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= 0124.0007.p (448 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... 739 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 208 7e-55 gi|300314016|ref|YP_003778108.1| two component transcription reg... 201 8e-53 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 161 8e-41 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 154 2e-38 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 739 bits (1908), Expect = 0.0, Method: Compositional matrix adjust. Identities = 392/502 (78%), Positives = 410/502 (81%), Gaps = 56/502 (11%) Query: 1 MKPIWIVDDDESIRWVLEKALARXLSYATHNLFSSARDAMQALETGTPQVLVSDIRMPGA 60 MKPIWIVDDDESIRWVLEKALAR + AT + FSSARDA+ AL+ GTPQVLVSDIRMPGA Sbjct: 1 MKPIWIVDDDESIRWVLEKALARE-NLATQS-FSSARDAIAALQNGTPQVLVSDIRMPGA 58 Query: 61 SGLELLQTIKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALE 120 SGLELLQT+KAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRAL+ Sbjct: 59 SGLELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRALD 118 Query: 121 ESLRETDVEQSSANAPEILGQAPAMQDVFRAIGRLSQSNVTVLITG-------------- 166 ESLRETD+EQ +A PEILGQAPAMQDVFRAIGRLSQSNVTVLITG Sbjct: 119 ESLRETDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALH 178 Query: 167 -------------------------------------XQAMRRGRFEQAEGGTLFLDEIG 189 QAMRRGRFEQAEGGTLFLDEIG Sbjct: 179 KHSPRASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIG 238 Query: 190 DMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEHRVREGLFREDLYHRLN 249 DMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLE RVREGLFREDLYHRLN Sbjct: 239 DMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLN 298 Query: 250 VIRLRLPSLRERSEDIPILARHFLTQSARQLGVEAKRLSPQAMQFLSQLELPGNVRQLEN 309 VIRLRLPSLRERSEDIPILAR+FL QSARQLGVEAKRLSPQAMQFLSQLE PGNVRQLEN Sbjct: 299 VIRLRLPSLRERSEDIPILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLEN 358 Query: 310 LCNWITVMAPGQTVEVKDLPQDLIEERSSNFQPAQTHAASSTAPAEAHSGAGVSAGY--- 366 LCNWITVMAPGQTVE+KDLPQDL+EER QPAQT AA ++A A + + G Sbjct: 359 LCNWITVMAPGQTVEIKDLPQDLVEERVHAPQPAQTVAAPASAAALPTAYTEPAPGVASA 418 Query: 367 DGDAGADRSWISLLETEAAQMLAEERPEVMDILGRQFEATLIKIALKHTHGRKNDAAVRL 426 D A SWI+LLETEAAQMLA E+PEVMDILGRQFEA LIK+ALKHTHGRKNDAAVRL Sbjct: 419 SADGAAGASWITLLETEAAQMLASEQPEVMDILGRQFEAALIKVALKHTHGRKNDAAVRL 478 Query: 427 GIGRNTITRKIQELGIGGAEDD 448 GIGRNTITRKIQELGIGGAEDD Sbjct: 479 GIGRNTITRKIQELGIGGAEDD 500 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 208 bits (530), Expect = 7e-55, Method: Compositional matrix adjust. Identities = 136/383 (35%), Positives = 200/383 (52%), Gaps = 64/383 (16%) Query: 1 MKPIWIVDDDESIRWVLEKALARXLSYATHNLFSSARDA--MQALETGTPQVLVSDIRMP 58 M I IVDDD + R +LA +S H++ + A ++ L + D+RMP Sbjct: 1 MARILIVDDDAAFR----GSLAETVSDLGHDVLEAGSTAAGLKLLAAHAVDAAIVDLRMP 56 Query: 59 GASGLELLQTIKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDKAVELIRRA 118 GL LQ A IP I++TA++ D+ + A + GAF++L KP VE + RA Sbjct: 57 DEDGLAFLQRAPAI-AAIPCIMLTAYASGDNTIEAIRLGAFDHLTKPVPRAALVETLERA 115 Query: 119 LEESLRETDVEQSSANA-PEILGQAPAMQDVFRAIGRLSQSNVTVLI------------- 164 L + + +++G++ AM+ VF+ IGR + S+ TVL+ Sbjct: 116 LRQGASTPAAASPATEERNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVAR 175 Query: 165 --------------------------------------TGXQAMRRGRFEQAEGGTLFLD 186 +G + R GRF++A+GGTLFLD Sbjct: 176 ALHRNGARAARPFVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLD 235 Query: 187 EIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEHRVREGLFREDLYH 246 EIGDM L Q ++LRVL + VGG+QS++ +VRVIAATH++L+H + +G FREDL++ Sbjct: 236 EIGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWY 295 Query: 247 RLNVIRLRLPSLRERSEDIPILARHFLTQSARQLGVEA-KRLSPQAMQFLSQLELPGNVR 305 RL V+ + +P+LRER DI +A HFL RQLG +A KR+SP A + L Q PGNVR Sbjct: 296 RLQVLTIMVPALRERPGDILTIAEHFL----RQLGGDAPKRISPAAARLLLQHAWPGNVR 351 Query: 306 QLENLCNWITVMAPGQTVEVKDL 328 +L N VM+ G +E +D+ Sbjct: 352 ELRNTMERAAVMSHGLCIEAEDI 374 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 201 bits (512), Expect = 8e-53, Method: Compositional matrix adjust. Identities = 123/334 (36%), Positives = 173/334 (51%), Gaps = 50/334 (14%) Query: 35 SARDAMQALETGTPQVLVSDIRMPGASGLELLQTIKAKHPGIPVIIITAFSDLDSAVSAF 94 SA A+ L P ++++D+R+PG GL L I++++P +PVI++TA + AV A Sbjct: 42 SAEAALAQLAISLPALVITDVRLPGMDGLALFAEIRSRYPALPVILLTAHGTIPDAVDAT 101 Query: 95 QGGAFEYLAKPFD----VDKAVELIRRALEESLR-----ETDVEQSSANAPEILGQAPAM 145 GAF YL KPFD +DK + + A L D+ S E+L +A + Sbjct: 102 TQGAFAYLTKPFDGHVLLDKVAQALSLAAPAPLSPDQSWRADILSRSQRVAELLAEARLV 161 Query: 146 ---------------------QDVFRAIGRLSQSNVTV--------------------LI 164 + + RA R Q + V Sbjct: 162 AASDASILIRGDSGTGKELLARAIHRASARAEQPFIAVNCGAIPEQLLESELFGHVKGAF 221 Query: 165 TGXQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVI 224 TG R G F+ A GGTLFLDEIGDMPL LQ +LLRVL + +VG +Q+ + +VR+I Sbjct: 222 TGAVEHREGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVRQVGANQAGEVDVRII 281 Query: 225 AATHQNLEHRVREGLFREDLYHRLNVIRLRLPSLRERSEDIPILARHFLTQSARQLGVEA 284 +ATH++LE +REG FREDLY+RLNV+ L LP+L ER EDI +LA HFL A + Sbjct: 282 SATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLANHFLKTIAAKYPKRL 341 Query: 285 KRLSPQAMQFLSQLELPGNVRQLENLCNWITVMA 318 +P A++ LS PGNVRQL N+ + ++ Sbjct: 342 TGFAPDALEILSLAHWPGNVRQLYNVVEQVCALS 375 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 161 bits (408), Expect = 8e-41, Method: Compositional matrix adjust. Identities = 125/395 (31%), Positives = 189/395 (47%), Gaps = 78/395 (19%) Query: 2 KP-IWIVDDD----ESIRWVLEKALARXLSYATHNLFSSARD-AMQALETGTPQVLVSDI 55 KP + IV+DD + +RW L+ A L + R+ A+ + P V+ D+ Sbjct: 5 KPKLLIVEDDPGLQKQLRWSLD---------AYEVLVAGDRESALAMVRRHEPAVVTMDL 55 Query: 56 RMP----GAS-GLELLQTIKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFDVDK 110 +P GAS G LQ + A P VI++T D AV A GA+++ KP +D+ Sbjct: 56 GLPPDPDGASEGFATLQQVLALAPDTKVIMLTGNQDHAHAVKAISMGAYDFHQKPC-IDE 114 Query: 111 AVELI-RRALE-ESLRETDVEQSSANAPEILG----QAPAMQDVFRAIGRLSQSNVTVLI 164 + L+ +RA +L+ + A LG + M V R+I +++ S+ +V++ Sbjct: 115 TLRLVVQRAFYLHALQRENQRMQQAGGHTALGGLITRDAGMLAVCRSIEKVAPSSASVML 174 Query: 165 -----TGXQAMRR----------------------------------------------G 173 TG + + R G Sbjct: 175 LGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQTIG 234 Query: 174 RFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEH 233 + E A GGT FLDE+GD+P+ LQ +LLR L + RVGGH + +VRVI ATHQNL+ Sbjct: 235 KVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQNLKE 294 Query: 234 RVREGLFREDLYHRLNVIRLRLPSLRERSEDIPILARHFLTQSARQLGVEAKRLSPQAMQ 293 G FREDLY+RL I +++P+L+ER D +LARHF+ + + G LS A+ Sbjct: 295 LTASGGFREDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKEGRATLHLSQDAVA 354 Query: 294 FLSQLELPGNVRQLENLCNWITVMAPGQTVEVKDL 328 + + E PGNVR++EN +MA GQ + +DL Sbjct: 355 AIERYEWPGNVREMENCVMRAVIMADGQQITAEDL 389 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 154 bits (388), Expect = 2e-38, Method: Compositional matrix adjust. Identities = 79/169 (46%), Positives = 109/169 (64%), Gaps = 3/169 (1%) Query: 165 TGXQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVI 224 TG R GRFE A+GGTLFLDE+G + L Q +LLRVL +G F RVG + +K +VRV+ Sbjct: 342 TGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVV 401 Query: 225 AATHQNLEHRVREGLFREDLYHRLNVIRLRLPSLRERSEDIPILARHFLTQSARQLGVEA 284 AAT+++L VREG FR+DL+ RLNV + LP LRER +DIP+L HFL ++ G+ Sbjct: 402 AATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAV 461 Query: 285 KRLSPQAMQFLSQLELPGNVRQLENLCNWITVMAPGQTVEVKDLPQDLI 333 + + +A+Q L PGN+R+L+NL ++A G + DLP I Sbjct: 462 RGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPL---DLPHMFI 507 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 0.134 0.378 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: 1,368,174 Number of extensions: 55847 Number of successful extensions: 381 Number of sequences better than 1.0e-08: 25 Number of HSP's gapped: 398 Number of HSP's successfully gapped: 29 Length of query: 448 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 360 Effective length of database: 1,203,190 Effective search space: 433148400 Effective search space used: 433148400 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)