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= 0013.0107.p (289 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptid... 290 6e-80 gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptid... 84 1e-17 gi|300311623|ref|YP_003775715.1| cytochrome c1 protein [Herbaspi... 57 2e-09 >gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 290 bits (743), Expect = 6e-80, Method: Compositional matrix adjust. Identities = 157/291 (53%), Positives = 192/291 (65%), Gaps = 8/291 (2%) Query: 1 VFFLIVTVFLYALWRAPRSTAITKADIHNQHSKRVHHIAIAWALGLSAAGLGSLFAVDML 60 VF L + AL+R R +A A + R+ AI WALGLSA GL +LFA D++ Sbjct: 60 VFLLTLLACAVALFRRRRYSAEAAA-----ATPRLTW-AIGWALGLSATGLLALFAADVV 113 Query: 61 TARQLSQLLPDDALRIDLTGHQWWWQATYLNSAGAPDFIVANELQLPVGRTVLINLRSDD 120 +R L QL AL++ LT QWWWQA Y + F ANEL LPVGR V+I+L S+D Sbjct: 114 ASRALDQLPTAGALQVKLTARQWWWQAQYHDPLTGQGFTTANELHLPVGRAVIIDLDSED 173 Query: 121 VIHSLWIPALHGKLDLIPGRTATLRLRADAPGSYRGQCAEFCGEQHALMALLAIAKPAEQ 180 VIHSLW+P LHGKLDLIPG+ A LRLRAD G+YRGQCAEFCG +HA MALL A+ Sbjct: 174 VIHSLWLPNLHGKLDLIPGKPAQLRLRADQAGTYRGQCAEFCGLEHARMALLVTAESPAD 233 Query: 181 YEAWAVSQ--RRPAAPPQTESAKHGLRVFLSNGCASCHTIRGTAAAGTLGPDLTHLAARE 238 Y WA Q + G VF+ GCA CH IRGT AAG GPDLTHLA+R Sbjct: 234 YARWASGQARAAAPVADAAATVARGRAVFMERGCAQCHAIRGTDAAGQNGPDLTHLASRS 293 Query: 239 TLAAGMLPNQRGHLAGWIANARAIKPGVAMPPSTLTPNDLHSLLDFMETLR 289 TLAAG+ PNQRG LAGWI +AR++K GV MPP+ L P++L++LLD++ETL+ Sbjct: 294 TLAAGIFPNQRGFLAGWITDARSLKTGVIMPPAQLPPDELNALLDYLETLQ 344 >gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 386 Score = 84.0 bits (206), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 68/265 (25%), Positives = 106/265 (40%), Gaps = 50/265 (18%) Query: 1 VFFLIVTVFLYALWRAPRSTAITKADIHNQHSKRVHHIAIAWALGLSAAGLGSLFAVDM- 59 +F + V Y++ + +S + H + + IAW + + L + M Sbjct: 65 IFVAVFGVMFYSIIKHRKSVGHKASTFHESTA-----VEIAWTV------VPFLIVIGMA 113 Query: 60 LTARQLSQLLPDDA---LRIDLTGHQWWWQATYLNSAGAPDFIVAN---------ELQLP 107 L A + + D + L I +TG QW W YL G ++N + L Sbjct: 114 LPATKTVVAMKDTSNADLTIKVTGMQWKWGYDYLKGEGEGISFLSNLATPREQVTDPSLK 173 Query: 108 VGRTVLINLR----------------SDDVIHSLWIPALHGKLDLIPGRTATLRLRADAP 151 LI + ++DVIHS IPA K D IPG RA+ Sbjct: 174 KNDNYLIEVDNPVVVPVNKKVRIVTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKI 233 Query: 152 GSYRGQCAEFCGEQHALMALLAIAKPAEQYEAWAVSQRRPAA-----PPQT----ESAKH 202 G+YRGQC E CG+ HA M ++ + Y+ W +++ A P +T E + Sbjct: 234 GTYRGQCVELCGKDHAFMPIVVNVVSEDDYKQWVDGKKKEMAAKADDPNKTWTVDELKQR 293 Query: 203 GLRVFLSNGCASCHTIRGTAAAGTL 227 G +V+ +N C +CH G G Sbjct: 294 GEKVYAAN-CVTCHQANGKGVPGAF 317 >gi|300311623|ref|YP_003775715.1| cytochrome c1 protein [Herbaspirillum seropedicae SmR1] Length = 124 Score = 56.6 bits (135), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 31/86 (36%), Positives = 49/86 (56%), Gaps = 2/86 (2%) Query: 201 KHGLRVFLSNGCASCHTIRGTAAAGTL-GPDLTHLAARETLAAGMLPNQRGHLAGWIANA 259 + G R+ ++GCA+CH+I G A TL GP L + A+ + AG+LPN + +LA WI + Sbjct: 30 QQGRRLLATHGCAACHSIPGIAPGQTLVGPPLDQV-AKASYVAGILPNSQANLARWIMHP 88 Query: 260 RAIKPGVAMPPSTLTPNDLHSLLDFM 285 R P AMP L+ + + ++ Sbjct: 89 RHFHPQSAMPELGLSEQEAADMAAYL 114 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 0.323 0.135 0.425 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: 931,639 Number of extensions: 37515 Number of successful extensions: 140 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 140 Number of HSP's successfully gapped: 4 Length of query: 289 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 205 Effective length of database: 1,222,130 Effective search space: 250536650 Effective search space used: 250536650 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 (22.0 bits) S2: 130 (54.7 bits)