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= 0002.0734.p (434 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/fu... 724 0.0 gi|300312253|ref|YP_003776345.1| GTP-binding protein [Herbaspiri... 69 9e-13 gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein [Herbas... 67 2e-12 gi|300312251|ref|YP_003776343.1| GTP-binding protein [Herbaspiri... 59 8e-10 >gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/furan oxidation) GTPase [Herbaspirillum seropedicae SmR1] Length = 479 Score = 724 bits (1870), Expect = 0.0, Method: Compositional matrix adjust. Identities = 371/468 (79%), Positives = 404/468 (86%), Gaps = 36/468 (7%) Query: 1 MTLDTSPIAAIATAPGRGGIGVVRLSGKNLWPVVQAICGKDESSLAPRHASYLPFKRADG 60 MT D+SPIAAIATAPGRGGIGVVRLSGKNL PV+QA+CG+ +SLAPRHA+YLPF DG Sbjct: 14 MTFDSSPIAAIATAPGRGGIGVVRLSGKNLAPVIQAVCGR--ASLAPRHATYLPFLNEDG 71 Query: 61 SLIDQGLAIYFKAPHSYTGEDVLELQGHGGPVVMQMLLARCLEAGVDIGLRL-------- 112 S IDQGLAI+F APHSYTGEDVLELQGHGGPVVMQMLLARC++AG +IGLRL Sbjct: 72 SAIDQGLAIHFPAPHSYTGEDVLELQGHGGPVVMQMLLARCVQAGSEIGLRLAEPGEFTQ 131 Query: 113 --------------------------AXKSASESLSGAFSKVIHDLVNKVTNLRMLVEAT 146 A KSASESLSGAFSKVIH+LV++VT LRMLVEAT Sbjct: 132 RAFLNDKIDLAQAEAVADLIEATTEAAAKSASESLSGAFSKVIHELVDQVTRLRMLVEAT 191 Query: 147 LDFPEEEIDFLEQSDARGQLAAIRATLDDVFMHASQGALLRDGLNVVLAGKPNVGKSSLL 206 LDFPEEEIDFL+QSDARGQLA IR+TL++VF HA+QGALLRDGLN VLAGKPNVGKSSLL Sbjct: 192 LDFPEEEIDFLKQSDARGQLATIRSTLEEVFKHAAQGALLRDGLNAVLAGKPNVGKSSLL 251 Query: 207 NVLAGSDVAIVTPIAGTTRDKVTETIQIEGMPLNIIDTAGIREAEEDGGGPDEVERIGIE 266 NVLAGSDVAIVTPIAGTTRDKVT+TIQIEGMPLNIIDTAGIREA +DG GPDEVERIGIE Sbjct: 252 NVLAGSDVAIVTPIAGTTRDKVTQTIQIEGMPLNIIDTAGIREAGDDGSGPDEVERIGIE 311 Query: 267 RTWGEVAKADVILHMLDADRGPTLEDEKITERFPDGVPVIRIWNKIDRSGHKPAVDKMSD 326 RTW EVAKADVILHMLDADRGPTLEDEKIT RFPDGVP+IRIWNKIDRSGHK AVDKM D Sbjct: 312 RTWAEVAKADVILHMLDADRGPTLEDEKITSRFPDGVPIIRIWNKIDRSGHKAAVDKMPD 371 Query: 327 ATHIYLSATDQVGIDLLRGELLRIAGWQQTVESRYLARERHLIALKAARDYLESAAMHAS 386 ATH+YLSA++ G+DLLR ELLRIAGWQQTVESRYLARERHL+ALKAA ++L AA HA+ Sbjct: 372 ATHVYLSASEGQGVDLLRAELLRIAGWQQTVESRYLARERHLLALKAADEHLAHAAAHAA 431 Query: 387 VDNQASDKSLDLFAEELRLAQERLSSITGKFTPDDLLGVIFSRFCIGK 434 +DN+A + +LDLFAEELRLAQERLSSITGKFTPDDLLGVIFSRFCIGK Sbjct: 432 LDNEAGEHALDLFAEELRLAQERLSSITGKFTPDDLLGVIFSRFCIGK 479 >gi|300312253|ref|YP_003776345.1| GTP-binding protein [Herbaspirillum seropedicae SmR1] Length = 447 Score = 68.6 bits (166), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 38/107 (35%), Positives = 61/107 (57%), Gaps = 3/107 (2%) Query: 189 GLNVVLAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTETIQIEGMPLNIIDTAGIR 248 G + + G+PNVGKS+L+N L G + I + GTTRD + + EG +IDTAGIR Sbjct: 180 GTKIAIVGRPNVGKSTLVNTLLGEERVIAFDMPGTTRDSIEIPFEREGRHYTLIDTAGIR 239 Query: 249 EAEEDGGGPDEVERIGIERTWGEVAKADVILHMLDADRGPTLEDEKI 295 G + +E+ + +T ++ A+V+L +LDA + + +D I Sbjct: 240 RR---GKVFEAIEKFSVVKTLKSISDANVVLLLLDAQQDISEQDAHI 283 Score = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 41/121 (33%), Positives = 64/121 (52%), Gaps = 6/121 (4%) Query: 192 VVLAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTETIQIEGMPLNIIDTAGIREAE 251 + L G+PNVGKS+L N L S A+V + G TRD+ ++ P +IDT G Sbjct: 5 IALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGFEPVA 64 Query: 252 EDGGGPDEVERIGIERTWGEVAKADVILHMLDADRGPTLEDEKITERFPD-GVPVIRIWN 310 +DG + ++T V +ADV++ ++D +G T D+ IT+ G PV+ + N Sbjct: 65 KDG-----IMYEMAKQTKQAVVEADVVVFIVDGRQGLTPHDKTITDFLRKCGRPVLLVVN 119 Query: 311 K 311 K Sbjct: 120 K 120 >gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein [Herbaspirillum seropedicae SmR1] Length = 309 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 51/169 (30%), Positives = 86/169 (50%), Gaps = 18/169 (10%) Query: 192 VVLAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTETIQIEGMPLNIIDTAGIREAE 251 + + G+PNVGKS+L+NVL G+ V+I + A TTR ++T IE +DT G + Sbjct: 24 IAIVGRPNVGKSTLMNVLVGAKVSITSRKAQTTRHRITGIQTIENTQYVYVDTPGFQTRH 83 Query: 252 EDGGGPDEVERIGIERT-WGEVAKADVILHMLDADR-GPTLEDEKITERFPDGVPVIRIW 309 + + RT + ADVIL +++A GP D+++ + P VP I + Sbjct: 84 SNALNK------TLNRTVTNTLTAADVILFVIEAGTFGPA--DKQVLDLLPANVPCILVL 135 Query: 310 NKIDRSGHKPAVDKMSD--ATH------IYLSATDQVGIDLLRGELLRI 350 NK DR+ K + + A+H + +SA + +D L+ E+ ++ Sbjct: 136 NKADRNKDKTTLMPFAREVASHHDFAAVVPVSAKQRFQLDRLQEEVRKL 184 >gi|300312251|ref|YP_003776343.1| GTP-binding protein [Herbaspirillum seropedicae SmR1] Length = 374 Score = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust. Identities = 52/166 (31%), Positives = 79/166 (47%), Gaps = 17/166 (10%) Query: 188 DGLNVVLAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTETIQI-EGMPLNIIDTAG 246 + +V L G N GKS++ N LA + V + T D + + + E + I DT G Sbjct: 188 ETFSVSLVGYTNAGKSTIFNALAKAGVYAANQLFATL-DTTSRRVYLGEVGHVVISDTVG 246 Query: 247 -IREAEEDGGGPDEVERIGIERTWGEVAKADVILHMLDADRGPTLEDEK-----ITERFP 300 IRE P ++ T E AD++LH++DA +E + + E Sbjct: 247 FIREL------PHQLVE-AFRATLEETIHADLLLHVVDAASPVRMEQIEEVNLVLKEIGA 299 Query: 301 DGVPVIRIWNKIDRSGHKPAV--DKMSDATHIYLSATDQVGIDLLR 344 D VP I +WNKID +G +P V D+ +++SA G+DLLR Sbjct: 300 DHVPQILVWNKIDAAGLEPTVEYDEYGKIQRVFVSAKSGAGLDLLR 345 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 0.388 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: 1,396,926 Number of extensions: 62091 Number of successful extensions: 273 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 268 Number of HSP's successfully gapped: 5 Length of query: 434 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 346 Effective length of database: 1,203,190 Effective search space: 416303740 Effective search space used: 416303740 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)