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= 0001.2893.p (561 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312224|ref|YP_003776316.1| peptide chain release factor 3 ... 1088 0.0 gi|300313617|ref|YP_003777709.1| translation elongation factor [... 176 4e-45 gi|300309453|ref|YP_003773545.1| elongation factor G1 [Herbaspir... 155 6e-39 gi|300311258|ref|YP_003775350.1| GTP-binding elongation factor p... 96 9e-21 gi|300312895|ref|YP_003776987.1| GTP-binding elongation factor p... 82 1e-16 >gi|300312224|ref|YP_003776316.1| peptide chain release factor 3 [Herbaspirillum seropedicae SmR1] Length = 530 Score = 1088 bits (2814), Expect = 0.0, Method: Compositional matrix adjust. Identities = 525/530 (99%), Positives = 530/530 (100%) Query: 32 LIAREVKRRRTFGIISHPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEK 91 +IAREVKRRRTFGIISHPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEK Sbjct: 1 MIAREVKRRRTFGIISHPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEK 60 Query: 92 QRGISVASSVMQFEYRDHVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQTI 151 QRGISVASSVMQFEYRDHVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQTI Sbjct: 61 QRGISVASSVMQFEYRDHVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQTI 120 Query: 152 KLLNVCRMRNTPIITFMNKLDRETRDSLELLDELESVLKIQCAPVTWPIGMGKNFRGVYH 211 KLLNVCRMRNTPIITFMNKLDRETRDSLELLDELESVLKIQCAPVTWPIGMGKNFRGVYH Sbjct: 121 KLLNVCRMRNTPIITFMNKLDRETRDSLELLDELESVLKIQCAPVTWPIGMGKNFRGVYH 180 Query: 212 LLRDEIMLFKAGEERANGSVEIIKGIDNPKLAEMFPLEIEQLKMEVELVHGASHPFNLDD 271 LLRDEIMLFKAGEERANG+VEIIKGIDNPKLAEMFPLEIEQLKMEVELVHGASHPFNLDD Sbjct: 181 LLRDEIMLFKAGEERANGNVEIIKGIDNPKLAEMFPLEIEQLKMEVELVHGASHPFNLDD 240 Query: 272 FLAGIQTPVFFGSAINNFGVREILDALLDWAPGPGGRDATVREVKPTEEPFSGFVFKIQA 331 FLAG+QTPVFFGSAINNFGVREILDALLDWAPGPGGRDATVREVKPTEEPFSGFVFKIQA Sbjct: 241 FLAGVQTPVFFGSAINNFGVREILDALLDWAPGPGGRDATVREVKPTEEPFSGFVFKIQA 300 Query: 332 NMDPAHRDRIAFLRVCSGRFERGMKLKHLRLNREIKVSSVVTFMASSREQVEEAYAGDII 391 NMDPAHRDRIAFLRVCSGRFERGMKLKHLRLNR+IKVSSVVTFMASSREQVEEAYAGDII Sbjct: 301 NMDPAHRDRIAFLRVCSGRFERGMKLKHLRLNRDIKVSSVVTFMASSREQVEEAYAGDII 360 Query: 392 GLPNHGNMQIGDSFSEGEMLQFTGIPYFAPDFFRVARIRNPLKIKQLHKGLQQLGEEGAV 451 GLPNHGNMQIGDSFSEGEMLQFTGIPYFAPDFFRVARIRNPLKIKQLHKGLQQLGEEGAV Sbjct: 361 GLPNHGNMQIGDSFSEGEMLQFTGIPYFAPDFFRVARIRNPLKIKQLHKGLQQLGEEGAV 420 Query: 452 QVFKPVTGSDLILGAVGVLQFEVVASRLLNEYGVDAVFEGTSISSARWISCDDKKKLADF 511 QVFKPVTGSDLILGAVGVLQFEVVASRLLNEYGVDAVFEGTSISSARWISCDDKKKLADF Sbjct: 421 QVFKPVTGSDLILGAVGVLQFEVVASRLLNEYGVDAVFEGTSISSARWISCDDKKKLADF 480 Query: 512 EKSSAGANLAIDAAGNLAYLASSGVNLRLTQERWPEITFHATREHAAKLD 561 EKSSAGANLAIDAAGN+AYLASSGVNLRLTQERWPEITFHATREHAAKLD Sbjct: 481 EKSSAGANLAIDAAGNMAYLASSGVNLRLTQERWPEITFHATREHAAKLD 530 >gi|300313617|ref|YP_003777709.1| translation elongation factor [Herbaspirillum seropedicae SmR1] Length = 701 Score = 176 bits (447), Expect = 4e-45, Method: Compositional matrix adjust. Identities = 139/524 (26%), Positives = 240/524 (45%), Gaps = 64/524 (12%) Query: 37 VKRRRTFGIISHPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEKQRGIS 96 ++ R GI +H DAGKTT TE++L ++G G V AT DWME E++RGI+ Sbjct: 7 IENYRNIGISAHIDAGKTTTTERILFYTGVNHKIGEV----HNGAATMDWMEQEQERGIT 62 Query: 97 VASSV-------MQFEYRDHVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQ 149 + S+ M Y +H +N++DTPGH DF+ + R + +D A+MV D+ GV+ Q Sbjct: 63 ITSAATTAFWKGMAGNYPEHRINIIDTPGHVDFTIEVERSMRVLDGAVMVYDSVGGVQPQ 122 Query: 150 TIKLLNVCRMRNTPIITFMNKLDRETRDSLELLDELESVLKIQCAPVTWPIGMGKNFRGV 209 + + P I F+NK+DR D + ++E LK + P+ P+G +F GV Sbjct: 123 SETVWRQANKYKVPRIAFVNKMDRIGADFFRVQKQIEERLKGKAVPIQIPVGAEDHFSGV 182 Query: 210 YHLLRDEIMLFKAGEERANGSVEIIKGIDNPKLAEMFPLEIE---------------QLK 254 L++ + +++ +E + G + + I PLE+E + Sbjct: 183 IDLVKMKAIIW---DEASQGVLFKYEDI---------PLELEDTARHWRDLMVEQAAEAN 230 Query: 255 MEVELVHGASHPFNLDDFLAGIQ--------TPVFFGSAINNFGVREILDALLDWAPGP- 305 E+ + + +P DD G++ P+ GSA N GV+ +LDA++D+ P P Sbjct: 231 EELLEKYLSGNPLTEDDIKRGLRLRTVANEIVPMLAGSAFKNKGVQAMLDAVIDYLPSPV 290 Query: 306 --------GGRDATVREVKPTEEPFSGFVFKIQANMDPAHRDRIAFLRVCSGRFERGMKL 357 G D+ + EEPFS FKI DP ++ F RV SG G + Sbjct: 291 DVPAIAGHGEDDSEIERHPSDEEPFSALAFKIMT--DP-FVGQLTFFRVYSGIVNSGDTV 347 Query: 358 KHLRLNREIKVSSVVTFMASSREQVEEAYAGDIIGLPNHGNMQIGDSFSEGE---MLQFT 414 + ++ ++ ++ A+ R++++E +AGDI ++ GD+ S+ E +L+ Sbjct: 348 YNPVKGKKERLGRILQMHANERKEIKEVFAGDIAAAVGLKDVTTGDTLSDPEHPIILERM 407 Query: 415 GIPYFAPDFFRVARIRNPLKIKQLHKGLQQLGEEG-AVQVFKPVTGSDLILGAVGVLQFE 473 P P + + +++ L +L +E + +V I+ +G L E Sbjct: 408 IFP--EPVISQAVEPKTKADQEKMGIALNRLAQEDPSFRVHTDEESGQTIMSGMGELHLE 465 Query: 474 VVASRLLNEYGVDAVFEGTSISSARWISCDDKKKLADFEKSSAG 517 ++ R+ E+ V+A ++ I + F K S G Sbjct: 466 ILVDRMKREFNVEATVGKPQVAYREAIRKAVEDVEGKFVKQSGG 509 >gi|300309453|ref|YP_003773545.1| elongation factor G1 [Herbaspirillum seropedicae SmR1] Length = 701 Score = 155 bits (393), Expect = 6e-39, Method: Compositional matrix adjust. Identities = 128/520 (24%), Positives = 231/520 (44%), Gaps = 56/520 (10%) Query: 37 VKRRRTFGIISHPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEKQRGIS 96 ++R R GI +H DAGKTT TE++L ++G G V AT DWME E++RGI+ Sbjct: 7 IERYRNIGISAHIDAGKTTTTERVLFYTGVNHKIGEVHDGA----ATMDWMEQEQERGIT 62 Query: 97 VASSV-------MQFEYRDHVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQ 149 + S+ M + H +N++DTPGH DF+ + R + +D A MV A GV+ Q Sbjct: 63 ITSAATTCYWKGMANNFPAHHINIIDTPGHVDFTIEVERSMRVLDGACMVYCAVGGVQPQ 122 Query: 150 TIKLLNVCRMRNTPIITFMNKLDRETRDSLELLDELESVLKIQCAPVTWPIGMGKNFRGV 209 + + P + F+NK+DR + ++ +++ + LK P+ PIG +NF GV Sbjct: 123 SETVWRQANKYKVPRLAFVNKMDRTGANFFKVYEQMRARLKANPIPMQVPIGAEENFEGV 182 Query: 210 YHLLRDEIMLFKAGEERANGSVEIIKGIDNPKLAEMFPLEIEQLKME-VELVHGASHPFN 268 L++ + + + D + E + ++ + VE AS Sbjct: 183 IDLVKMRAIYWDDASQGMK--------FDYRDIPEHLKADAQKWRENLVETAAEASEDL- 233 Query: 269 LDDFL-------------------AGIQTPVFFGSAINNFGVREILDALLDWAPGP---- 305 ++ +L +G P+ G+A N GV+ +LD ++++ P P Sbjct: 234 MNKYLEEGDLTEAEIKGAIRQRTISGEIVPMMCGTAFKNKGVQAMLDGVVEYLPSPVDIP 293 Query: 306 ------GGRDATVREVKPTEEPFSGFVFKIQANMDPAHRDRIAFLRVCSGRFERGMKLKH 359 + VRE K +E FS FKI DP ++ F+R SG G + + Sbjct: 294 PVPGLNEDDEPVVREAK-DDEKFSALAFKIAT--DP-FVGQLCFIRCYSGTLNSGDTVLN 349 Query: 360 LRLNREIKVSSVVTFMASSREQVEEAYAGDIIGLPNHGNMQIGDSFSEGE-MLQFTGIPY 418 +++ ++ +V A+ RE+++E AGDI + + GD+ + + M+ + + Sbjct: 350 SVKSKKERIGRIVQMHANQREEIKEMMAGDIAAVVGLKDTTTGDTLCDDKAMVVLERMVF 409 Query: 419 FAPDFFRVARIRNPLKIKQLHKGLQQL-GEEGAVQVFKPVTGSDLILGAVGVLQFEVVAS 477 P + + +++ L +L E+ + +V I+ +G L +++ Sbjct: 410 PEPVISQAVEPKTKADQEKMGLALNRLAAEDPSFRVRTDEESGQTIIAGMGELHLDIIVD 469 Query: 478 RLLNEYGVDAVFEGTSISSARWISCDDKKKLADFEKSSAG 517 R+ E+ V+A ++ I ++ F K S G Sbjct: 470 RMKREFNVEATVGKPQVAYRETIRKTCEESEGKFVKQSGG 509 >gi|300311258|ref|YP_003775350.1| GTP-binding elongation factor protein [Herbaspirillum seropedicae SmR1] Length = 597 Score = 95.9 bits (237), Expect = 9e-21, Method: Compositional matrix adjust. Identities = 57/171 (33%), Positives = 92/171 (53%), Gaps = 15/171 (8%) Query: 41 RTFGIISHPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEKQRGISVASS 100 R F II+H D GK+TL +++ IQL G + R+ D M+IE++RGI++ + Sbjct: 5 RNFSIIAHIDHGKSTLADRI------IQLCGGLSNREMEAQVL-DSMDIERERGITIKAQ 57 Query: 101 VMQFEYRD-----HVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQTIKLLN 155 Y+ + +NL+DTPGH DFS + R L+A + AL+V+DA++GVE QT+ Sbjct: 58 TAALSYKAKDGQIYNLNLIDTPGHVDFSYEVSRSLSACEGALLVVDASQGVEAQTVANCY 117 Query: 156 VCRMRNTPIITFMNKLDRETRDSLELLDELESVLKIQCA---PVTWPIGMG 203 ++ +NK+D + D E+E V+ I + P + G+G Sbjct: 118 TALDLGVEVVPVLNKIDLPSADPDNAKSEIEDVIGIDASDATPCSAKTGLG 168 >gi|300312895|ref|YP_003776987.1| GTP-binding elongation factor protein [Herbaspirillum seropedicae SmR1] Length = 627 Score = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 55/162 (33%), Positives = 81/162 (50%), Gaps = 13/162 (8%) Query: 48 HPDAGKTTLTEKLLLFSGAIQLAGTVKARKSGRHATSDWMEIEKQRGISVASSVMQFEYR 107 H D GKTTL ++LL SG + V R D +IEK+RGI++ S EY+ Sbjct: 30 HVDHGKTTLVDQLLRQSGTFRDNQQVDNR------VMDSNDIEKERGITILSKNCAVEYK 83 Query: 108 DHVVNLLDTPGHQDFSEDTYRVLTAVDSALMVIDAAKGVEEQTIKLLNVCRMRNTPIITF 167 +N++DTPGH DF + RVL+ VDS L+++DA +G QT + I Sbjct: 84 GTHINIVDTPGHADFGGEVERVLSMVDSVLLLVDAQEGPMPQTRFVTRKALALGLKPIVV 143 Query: 168 MNKLDRE-------TRDSLELLDELESVLKIQCAPVTWPIGM 202 +NK+DR + EL D+L + + PV + G+ Sbjct: 144 LNKIDRPGARAEWAINATFELFDKLGATEEQLDFPVIYASGL 185 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 0.135 0.389 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: 1,611,512 Number of extensions: 64435 Number of successful extensions: 214 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 8 Length of query: 561 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 471 Effective length of database: 1,193,720 Effective search space: 562242120 Effective search space used: 562242120 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: 133 (55.8 bits)