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= 0003.0071.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|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pil... 468 e-133 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 172 5e-44 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 112 6e-26 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 107 1e-24 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 468 bits (1204), Expect = e-133, Method: Compositional matrix adjust. Identities = 251/338 (74%), Positives = 286/338 (84%) Query: 1 MDIATLLAFAVRNQASDLHLCAGLAPLLRVHGAIRRINLQPLDGAHLQQSLLAVMPAPLQ 60 MDIA LLAFAVRNQASDLHLCAG+ PLLRVHGA+RR+NLQ G LQQ L A+MPA L Sbjct: 1 MDIAVLLAFAVRNQASDLHLCAGMPPLLRVHGALRRVNLQAPTGPQLQQWLQALMPAALH 60 Query: 61 PHYRAGTDCDFALALPGLGRFRIHAFHQQRGPAAAIRPLGQQPPALAELHAPPACAELAT 120 P Y G +CDFA+ L LGRFR+HAF +Q GPA AIR LG++PP LA+L APP CAELA Sbjct: 61 PRYAQGRECDFAIELAALGRFRVHAFLRQGGPAVAIRHLGREPPTLAQLGAPPLCAELAE 120 Query: 121 RPHGLVLVSGPTGSGKSSTLAAMVRLINETRPVHILTLEDPIEFLHTPCRALVSQREIGT 180 R GLVLV+GPTG+GKSSTLAAM+R +NETR +HILT+EDPIEF+HTP RAL+SQRE+GT Sbjct: 121 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGT 180 Query: 181 HVASFAQALRAALREDPDVLLVGELRDTETIRLALTAAETGHLVLATLHAASAARAVDRI 240 H A ALRAALR DPDVLLVGELRD +TIRLALTAAETGHLVL TLHAASAAR V+R+ Sbjct: 181 HTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERM 240 Query: 241 IDAFPEGEKDTARALLAEALQGVVAQVLVPSADGAARVAAHEVLVATAAVRNLIREGRSA 300 +D FP GEK+ ARA+LAE+LQGV+AQ L+P+ADG ARVAAHE+LVAT AVRNLIREGRSA Sbjct: 241 LDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIREGRSA 300 Query: 301 QLLSAMQAGAAQGMQTLQASLSLLVQQGRISAASAREH 338 QLLS MQAGAAQGMQTL+A+L L QQGRISA + R+H Sbjct: 301 QLLSLMQAGAAQGMQTLEAALQRLHQQGRISAQTLRQH 338 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 172 bits (435), Expect = 5e-44, Method: Compositional matrix adjust. Identities = 103/272 (37%), Positives = 153/272 (56%), Gaps = 7/272 (2%) Query: 68 DCDFALALPGLGRFRIHAFHQQRGP--AAAIRPLGQQPPALAELHAPPACAELATRPHGL 125 DC + L G R R + + RG A +IR +P AL P + G+ Sbjct: 78 DCPYVL---GEWRLRCNIYRMARGSKVAVSIRRFPLEPLALERTGLPSYVKTVLEATKGI 134 Query: 126 VLVSGPTGSGKSSTLAAMVRLINETRPVHILTLEDPIEFLHTPCRALVSQREIGTHVASF 185 +LV+GPTG+GK++T+A+M+ IN +R HI+T+E+PIE+ ++++SQ+E+ T SF Sbjct: 135 ILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQSMISQKEVPTDTESF 194 Query: 186 AQALRAALREDPDVLLVGELRDTETIRLALTAAETGHLVLATLHAASAARAVDRIIDAFP 245 + LR ALR+ PDVL+VGE+RD +T L A E+GHLVLATLH +SA RA+ +++ FP Sbjct: 195 SSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKLLGFFP 254 Query: 246 EGEKDTARALLAEALQGVVAQVLVPSADGAARVAAHE-VLVATAAVRNLIREGRSAQLLS 304 + ++ A LAE+L GV+ Q L+PS DG V A E V + I + L+ Sbjct: 255 QEQRAQRAATLAESLVGVIFQSLLPSEDGEHHVMASEMVFNNNQQIAAFISDPAKLHLIG 314 Query: 305 AMQAGAAQGM-QTLQASLSLLVQQGRISAASA 335 M ++L L LV + +SA A Sbjct: 315 DFMKRKEDNMSRSLNEVLLQLVHKKSVSARDA 346 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 112 bits (279), Expect = 6e-26, Method: Compositional matrix adjust. Identities = 94/256 (36%), Positives = 133/256 (51%), Gaps = 26/256 (10%) Query: 3 IATLLAFAVRNQASDLHLCAGLAPL-------LRVHGAIRRINLQPLDGAHLQQSLLAVM 55 + LLA AV ASDLH P LR+ G + + PL + L ++ Sbjct: 18 LYKLLADAVSMGASDLHF----EPFEHYCRVRLRIDGILHELAQPPLSLKDKLATRLKIL 73 Query: 56 PAPLQPHYRAGTDCDFALALPGLG-RFRIHAFHQQRGPAAAIRPLG--QQPPALAELHAP 112 R D LAL FR+ Q G +R L Q AL +L Sbjct: 74 ARLDIAEKRLPQDGKMRLALETRTVDFRVSTLPTQFGEKIVLRILDTEQATLALEQLGYE 133 Query: 113 PA----CAELATRPHGLVLVSGPTGSGKSSTLAAMVRLINETRP-VHILTLEDPIEFLHT 167 PA + RPHG+VL++GPTGSGK+ +L A ++ +N RP ++I T EDP+E ++ Sbjct: 134 PAQLQALQQAIARPHGMVLMTGPTGSGKTVSLYACLQRLN--RPGINIATAEDPVE-INL 190 Query: 168 PCRALVSQREIGTHVA-SFAQALRAALREDPDVLLVGELRDTETIRLALTAAETGHLVLA 226 P ++Q I +FA ALRA LR+DPDVL+VGE+RD +T +A+ AA+TGHLVL+ Sbjct: 191 PG---INQVSINERAGLNFAVALRAFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLS 247 Query: 227 TLHAASAARAVDRIID 242 TLH A + R+++ Sbjct: 248 TLHTNDAPATLTRLLN 263 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 107 bits (268), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 86/263 (32%), Positives = 131/263 (49%), Gaps = 32/263 (12%) Query: 6 LLAFAVRNQASDLHL-----CAGLAPLLRVHGAIRRINLQPLD-GAHLQQSLLAVMPAPL 59 LL A R++ASD+HL C + R+H + ++ Q + G L +L M + Sbjct: 124 LLNKACRSRASDIHLRVRKNCTEI--YFRIHNDLVQVGGQTREYGERLLATLYGAMTSVS 181 Query: 60 QPHYRAGTDCDFALAL-----PGLGRFRIHAFHQQRGPAAAIRPLGQ--------QPPAL 106 Y+ D A+A P L RI G +R L +P Sbjct: 182 DSSYKPTERQDAAIADRDKLPPALYGVRIATVPTSEGSVMVLRLLYNDAGDNIDLRPLGF 241 Query: 107 AELHAPPACAELATRPHGLVLVSGPTGSGKSSTLAAMV--RLINETRPVHILTLEDPIEF 164 +E HA A +L +P G+ ++SGPTGSGKS+TL ++ +I +H+LT+EDP+E+ Sbjct: 242 SEAHAS-ALQKLKEQPVGMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPVEY 300 Query: 165 -----LHTPCRALVSQREIGTHVASFAQALRAALREDPDVLLVGELRDTETIRLALTAAE 219 + T S+ E +FA A+ A+R DPD +++GE+RD T + AL A+ Sbjct: 301 PIDGAVQTAVTNAGSEEE---RSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASM 357 Query: 220 TGHLVLATLHAASAARAVDRIID 242 TGH V T+HA SA +DR++D Sbjct: 358 TGHQVWTTVHANSALAIIDRLLD 380 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 0.321 0.133 0.377 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: 899,016 Number of extensions: 34063 Number of successful extensions: 258 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 254 Number of HSP's successfully gapped: 4 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 131 (55.1 bits)