PDPDGASEGFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPC-IDETLR 117 Query: 112 LI-RRA--LDESLRETD-IEQGAAQTP--EILGQAPAMQDVFRAIGRLSQSNVTVLITGE 165 L+ +RA L RE ++Q T ++ + M V R+I +++ S+ +V++ G Sbjct: 118 LVVQRAFYLHALQRENQRMQQAGGHTALGGLITRDAGMLAVCRSIEKVAPSSASVMLLGS 177 Query: 166 SGSGKELVARALHKHSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFE 225 SG+GKE++ARALH+ SPR+ + F+A+N AAIP++LLESELFG+E+GAFTGA G+ E Sbjct: 178 SGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIGKVE 237 Query: 226 QAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVR 285 A GGT FLDE+GD+P+ LQ +LLR L + RVGGH + +VRVI ATHQNL++ Sbjct: 238 LAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKELTA 297 Query: 286 EGLFREDLYHRLNVIRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLS 345 G FREDLY+RL I +++P+L+ER D +LAR+F+ + + G LS A+ + Sbjct: 298 SGGFREDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVAAIE 357 Query: 346 QLEFPGNVRQLENLCNWITVMAPGQTVEIKDL 377 + E+PGNVR++EN +MA GQ + +DL Sbjct: 358 RYEWPGNVREMENCVMRAVIMADGQQITAEDL 389 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 0.318 0.133 0.373 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: 1,363,309 Number of extensions: 52648 Number of successful extensions: 435 Number of sequences better than 1.0e-08: 30 Number of HSP's gapped: 435 Number of HSP's successfully gapped: 30 Length of query: 499 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 410 Effective length of database: 1,198,455 Effective search space: 491366550 Effective search space used: 491366550 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 (21.7 bits) S2: 132 (55.5 bits)