RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780375|ref|YP_003064788.1| hypothetical protein CLIBASIA_01300 [Candidatus Liberibacter asiaticus str. psy62] (175 letters) >gnl|CDD|152532 pfam12097, DUF3573, Protein of unknown function (DUF3573). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 372 to 530 amino acids in length. Length = 375 Score = 31.0 bits (70), Expect = 0.16 Identities = 32/136 (23%), Positives = 54/136 (39%), Gaps = 20/136 (14%) Query: 8 YYYKKRDMLSQLLFLLFFFLQGFANQSYGDPTLVDREIQQYCTNVIDSVRERDYLSQKKV 67 + KK +L L + F F G + V IQQ +N ID ++D +K Sbjct: 1 MFIKKLLILIFFLTISFLFFIGRSYA-------VVNAIQQTDSNQID---KKDISKLQKQ 50 Query: 68 LEDLQKDIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQID 127 ++ LQ I NH +E +Y+ + D + ++ L L Q + Sbjct: 51 IKSLQAQI--------NHLEEQTNSNLSSQ--FATYSSKVNDSTLTGNGETKVLSLGQRN 100 Query: 128 PDISSHILMRLSPRQS 143 +I+S I+ + QS Sbjct: 101 NNIASDIMSNETFDQS 116 >gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. Length = 1164 Score = 30.4 bits (69), Expect = 0.23 Identities = 21/101 (20%), Positives = 48/101 (47%), Gaps = 13/101 (12%) Query: 43 REIQQYCTNVIDSVRER--DYLSQKKVLEDLQKDIEQRVILLENHKKEYNLWFQKYDSFI 100 IQ+Y + V +R + ++ LE+ +K I +R+ E K+E ++ + +++ Sbjct: 976 LAIQEY-----EEVLKRLDELKEKRAKLEEERKAILERIEEYEKKKRE--VFMEAFEAI- 1027 Query: 101 MSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPR 141 N+N +I+ ++ + L LE D + + + P+ Sbjct: 1028 ---NENFNEIFAELSGGTGELILENPDDPFAGGLELSAKPK 1065 >gnl|CDD|168632 PRK06633, PRK06633, acetyl-CoA acetyltransferase; Provisional. Length = 392 Score = 26.9 bits (59), Expect = 2.7 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 14/75 (18%) Query: 80 ILLENHKKEYNLWFQKYDSFIMSYNKN-------------ILDIYKKMDSDSAALQL-EQ 125 I EN K++N+ Q+ D F +S +K IL I + ++ E Sbjct: 159 ITAENISKQFNISRQEQDEFALSSHKKAAKAQLAGIFKDEILPIEVTIKKTTSLFDHDET 218 Query: 126 IDPDISSHILMRLSP 140 + PD S IL +L P Sbjct: 219 VRPDTSLEILSKLRP 233 >gnl|CDD|185341 PRK15444, pduC, propanediol dehydratase large subunit; Provisional. Length = 554 Score = 26.9 bits (60), Expect = 2.8 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 7/79 (8%) Query: 78 RVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMR 137 +V+ L+ +E F D FI Y ++ + M DS L +DP++ ++R Sbjct: 47 KVVELDGKPRED---FDLIDHFIARYGIDLERAEEVMAMDSVKLARMLVDPNVPREEIVR 103 Query: 138 L----SPRQSSLIMSKMNP 152 L +P + ++S+MN Sbjct: 104 LTTAMTPAKIVEVVSQMNV 122 >gnl|CDD|180417 PRK06132, PRK06132, hypothetical protein; Provisional. Length = 359 Score = 26.9 bits (60), Expect = 3.2 Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%) Query: 115 DSDSAALQLEQIDPDISSHILMRLSPRQSSLIMS 148 DS + AL I PD I L+P S+L+++ Sbjct: 308 DSPAEALDRITIPPDFRRRIAALLTP-GSTLVIT 340 >gnl|CDD|161765 TIGR00207, fliG, flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family. Length = 338 Score = 26.3 bits (58), Expect = 3.9 Identities = 13/58 (22%), Positives = 25/58 (43%) Query: 108 LDIYKKMDSDSAALQLEQIDPDISSHILMRLSPRQSSLIMSKMNPKSATMITNVVANM 165 + +K + A ++Q P + IL L P Q++ I+S + + +A M Sbjct: 112 FEFLRKAEPQQIADFIQQEHPQTIALILSHLDPAQAADILSLFPEEVQAEVARRIATM 169 >gnl|CDD|183821 PRK12899, secA, preprotein translocase subunit SecA; Reviewed. Length = 970 Score = 26.3 bits (58), Expect = 4.1 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 8/83 (9%) Query: 66 KVLEDLQKDIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNIL---DIYKKMDSDSAALQ 122 +++E QK +E R + H EY+ K I ++ ++L DI+ A Sbjct: 715 RLIETAQKRVEGRNYTIRKHTLEYDDVMNKQRQTIYAFRNDVLHAEDIF-----VVAKEI 769 Query: 123 LEQIDPDISSHILMRLSPRQSSL 145 +E + ++S IL SL Sbjct: 770 IEHVALMLASLILKDRHADGCSL 792 >gnl|CDD|183409 PRK12291, PRK12291, apolipoprotein N-acyltransferase; Reviewed. Length = 418 Score = 26.1 bits (58), Expect = 5.1 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 8/89 (8%) Query: 1 MILLPIIYYYKKRDMLSQLLFLLFFFLQGFANQSYGDPTLVDREIQQYCTNVIDSVR-ER 59 + L I Y K + + LL F F D LV+ E+ TN+ ++ ++ Sbjct: 155 IFLAAIFLYKKYKKKYKIIGVLLLLFALDFKPFKTSDLPLVNIELVN--TNIPQDLKWDK 212 Query: 60 DYLSQ--KKVLEDLQKDIEQR---VILLE 83 + L + L+++ K I+++ ++L E Sbjct: 213 ENLKSIINENLKEIDKAIDEKKDLIVLPE 241 >gnl|CDD|117782 pfam09231, RDV-p3, Rice dwarf virus p3. Members of this family are core structural proteins found in the double-stranded RNA virus Phytoreovirus. They are large proteins without apparent domain division, with a number of all-alpha regions and one all beta domain near the C-terminal end. Length = 963 Score = 25.7 bits (56), Expect = 6.9 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 14/64 (21%) Query: 98 SFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPRQSSLIMSKMNPKSATM 157 +FI+SY K+I D + ++ DSA +P ++ H + +I S +N A M Sbjct: 43 TFIVSYAKDIYDKFMCIEHDSA------YEPSLTMHRV--------RVIYSMLNDYCAKM 88 Query: 158 ITNV 161 I+ V Sbjct: 89 ISEV 92 >gnl|CDD|182988 PRK11133, serB, phosphoserine phosphatase; Provisional. Length = 322 Score = 25.7 bits (57), Expect = 7.4 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 114 MDSDSAALQLEQID 127 MD DS A+Q+E ID Sbjct: 115 MDMDSTAIQIECID 128 >gnl|CDD|150912 pfam10316, 7TM_GPCR_Srbc, Serpentine type 7TM GPCR chemoreceptor Srbc. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srbc is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. Length = 273 Score = 25.2 bits (56), Expect = 8.4 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 13/50 (26%) Query: 7 IYYYKKRDMLSQLLFLLFFFLQGFANQS--YGDPTLVDREIQQYCTNVID 54 I+Y+ R + + L+ G Q +G +C NVID Sbjct: 114 IFYHNYRPKIPNFIILILAISYGLFEQYVLFG-----------FCDNVID 152 >gnl|CDD|185659 PTZ00481, PTZ00481, Membrane attack complex/ Perforin (MACPF) Superfamily; Provisional. Length = 524 Score = 25.5 bits (56), Expect = 8.5 Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 2/36 (5%) Query: 41 VDREIQQYCTNVIDSVRERDYLSQKKVLEDLQKDIE 76 V +QQ N I+S+++R Q++V E Q+ IE Sbjct: 335 VKANLQQAIMNRIESMKQRQISYQQQVRE--QRRIE 368 >gnl|CDD|178117 PLN02501, PLN02501, digalactosyldiacylglycerol synthase. Length = 794 Score = 25.3 bits (55), Expect = 8.8 Identities = 11/44 (25%), Positives = 18/44 (40%) Query: 98 SFIMSYNKNILDIYKKMDSDSAALQLEQIDPDISSHILMRLSPR 141 S S +D KK+ + + P+IS +L + PR Sbjct: 68 SPSASSFPTEIDFVKKLQPKISEFRRVYSAPEISRKVLEKWGPR 111 >gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional. Length = 895 Score = 25.2 bits (55), Expect = 9.5 Identities = 23/103 (22%), Positives = 47/103 (45%), Gaps = 6/103 (5%) Query: 60 DYLSQKKVLEDLQKDIEQRVILLENHKKEYNLWFQKYDSFIMSYNKNILDIYKKMDSDSA 119 DY+ +K +DL I + LE ++ +YN + + +S + +I + S Sbjct: 340 DYIKKKSRYDDLNNQILE----LEGYEMDYNSYLKSIESLKKKIEEYSKNIERMSAFISE 395 Query: 120 ALQLEQIDPDISSHIL--MRLSPRQSSLIMSKMNPKSATMITN 160 L++++IDPD L + + + S +S +N + + N Sbjct: 396 ILKIQEIDPDAIKKELNEINVKLQDISSKVSSLNQRIRALREN 438 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 0.322 0.136 0.379 Gapped Lambda K H 0.267 0.0697 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,808,835 Number of extensions: 171501 Number of successful extensions: 470 Number of sequences better than 10.0: 1 Number of HSP's gapped: 466 Number of HSP's successfully gapped: 41 Length of query: 175 Length of database: 5,994,473 Length adjustment: 87 Effective length of query: 88 Effective length of database: 4,114,577 Effective search space: 362082776 Effective search space used: 362082776 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 (21.9 bits) S2: 54 (24.6 bits)