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= 0001.4028.p (386 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134096078|ref|YP_001101153.1| cytochrome C oxidase polypeptid... 660 0.0 gi|134094346|ref|YP_001099421.1| putative cytochrome cbb3 subuni... 106 2e-24 gi|134095986|ref|YP_001101061.1| putative cytochrome C [Herminii... 68 7e-13 >gi|134096078|ref|YP_001101153.1| cytochrome C oxidase polypeptide II (cytochrome AA3 subunit 2) transmembrane protein [Herminiimonas arsenicoxydans] Length = 386 Score = 660 bits (1704), Expect = 0.0, Method: Compositional matrix adjust. Identities = 321/386 (83%), Positives = 351/386 (90%) Query: 1 MKLAKRLQTLSLGASLLAAGLPAWAVVDSPGGPAVLQTNFQPPVTKIAEQIYDLHIMMLV 60 MK AKRLQ+L LGASLL AGLP+WAV DSPGGPAV Q NF PVT+IAEQIY LH ++LV Sbjct: 1 MKHAKRLQSLMLGASLLTAGLPSWAVTDSPGGPAVRQLNFHQPVTQIAEQIYSLHTLLLV 60 Query: 61 ICLLIFVAVFGVMFYSIIKHRKSVGHKAASFHESTTVEIAWTVVPFLIVIGMALPATKTV 120 ICL+IF+AVFGVMFYSI+KHRKSVGHK+A+FHEST VEIAWTVVPFLIVIGMALPATKTV Sbjct: 61 ICLVIFLAVFGVMFYSIVKHRKSVGHKSATFHESTAVEIAWTVVPFLIVIGMALPATKTV 120 Query: 121 VAMKDTSNADLTIKVTGMQWKWGYDYLKGEGEGISFLSSLATPREQITDPALKKNDNYLI 180 VAMKDTSNAD+TIK TGMQWKWGYDYL GEG+GI FLS+LATPREQITDP L KN+NYLI Sbjct: 121 VAMKDTSNADITIKATGMQWKWGYDYLAGEGQGIGFLSNLATPREQITDPTLTKNENYLI 180 Query: 181 EVDNPVVVPVNKKVRLVTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKIGTYRGQC 240 EVDNPVVVPVNKK+R+V TANDVIHSW IP+FGVKQDAIPGFVRDTWF+AEKIGTYRGQC Sbjct: 181 EVDNPVVVPVNKKIRIVLTANDVIHSWMIPSFGVKQDAIPGFVRDTWFKAEKIGTYRGQC 240 Query: 241 VELCGKDHAFMPIVVNVVSDDDYKKWVEGKKKEMAAKADDPSKVWTVDELKQRGEKVYAA 300 ELCGKDHAFMPIVVNVVSD+DYK WV+GKKKEMAA ADDP+K WTVDEL QRGEKVY A Sbjct: 241 AELCGKDHAFMPIVVNVVSDEDYKVWVDGKKKEMAANADDPNKTWTVDELVQRGEKVYTA 300 Query: 301 NCVVCHQANGKGVPGAFPALDGSAVVNGPKDGQIHILLNGKNAMPAWKGILNDTEIAAVI 360 NC+ CHQANGKGVPG+FPALD S +V GPK IH+++ GK AMPAWK +L+DTEIAAVI Sbjct: 301 NCIACHQANGKGVPGSFPALDASPIVTGPKAANIHMVMEGKGAMPAWKPVLSDTEIAAVI 360 Query: 361 TYTRNNWSNKAQENIVQPAEVLAARK 386 TYTRN+WSNKA ENIVQPAEVLAARK Sbjct: 361 TYTRNHWSNKAAENIVQPAEVLAARK 386 >gi|134094346|ref|YP_001099421.1| putative cytochrome cbb3 subunit 2 [Herminiimonas arsenicoxydans] Length = 400 Score = 106 bits (264), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 85/347 (24%), Positives = 150/347 (43%), Gaps = 27/347 (7%) Query: 43 PVTKIAEQIYDLHIMMLVICLLIFVAVFGVMFYSIIKHRKSVGHKAASFHESTTVEIAWT 102 P+ +Q+ D + VI + FVA+ ++ Y +++ R G +AA ++ +E Sbjct: 27 PLASNWQQMDDTLAITFVITGIFFVAINFLLVYMLLRFRHREGSRAAYAPDNKKLERWLI 86 Query: 103 VVPFLIVIGMALPATKTVVAMKDTSNADLTIKVTGMQWKWGYDYLKGEGE-GISFLSSLA 161 L ++ + P A L ++V G QW+W + + G+ G+S ++ Sbjct: 87 GGTTLAIMALLAPGLFVYAAYIKPPPDALHLEVLGQQWQWRFRFPDQNGKLGLSDARLVS 146 Query: 162 TPREQITDPALKKNDNYLIEVDNPVVVPVNKKVRLVTTANDVIHSWTIPAFGVKQDAIPG 221 DP N ++ N V +P+NK V+++ + DV+H + +P F + + +PG Sbjct: 147 AANPFGLDPKDPNGQNNILINSNEVHLPLNKPVKMLLRSQDVLHDFYVPQFRARMNMVPG 206 Query: 222 FVRDTWFRAEKIGTYRGQCVELCGKDHAFMPIVVNVVSDDDYKKWVEGKKKEMAAKADDP 281 V WF K G Y C +LCG H M VV V + ++KW++ + A P Sbjct: 207 MVTSFWFTPTKAGRYEILCAQLCGVGHYTMRGVVVVEDEAAFQKWLQAQPT-FAMTLAAP 265 Query: 282 SKVWTVDE-------LKQRGEKVYAANCVVCHQANG--------KGVPGAFPAL-DGSAV 325 + V + L+Q + + CV CH +G K + G +L DG +V Sbjct: 266 AVVAGAHDQGAPDAKLEQGKQLAQSKGCVACHSLDGSSGVGPSWKNLFGHTTSLSDGKSV 325 Query: 326 VNGPK-------DGQIHILLNGKNAMPAWKGILNDTEIAAVITYTRN 365 + D I+ MP + ++D E+AA+I Y + Sbjct: 326 LADEAYLKKSILDPSAQIVKGFAPIMPKLE--MSDAELAALIVYIES 370 >gi|134095986|ref|YP_001101061.1| putative cytochrome C [Herminiimonas arsenicoxydans] Length = 429 Score = 68.2 bits (165), Expect = 7e-13, Method: Compositional matrix adjust. Identities = 36/90 (40%), Positives = 48/90 (53%), Gaps = 12/90 (13%) Query: 294 GEKVYAANCVVCHQANGKGVPGAFPALDGSAVVNGP-KDGQIHILLNGKNA--------- 343 G K+Y C+ CHQA+GKGVP +PAL GS + P I ++L G A Sbjct: 325 GAKLYEDQCISCHQASGKGVPSIYPALAGSRAITTPVATNAIRMVLYGGYAPSTGGNPRP 384 Query: 344 --MPAWKGILNDTEIAAVITYTRNNWSNKA 371 MP + + D E+AAV+TY RN W N+ Sbjct: 385 YGMPPFGQSMTDEEVAAVVTYIRNAWGNQG 414 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 Lambda K H 0.319 0.134 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 3295 Number of Hits to DB: 716,364 Number of extensions: 28610 Number of successful extensions: 96 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 94 Number of HSP's successfully gapped: 3 Length of query: 386 Length of database: 1,000,347 Length adjustment: 83 Effective length of query: 303 Effective length of database: 726,862 Effective search space: 220239186 Effective search space used: 220239186 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: 129 (54.3 bits)