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= 0048.0001.p (342 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310378|ref|YP_003774470.1| transcription regulator protein... 289 3e-79 gi|300310376|ref|YP_003774468.1| outer membrane porin [Herbaspir... 244 9e-66 gi|300310493|ref|YP_003774585.1| transcription regulator protein... 66 5e-12 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 57 2e-09 gi|300309916|ref|YP_003774008.1| transcription regulator protein... 55 9e-09 >gi|300310378|ref|YP_003774470.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 282 Score = 289 bits (739), Expect = 3e-79, Method: Compositional matrix adjust. Identities = 141/162 (87%), Positives = 150/162 (92%) Query: 173 NNGGGNANXPPPLDKGLDILELLSKSEQMLTLNQISKQLGRSVNEIFRMVVTLEQRGYLI 232 ++ G P LDKGLDILELLS+SEQMLTLNQIS+QLGRSVNEIFRMVVTLEQRGYLI Sbjct: 24 SSSGKTRYAAPALDKGLDILELLSRSEQMLTLNQISRQLGRSVNEIFRMVVTLEQRGYLI 83 Query: 233 ADNDQYRLSLKLFELAHNNQPIRSLVSTALPHMRELANRTMQSTHLTVYEAGRVIVVAQV 292 ADND YRLSLKLFELAH++QPIRSLVSTALPHMRELA+R +QSTHLTVYEAGRVIVVAQV Sbjct: 84 ADNDHYRLSLKLFELAHHHQPIRSLVSTALPHMRELASRAVQSTHLTVYEAGRVIVVAQV 143 Query: 293 DSPERWAFGLKVGALVSLTDTASGHVLLSFRDEAERGRMLAA 334 DSPERWAFGLKVGALVSLTDTASGHVLL+FRDEAER MLAA Sbjct: 144 DSPERWAFGLKVGALVSLTDTASGHVLLAFRDEAERAAMLAA 185 >gi|300310376|ref|YP_003774468.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 355 Score = 244 bits (622), Expect = 9e-66, Method: Compositional matrix adjust. Identities = 123/176 (69%), Positives = 134/176 (76%), Gaps = 19/176 (10%) Query: 4 NDVWFLDPTGQQFIGTATLVRGRNWQGADNVIEYQTPTWGGFNATFQTALGEQAGSI--- 60 NDVWFLDPTGQQ+IGTA LVRGRNW GA NVIEY TPT+GGF AT QT+LGE AGS Sbjct: 122 NDVWFLDPTGQQWIGTANLVRGRNWPGASNVIEYTTPTFGGFGATVQTSLGEAAGSFSKG 181 Query: 61 ----KNKRKDGVSLVYQNQGLELRAIYDLIRDSNGKYGSGLNSDGTRNTVFDTSKELILG 116 K RKDG+SLVYQN GLELR IYD+IRD+NG+Y V+DTSKELILG Sbjct: 182 GTSTKYGRKDGLSLVYQNNGLELRGIYDVIRDANGRY----------TDVYDTSKELILG 231 Query: 117 GTYTIDKLKLFLGYENLRAPD--VAPGSPDKVNHYWLGANYQVTPALTLIGSVFRV 170 GTY IDKLK+FLGYENLRAPD A G PD+VNHYWLGANY VTP L+GSVF V Sbjct: 232 GTYKIDKLKMFLGYENLRAPDANTASGVPDRVNHYWLGANYDVTPQFQLVGSVFHV 287 >gi|300310493|ref|YP_003774585.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 263 Score = 65.9 bits (159), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 47/160 (29%), Positives = 79/160 (49%), Gaps = 2/160 (1%) Query: 185 LDKGLDILELLSKSEQMLTLNQISKQLGRSVNEIFRMVVTLEQRGYLIA--DNDQYRLSL 242 L+KGL +L + + +TL ++ G S + RMV TLE GY+ +Y+L+ Sbjct: 17 LEKGLAVLRAFNAQHRTMTLGDVASATGISKSSAQRMVHTLETLGYICKHPKTRRYQLTP 76 Query: 243 KLFELAHNNQPIRSLVSTALPHMRELANRTMQSTHLTVYEAGRVIVVAQVDSPERWAFGL 302 K+ E+ +N LV A P + ELAN T ++ +LT G ++ VA+ + + + Sbjct: 77 KVMEVGYNYLAADILVDVANPFLSELANITGETVNLTEPYDGEMVYVARFVASKFIPIHM 136 Query: 303 KVGALVSLTDTASGHVLLSFRDEAERGRMLAAXAGVFHFP 342 +G+ + + TASG LS + E +L + H P Sbjct: 137 PIGSRIPMYCTASGRAYLSALEPEEAQAILESSERTVHTP 176 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 52/182 (28%), Positives = 80/182 (43%), Gaps = 18/182 (9%) Query: 30 GADNVIEYQTPTWGGFNATFQTALGEQAGSIKNKRKDGVSLVYQNQGLELRAIYDLIRDS 89 G N+++YQ + G GE AG +N K GV L + + A YD R+ Sbjct: 158 GVSNLVKYQGE-FSGVKIGAMYGFGEVAGETRNGAKYGVGLGWGTGPFSVVATYD--RN- 213 Query: 90 NGKYGSGLNSDGTRNTVFDTSKELILGGTYT-IDKLKLFLGYENLRAPDVAPGSPD-KVN 147 NS NT +D + L Y + K LGY + +A G+ D + + Sbjct: 214 --------NSATATNTPYDRATSAHLAAGYQPSEAWKFNLGYRYYK-KSLATGAADLRSD 264 Query: 148 HYWLGANYQVTPALTLIGSVFRVNVNNGGGNANXPPPLDKGLDILELLSKSEQMLTLNQI 207 +W GA Y+ TPA+TLIG+++ N+ N AN P+ L + +SK + Sbjct: 265 FFWGGAAYKFTPAMTLIGAIYYQNIKN---VANDADPIMYSLRLKYAMSKRTDLYLSTAY 321 Query: 208 SK 209 +K Sbjct: 322 AK 323 >gi|300309916|ref|YP_003774008.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 265 Score = 55.1 bits (131), Expect = 9e-09, Method: Compositional matrix adjust. Identities = 34/150 (22%), Positives = 76/150 (50%), Gaps = 2/150 (1%) Query: 185 LDKGLDILELLSKSEQMLTLNQISKQLGRSVNEIFRMVVTLEQRGYLIAD--NDQYRLSL 242 K + +L+L++ + L + Q++ G ++R++ L G ++ + N QY + Sbjct: 20 FSKFMVVLQLIADQDAPLNIAQLAALSGYPRPTVYRILAALMAEGMVVENPRNKQYEVGP 79 Query: 243 KLFELAHNNQPIRSLVSTALPHMRELANRTMQSTHLTVYEAGRVIVVAQVDSPERWAFGL 302 +L LA + +TA+ +R+L + T ++ HL V ++ + +++SP+ Sbjct: 80 RLINLASRAWDRSDIRTTAIESLRQLRDLTRETVHLAVPSDHSMVYIEKLESPQAVRMDS 139 Query: 303 KVGALVSLTDTASGHVLLSFRDEAERGRML 332 ++G V+L ++ G L+ +EA R R++ Sbjct: 140 RIGTRVTLYSSSVGKAYLAGLEEAHRERLM 169 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 0.136 0.399 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: 996,284 Number of extensions: 38924 Number of successful extensions: 137 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 135 Number of HSP's successfully gapped: 6 Length of query: 342 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 256 Effective length of database: 1,212,660 Effective search space: 310440960 Effective search space used: 310440960 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: 131 (55.1 bits)