RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780471|ref|YP_003064884.1| cytochrome o ubiquinol oxidase subunit IV [Candidatus Liberibacter asiaticus str. psy62] (119 letters) >gnl|CDD|182568 PRK10582, PRK10582, cytochrome o ubiquinol oxidase subunit IV; Provisional. Length = 109 Score = 99.4 bits (248), Expect = 2e-22 Identities = 49/98 (50%), Positives = 74/98 (75%), Gaps = 1/98 (1%) Query: 13 SYGTKKQCLVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMS 72 S+G+ K + GFILS+ILT+IPF +VM G ++ TI+ A+ QI+VHLV FLHM+ Sbjct: 11 SHGSVKTYMTGFILSIILTVIPFWMVMTGAA-SPAVILGTILAMAVVQILVHLVCFLHMN 69 Query: 73 TKVEDGWSIMAMIFTIIMVAICFVGSMWVMYHLNNNMM 110 TK ++GW++ A +FT++++AI VGS+W+M++LN NMM Sbjct: 70 TKSDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNMM 107 >gnl|CDD|131894 TIGR02847, CyoD, cytochrome o ubiquinol oxidase subunit IV. Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilize cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant. Length = 96 Score = 98.1 bits (245), Expect = 5e-22 Identities = 46/97 (47%), Positives = 74/97 (76%), Gaps = 1/97 (1%) Query: 14 YGTKKQCLVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMST 73 +G+ K L+GF+LS+ILT IPFG+VM G K + + I++ A+ QI+VHLVFFLH++T Sbjct: 1 HGSLKSYLIGFVLSVILTAIPFGLVMSGTL-SKGLTLVIIIVLAVVQILVHLVFFLHLNT 59 Query: 74 KVEDGWSIMAMIFTIIMVAICFVGSMWVMYHLNNNMM 110 E W++++++FTI+++ I GS+W+M++LN+NMM Sbjct: 60 SSEQRWNLISLLFTILIIFILIGGSIWIMHNLNHNMM 96 >gnl|CDD|131947 TIGR02901, QoxD, cytochrome aa3 quinol oxidase, subunit IV. This family (QoxD) encodes subunit IV of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site. Length = 94 Score = 37.1 bits (86), Expect = 0.001 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%) Query: 21 LVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWS 80 + GFILSL+LT + + + L + I++ A Q + L+ F+H + Sbjct: 10 VNGFILSLLLTFLALWVALYSD-LPLAMGLTIIIIFAFIQAGLQLIMFMHAGESEDGKVQ 68 Query: 81 IMAMIFTIIMVAICFVGSMWVM 102 I + ++ + + GS+WVM Sbjct: 69 IYNIYYSAFIALVTVFGSLWVM 90 >gnl|CDD|131954 TIGR02908, CoxD_Bacillus, cytochrome c oxidase, subunit IVB. This model represents a small clade of cytochrome oxidase subunit IV's found in the Bacilli. Length = 110 Score = 30.6 bits (69), Expect = 0.086 Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 3/85 (3%) Query: 18 KQCLVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVED 77 K+ +V F L + LT+I F VM DK + I+L A Q+ L +F+HM K + Sbjct: 26 KKQIVTFALMIFLTLIAFFAVMLDEI-DKWFVIPFILLLAAVQVAFQLYYFMHMKDKGHE 84 Query: 78 GWS--IMAMIFTIIMVAICFVGSMW 100 + I +F ++V + F W Sbjct: 85 VPAQFIYGGVFVTMLVVLAFTTITW 109 >gnl|CDD|132323 TIGR03280, methan_mark_11, putative methanogenesis marker protein 11. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. Length = 292 Score = 27.4 bits (61), Expect = 0.86 Identities = 6/11 (54%), Positives = 7/11 (63%) Query: 94 CFVGSMWVMYH 104 C GS WV+Y Sbjct: 24 CPSGSEWVIYQ 34 >gnl|CDD|149146 pfam07907, YibE_F, YibE/F-like protein. The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE and YibF. Most of the members of this family are annotated as being putative membrane proteins, and in fact the sequences contain a high proportion of hydrophobic residues. Length = 244 Score = 27.4 bits (62), Expect = 1.0 Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 7/92 (7%) Query: 25 ILSLILT-IIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWSIMA 83 +LSL+L ++ F +++ N + +TI+L I V L + K ++ A Sbjct: 26 LLSLVLNFVLLFLVLIPIILAGFNPILVTIILAIII-TAVTLFLVNGFNKK-----TLAA 79 Query: 84 MIFTIIMVAICFVGSMWVMYHLNNNMMSMEGM 115 + T++ V + + ++ V+ + + E Sbjct: 80 FLGTLLGVLLAGILALLVIKLTHLQGLGYEEA 111 >gnl|CDD|163109 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose phosphotransferase. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier, knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity. Length = 451 Score = 27.2 bits (61), Expect = 1.1 Identities = 6/46 (13%), Positives = 18/46 (39%) Query: 61 IIVHLVFFLHMSTKVEDGWSIMAMIFTIIMVAICFVGSMWVMYHLN 106 I+ L F L + W ++ + + ++ + + ++ L Sbjct: 77 ILALLAFLLKTGGEFSRLWLLLWFLLALALLLLGRLILRLLLRRLR 122 >gnl|CDD|152872 pfam12438, DUF3679, Protein of unknown function (DUF3679). This domain family is found in bacteria, and is approximately 60 amino acids in length. Length = 56 Score = 26.1 bits (58), Expect = 2.2 Identities = 10/30 (33%), Positives = 14/30 (46%) Query: 87 TIIMVAICFVGSMWVMYHLNNNMMSMEGMR 116 I+ V I G + M N+ M SM+G Sbjct: 2 CILAVIILLFGVLLGMQQANHGMKSMKGYD 31 >gnl|CDD|162944 TIGR02600, TIGR02600, Verrucomicrobium spinosum paralogous protein TIGR02600. In Verrucomicrobium spinosum, a five-gene operon that includes proteins with an N-terminal signal sequence for cleavage and methylation recurs over twenty times. Each operon is likely to encode a membrane complex, the function of which is unknown. This model represents a long paralogous protein from this putative membrame complex, with members averaging about 1300 amino acids. The N-terminal region includes an apparent signal sequence. The function is unknown. Length = 1265 Score = 26.0 bits (57), Expect = 2.4 Identities = 9/25 (36%), Positives = 14/25 (56%) Query: 49 MCLTIVLCAIAQIIVHLVFFLHMST 73 M L +VL +A I + ++ FL M Sbjct: 1 MALIMVLIILALITILVLGFLSMVR 25 >gnl|CDD|177754 PLN00151, PLN00151, potassium transporter; Provisional. Length = 852 Score = 25.9 bits (57), Expect = 2.8 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%) Query: 51 LTIVLC-AIAQIIVHLVFFLHMSTKVEDG-WSIMAMIFTIIMVAICFV 96 + +VLC + + V LVFF + + V DG W ++F + + I ++ Sbjct: 526 IFLVLCFPVVFLSVELVFFSSVLSSVGDGGWIP--LVFASVFLCIMYI 571 >gnl|CDD|162339 TIGR01399, hrcV, type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane. Length = 677 Score = 25.4 bits (56), Expect = 3.3 Identities = 9/20 (45%), Positives = 15/20 (75%) Query: 22 VGFILSLILTIIPFGIVMKG 41 VG ++ LI+TI+ F ++ KG Sbjct: 103 VGLVIFLIITIVQFIVITKG 122 >gnl|CDD|178625 PLN03076, PLN03076, ARF guanine nucleotide exchange factor (ARF-GEF); Provisional. Length = 1780 Score = 25.2 bits (55), Expect = 4.4 Identities = 7/13 (53%), Positives = 9/13 (69%) Query: 75 VEDGWSIMAMIFT 87 V+ GW M M+FT Sbjct: 1218 VKSGWKSMFMVFT 1230 >gnl|CDD|180350 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated. Length = 697 Score = 25.1 bits (56), Expect = 4.5 Identities = 9/21 (42%), Positives = 15/21 (71%) Query: 21 LVGFILSLILTIIPFGIVMKG 41 +VG ++ +IL II F ++ KG Sbjct: 123 VVGIVVFIILVIINFVVITKG 143 >gnl|CDD|130267 TIGR01200, TIGR01200, Porphyromonas gingivalis paralogous family TIGR01200. No identifiable homologs outside Porphyromonas gingivalis. Length = 292 Score = 24.9 bits (54), Expect = 5.0 Identities = 7/34 (20%), Positives = 20/34 (58%) Query: 83 AMIFTIIMVAICFVGSMWVMYHLNNNMMSMEGMR 116 ++ ++ + ICF+ S+ + ++++EGM+ Sbjct: 1 SLFRILLYILICFLLSIVGIQSPVPRIITLEGMK 34 >gnl|CDD|185010 PRK15050, PRK15050, 2-aminoethylphosphonate transport system permease PhnU; Provisional. Length = 296 Score = 25.0 bits (55), Expect = 5.1 Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 2/28 (7%) Query: 20 CLV-GFILSLILTIIPF-GIVMKGFFLD 45 CLV G +L+L+L +PF G + G F+D Sbjct: 89 CLVLGVLLALVLAFVPFPGASLVGRFID 116 >gnl|CDD|162106 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis. Length = 1204 Score = 24.8 bits (54), Expect = 5.1 Identities = 7/49 (14%), Positives = 21/49 (42%), Gaps = 3/49 (6%) Query: 52 TIVLCAIAQIIVHLVFFLHMSTKVEDGWSIMAMIFTIIMVAICFVGSMW 100 ++ I+ + +V + + S + ++ ++ M+ + VG M Sbjct: 1050 ALINLGISLGAIFIVTLVLLGLNA---LSAVNVVISVGMIVVNLVGIMH 1095 >gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated. Length = 156 Score = 24.7 bits (55), Expect = 5.1 Identities = 6/20 (30%), Positives = 10/20 (50%) Query: 82 MAMIFTIIMVAICFVGSMWV 101 M + T+I I F+ +W Sbjct: 1 MNLNGTLIGQLIAFLILVWF 20 >gnl|CDD|162292 TIGR01301, GPH_sucrose, GPH family sucrose/H+ symporter. This model represents sucrose/proton symporters, found in plants, from the Glycoside-Pentoside-Hexuronide (GPH)/cation symporter family. These proteins are predicted to have 12 transmembrane domains. Members may export sucrose (e.g. SUT1, SUT4) from green parts to the phloem for long-distance transport or import sucrose (e.g SUT2) to sucrose sinks such as the tap root of the carrot. Length = 477 Score = 24.4 bits (53), Expect = 6.5 Identities = 7/19 (36%), Positives = 11/19 (57%) Query: 89 IMVAICFVGSMWVMYHLNN 107 I++AIC ++ V Y N Sbjct: 344 IILAICLAATVLVTYVAKN 362 >gnl|CDD|162465 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase, flippase. This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes. Length = 1057 Score = 24.6 bits (54), Expect = 6.6 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 3/49 (6%) Query: 49 MCLTIVLCAIAQIIVHLVFFL---HMSTKVEDGWSIMAMIFTIIMVAIC 94 M I + + L S ++D S+ ++FT ++V + Sbjct: 920 MLDGIYQSLVIFFFPMFAYILGDFVSSGSLDDFSSVGVIVFTALVVIVN 968 >gnl|CDD|163048 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs. Length = 764 Score = 24.3 bits (53), Expect = 7.2 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 6/80 (7%) Query: 24 FILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWSIMA 83 L L+ II V+K K + IV+ + V+ +F + V + + Sbjct: 61 KYLLLVAVIILLSYVLKNLTDKKKTVVPPIVV--FLEAAVYAIFGYLQNKLV----TPLD 114 Query: 84 MIFTIIMVAICFVGSMWVMY 103 I +I+ ++ FV Y Sbjct: 115 FILSIVEASLSFVLYYIFNY 134 >gnl|CDD|181866 PRK09450, cyaA, adenylate cyclase; Provisional. Length = 830 Score = 24.1 bits (53), Expect = 8.5 Identities = 6/18 (33%), Positives = 13/18 (72%) Query: 6 IHNMNMHSYGTKKQCLVG 23 N+++ S+G +++ LVG Sbjct: 577 FRNLDVFSFGGEQENLVG 594 >gnl|CDD|178466 PLN02878, PLN02878, homogentisate phytyltransferase. Length = 280 Score = 23.9 bits (52), Expect = 9.2 Identities = 10/19 (52%), Positives = 13/19 (68%) Query: 57 AIAQIIVHLVFFLHMSTKV 75 A+ ++V L FFLHM T V Sbjct: 129 AVRAVVVQLAFFLHMQTHV 147 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.336 0.143 0.457 Gapped Lambda K H 0.267 0.0744 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,852,834 Number of extensions: 105450 Number of successful extensions: 617 Number of sequences better than 10.0: 1 Number of HSP's gapped: 608 Number of HSP's successfully gapped: 121 Length of query: 119 Length of database: 5,994,473 Length adjustment: 81 Effective length of query: 38 Effective length of database: 4,244,225 Effective search space: 161280550 Effective search space used: 161280550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.7 bits) S2: 51 (23.4 bits)