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= 0001.3715.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... 480 e-137 gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein... 172 4e-44 gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum ser... 110 2e-25 gi|300310145|ref|YP_003774237.1| general secretion pathway prote... 97 2e-21 >gi|300313098|ref|YP_003777190.1| Tfp pilus assembly protein, pilus retraction ATPase PilT protein [Herbaspirillum seropedicae SmR1] Length = 351 Score = 480 bits (1235), Expect = e-137, Method: Compositional matrix adjust. Identities = 258/336 (76%), Positives = 292/336 (86%) Query: 1 MDIATLLAFAVRNQASDLHLCAGLAPLLRVHGAIRRINLQPLEAAQLQQALHAVMPSALH 60 MDIA LLAFAVRNQASDLHLCAG+ PLLRVHGA+RR+NLQ QLQQ L A+MP+ALH Sbjct: 1 MDIAVLLAFAVRNQASDLHLCAGMPPLLRVHGALRRVNLQAPTGPQLQQWLQALMPAALH 60 Query: 61 RRHAAGADCDFSFALPTLGRFRVHAFHQQRGPAAAIRCLGQQPPSLSELAAPPLCAELAL 120 R+A G +CDF+ L LGRFRVHAF +Q GPA AIR LG++PP+L++L APPLCAELA Sbjct: 61 PRYAQGRECDFAIELAALGRFRVHAFLRQGGPAVAIRHLGREPPTLAQLGAPPLCAELAE 120 Query: 121 RPRGLVLVSGPTGAGKSSTLAAMVRHINEMRPVHILTIEDPIEFIHEPRRALVTQREIGT 180 R GLVLV+GPTGAGKSSTLAAM+RH+NE R +HILTIEDPIEFIH P+RAL++QRE+GT Sbjct: 121 RAGGLVLVTGPTGAGKSSTLAAMIRHLNETRALHILTIEDPIEFIHTPQRALISQRELGT 180 Query: 181 HVADFAQALRAALREDPDVLLVGELRDADTIGLALTAAETGHLVLGTLHAASAAKTVDRI 240 H AD ALRAALR DPDVLLVGELRDADTI LALTAAETGHLVLGTLHAASAA+TV+R+ Sbjct: 181 HTADLPAALRAALRADPDVLLVGELRDADTIRLALTAAETGHLVLGTLHAASAARTVERM 240 Query: 241 IDVFPAGEKEAARALLAEALEGVIAQTLLPTVDGLGRVAAHELLVATPAVRNLIREGRNA 300 +DVFPAGEKE ARA+LAE+L+GVIAQTLLPT DG RVAAHELLVATPAVRNLIREGR+A Sbjct: 241 LDVFPAGEKEPARAMLAESLQGVIAQTLLPTADGRARVAAHELLVATPAVRNLIREGRSA 300 Query: 301 QLVSVMQAGGAQAMQTLEASLAALVRQGRISEQTAR 336 QL+S+MQAG AQ MQTLEA+L L +QGRIS QT R Sbjct: 301 QLLSLMQAGAAQGMQTLEAALQRLHQQGRISAQTLR 336 >gi|300310151|ref|YP_003774243.1| twitching mobility PilT protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 172 bits (436), Expect = 4e-44, Method: Compositional matrix adjust. Identities = 101/282 (35%), Positives = 159/282 (56%), Gaps = 6/282 (2%) Query: 6 LLAFAVRNQA-SDLHLCAGLAPLLRVHGAIRRINLQPLEAAQLQQALHAVMPSALHRRHA 64 LLA +Q SD+H+ +L+ + ++ P+ QL L A+ + Sbjct: 15 LLALVNSSQTFSDIHIEQDQPLMLKTPRGWQPVHDMPVVIEQLAPLLSAIDEDWEDKIID 74 Query: 65 AGADCDFSFALPTLGRFRVHAFHQQRGP--AAAIRCLGQQPPSLSELAAPPLCAELALRP 122 DC + R R + + RG A +IR +P +L P + Sbjct: 75 GALDCPYVLGE---WRLRCNIYRMARGSKVAVSIRRFPLEPLALERTGLPSYVKTVLEAT 131 Query: 123 RGLVLVSGPTGAGKSSTLAAMVRHINEMRPVHILTIEDPIEFIHEPRRALVTQREIGTHV 182 +G++LV+GPTGAGK++T+A+M+ +IN R HI+TIE+PIE+ + ++++++Q+E+ T Sbjct: 132 KGIILVTGPTGAGKTTTIASMLDYINASRRGHIITIEEPIEYELQRKQSMISQKEVPTDT 191 Query: 183 ADFAQALRAALREDPDVLLVGELRDADTIGLALTAAETGHLVLGTLHAASAAKTVDRIID 242 F+ LR ALR+ PDVL+VGE+RD DT L A E+GHLVL TLH +SA + + +++ Sbjct: 192 ESFSSGLREALRQKPDVLMVGEIRDFDTADTVLHAGESGHLVLATLHTSSAVRAITKLLG 251 Query: 243 VFPAGEKEAARALLAEALEGVIAQTLLPTVDGLGRVAAHELL 284 FP ++ A LAE+L GVI Q+LLP+ DG V A E++ Sbjct: 252 FFPQEQRAQRAATLAESLVGVIFQSLLPSEDGEHHVMASEMV 293 >gi|300309699|ref|YP_003773791.1| ATPase PilB [Herbaspirillum seropedicae SmR1] Length = 377 Score = 110 bits (275), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 92/261 (35%), Positives = 136/261 (52%), Gaps = 24/261 (9%) Query: 81 FRVHAFHQQRGPAAAIRCLGQQPPSLS--ELAAPPLCAELAL------RPRGLVLVSGPT 132 FRV Q G +R L + +L+ +L P A+L RP G+VL++GPT Sbjct: 100 FRVSTLPTQFGEKIVLRILDTEQATLALEQLGYEP--AQLQALQQAIARPHGMVLMTGPT 157 Query: 133 GAGKSSTLAAMVRHINEMRP-VHILTIEDPIEFIHEPRRALVTQREIGTHVA-DFAQALR 190 G+GK+ +L A ++ +N RP ++I T EDP+E I+ P + Q I +FA ALR Sbjct: 158 GSGKTVSLYACLQRLN--RPGINIATAEDPVE-INLPG---INQVSINERAGLNFAVALR 211 Query: 191 AALREDPDVLLVGELRDADTIGLALTAAETGHLVLGTLHAASAAKTVDRIIDV-FPAGEK 249 A LR+DPDVL+VGE+RD DT +A+ AA+TGHLVL TLH A T+ R++++ PA Sbjct: 212 AFLRQDPDVLMVGEIRDLDTADIAIKAAQTGHLVLSTLHTNDAPATLTRLLNMGVPAYNI 271 Query: 250 EAARALL-AEALEGVIAQTLLPTVDGLGRVAAHELLVATPAVRNLIREGRNAQLVSVMQA 308 A+ +L+ A+ L + P D G H PA + GR + + Sbjct: 272 AASVSLIVAQRLVRRLCSCRRPARDASGSFVPH----GCPACSHTGYRGRTGIYQVMPVS 327 Query: 309 GGAQAMQTLEASLAALVRQGR 329 Q++ +A + RQ R Sbjct: 328 ATMQSLIQAQAGTQDIARQAR 348 >gi|300310145|ref|YP_003774237.1| general secretion pathway protein E [Herbaspirillum seropedicae SmR1] Length = 541 Score = 97.1 bits (240), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 97/292 (33%), Positives = 146/292 (50%), Gaps = 40/292 (13%) Query: 6 LLAFAVRNQASDLHL-----CAGLAPLLRVHGAIRRINLQPLEA-----AQLQQALHAVM 55 LL A R++ASD+HL C + R+H + ++ Q E A L A+ +V Sbjct: 124 LLNKACRSRASDIHLRVRKNCTEI--YFRIHNDLVQVGGQTREYGERLLATLYGAMTSVS 181 Query: 56 PSAL---HRRHAAGADCDFSFALPTLGRFRVHAFHQQRGPAAAIRCLGQ--------QPP 104 S+ R+ AA AD D P L R+ G +R L +P Sbjct: 182 DSSYKPTERQDAAIADRDK--LPPALYGVRIATVPTSEGSVMVLRLLYNDAGDNIDLRPL 239 Query: 105 SLSELAAPPLCAELALRPRGLVLVSGPTGAGKSSTLAAMVRH--INEMRPVHILTIEDPI 162 SE A L +L +P G+ ++SGPTG+GKS+TL ++ I +H+LTIEDP+ Sbjct: 240 GFSEAHASAL-QKLKEQPVGMNIISGPTGSGKSTTLQRVLTGEIIEAEGKLHVLTIEDPV 298 Query: 163 EF-IHEPRRALVTQREIGTHVAD-FAQALRAALREDPDVLLVGELRDADTIGLALTAAET 220 E+ I + VT + FA A+ A+R DPD +++GE+RD T AL A+ T Sbjct: 299 EYPIDGAVQTAVTNAGSEEERSRAFAAAISNAMRLDPDTIMIGEVRDRATAQNALRASMT 358 Query: 221 GHLVLGTLHAASAAKTVDRIIDV-FPAGEKEAARALLAE--ALEGVIAQTLL 269 GH V T+HA SA +DR++D+ PA +L+A+ + G+I+Q L+ Sbjct: 359 GHQVWTTVHANSALAIIDRLLDLGLPA-------SLVADHAVVTGLISQRLV 403 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 0.322 0.134 0.380 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: 891,871 Number of extensions: 31690 Number of successful extensions: 240 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 236 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)