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= 0124.0004.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|300312421|ref|YP_003776513.1| propionate catabolism operon re... 497 e-142 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 89 4e-19 gi|300313916|ref|YP_003778008.1| two component response regulato... 86 3e-18 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 84 2e-17 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 80 2e-16 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 497 bits (1279), Expect = e-142, Method: Compositional matrix adjust. Identities = 248/315 (78%), Positives = 275/315 (87%), Gaps = 4/315 (1%) Query: 1 MKRHSPQHRDQGDKPVIWTVSVSRLFELFRDITLEFDDQAEIEPIPLGFEDAVRHIRERL 60 MKR +P R DKPVIWTVSVSRL ELFRDITLEFD A+IEPI LGF+DAVR IRERL Sbjct: 1 MKRPAPVDR-HADKPVIWTVSVSRLSELFRDITLEFDALADIEPIHLGFDDAVREIRERL 59 Query: 61 ATERCDAVIAAGSNGAYLKSRLSVPVIIAKASGFDVMQALARARKITPDIGLITYQETMP 120 ATERCD VI+AGSNGAYLKSRL VPVI+A+ASGFDVMQALARAR++T I L+TYQE MP Sbjct: 60 ATERCDVVISAGSNGAYLKSRLPVPVIVARASGFDVMQALARARQLTRRIALVTYQEAMP 119 Query: 121 ALSEFQSTFGLNIAQRTYATEEDARSQISELKAAGIKAIVGAGLITDLAEEAGLAGIFVY 180 AL+EF FGL I QRTYATEEDAR+ ++ELKAAGI+A+ GAGLITDLAEEAG+ GIF+Y Sbjct: 120 ALAEFGQRFGLEIVQRTYATEEDARAVVNELKAAGIEAVAGAGLITDLAEEAGMRGIFLY 179 Query: 181 SAASIRQAFDDALELARLTQLESTRGRSFPVADTLRAKHHINDLRGDSAAMESVRQSVTL 240 SAA++RQAF+DALELARLTQLESTR PVAD+LRA+HH+ DLRGDSA ME+VRQS+TL Sbjct: 180 SAATVRQAFEDALELARLTQLESTRSPILPVADSLRARHHLKDLRGDSAEMETVRQSITL 239 Query: 241 FAKSPATVLIQGETGTGKELAAQAIHRAHPQMQGKVQAHHPFVAVNCGALAESLLESELF 300 FA+SPA VLIQGETGTGKELAAQAIHRAHP MQGK QA HPFVA+NCGALAESLLESELF Sbjct: 240 FARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAESLLESELF 299 Query: 301 GYEEGALXG---GGR 312 GYEEGA G GGR Sbjct: 300 GYEEGAFTGSRRGGR 314 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 89.4 bits (220), Expect = 4e-19, Method: Compositional matrix adjust. Identities = 47/103 (45%), Positives = 68/103 (66%), Gaps = 6/103 (5%) Query: 215 LRAKHHINDLRGDSAAMESVRQSVTLFAKSPATVLIQGETGTGKELAAQAIHRAHPQMQG 274 L+ K+ ++++ G S AM+ V V A S +T+L++GE+GTGKE+ A+AIH P+ G Sbjct: 194 LQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDG 253 Query: 275 KVQAHHPFVAVNCGALAESLLESELFGYEEGALXGGGRPRRSR 317 PF+ VNC AL+E+LLESELFG+E+GA G R+ R Sbjct: 254 ------PFIKVNCAALSETLLESELFGHEKGAFTGAQGERKGR 290 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 86.3 bits (212), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 48/96 (50%), Positives = 59/96 (61%), Gaps = 6/96 (6%) Query: 222 NDLRGDSAAMESVRQSVTLFAKSPATVLIQGETGTGKELAAQAIHRAHPQMQGKVQAHHP 281 N L G+S AM V + + A S ATVL+ GETGTGKEL A+A+HR +A P Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHR------NGARAARP 187 Query: 282 FVAVNCGALAESLLESELFGYEEGALXGGGRPRRSR 317 FVAVNC A+ L+ESELFG+ +GA G PR R Sbjct: 188 FVAVNCAAIPAELIESELFGHVKGAFSGATSPRLGR 223 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 83.6 bits (205), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 63/172 (36%), Positives = 86/172 (50%), Gaps = 14/172 (8%) Query: 147 QISELKAAGIKAIVGAGLIT-DLAEEAGLAGIFVYSAASIRQAFDDALELARLTQLESTR 205 Q + K GI I+ D A A G F Y A D A+EL R ES R Sbjct: 65 QTVKAKHPGIPVIIITAFSDLDSAVSAFQGGAFEYLAKPFD--VDKAVELIRRALDESLR 122 Query: 206 GRSFPVADTLRAKHHINDLRGDSAAMESVRQSVTLFAKSPATVLIQGETGTGKELAAQAI 265 D + ++ G + AM+ V +++ ++S TVLI GE+G+GKEL A+A+ Sbjct: 123 E-----TDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARAL 177 Query: 266 HRAHPQMQGKVQAHHPFVAVNCGALAESLLESELFGYEEGALXGGGRPRRSR 317 H+ P+ A PFVA+N A+ + LLESELFG+E GA G RR R Sbjct: 178 HKHSPR------ASQPFVALNTAAIPKDLLESELFGHERGAFTGAQAMRRGR 223 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 43/95 (45%), Positives = 58/95 (61%), Gaps = 6/95 (6%) Query: 223 DLRGDSAAMESVRQSVTLFAKSPATVLIQGETGTGKELAAQAIHRAHPQMQGKVQAHHPF 282 +L G S A + Q + + A S TVL+ GETGTGKEL A A+H A P +AH P Sbjct: 199 ELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASP------RAHKPM 252 Query: 283 VAVNCGALAESLLESELFGYEEGALXGGGRPRRSR 317 +++NC AL ++L+ESELFG+ GA G RR + Sbjct: 253 ISLNCAALPDTLVESELFGHVRGAFSGAVADRRGK 287 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 0.133 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: 828,048 Number of extensions: 30874 Number of successful extensions: 170 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 159 Number of HSP's successfully gapped: 12 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 130 (54.7 bits)