RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780496|ref|YP_003064909.1| integration host factor subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (114 letters) >gnl|CDD|143973 pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein. Length = 90 Score = 89.9 bits (224), Expect = 1e-19 Identities = 31/89 (34%), Positives = 59/89 (66%) Query: 5 ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64 +T+ +L+K+I+++ GLS+KD+ V + I ++ +GE +++ F TF V+++ +R G Sbjct: 1 MTKKELIKAIAEKTGLSKKDAEAIVDAFLDVITEALKKGEKVELRGFGTFEVRERKARTG 60 Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93 RN +T +E+KI ++VV FK LK+ + Sbjct: 61 RNPKTGEEIKIPAKKVVKFKPGKELKEAV 89 >gnl|CDD|29683 cd00591, HU_IHF, Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.. Length = 87 Score = 87.4 bits (217), Expect = 7e-19 Identities = 31/87 (35%), Positives = 57/87 (65%) Query: 6 TRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGR 65 T+S+L+++I+++ GLS+KD+ V + I ++ +GE +++ F TF V+++ +R GR Sbjct: 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLDVITEALAKGEKVELPGFGTFEVRERAARTGR 60 Query: 66 NLQTNQEVKIDPRRVVVFKASSILKKR 92 N +T +E+KI ++VV FK LK Sbjct: 61 NPKTGEEIKIPAKKVVKFKPGKALKDA 87 >gnl|CDD|31119 COG0776, HimA, Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]. Length = 94 Score = 86.7 bits (215), Expect = 1e-18 Identities = 32/90 (35%), Positives = 58/90 (64%) Query: 4 TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRV 63 T+T+S+L+ +I+++ GLS+KD+ V EI ++ +GE +++ F TF V+++ +R Sbjct: 1 TMTKSELIDAIAEKAGLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAART 60 Query: 64 GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93 GRN +T +E+KI ++V FK LK + Sbjct: 61 GRNPKTGEEIKIPAKKVPKFKPGKALKDAV 90 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 26.4 bits (59), Expect = 1.8 Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%) Query: 30 TTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVGRNL 67 TTL ++ + ++ E +K+ F T V++ G R+G ++ Sbjct: 13 TTLVKKVIE-LLKSEGVKVGGFYTPEVREGGRRIGFDI 49 >gnl|CDD|37330 KOG2119, KOG2119, KOG2119, Predicted bile acid beta-glucosidase [Carbohydrate transport and metabolism]. Length = 879 Score = 25.0 bits (54), Expect = 4.8 Identities = 11/43 (25%), Positives = 19/43 (44%) Query: 16 KEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQ 58 +EF LS +++ + V L+ + A G I F + K Sbjct: 40 REFFLSIREAIKLVPRLWLYTREEAWNGRKAFIDIFNKENHKS 82 >gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor) [Signal transduction mechanisms]. Length = 5019 Score = 25.0 bits (54), Expect = 4.9 Identities = 16/49 (32%), Positives = 24/49 (48%) Query: 44 EAIKISSFATFHVKQKGSRVGRNLQTNQEVKIDPRRVVVFKASSILKKR 92 E + + A FH++QK RVGR E + ++ V K S +KR Sbjct: 3572 ERVLDIAAALFHLEQKSKRVGRRHYCLVEHPLRSKKAVWHKLLSKQRKR 3620 >gnl|CDD|144883 pfam01454, MAGE, MAGE family. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis. Length = 171 Score = 24.5 bits (54), Expect = 6.1 Identities = 6/18 (33%), Positives = 13/18 (72%) Query: 1 MSKTITRSDLVKSISKEF 18 + ITR++++K + KE+ Sbjct: 11 KKEPITRAEILKIVIKEY 28 >gnl|CDD|144535 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family. Length = 229 Score = 24.4 bits (54), Expect = 7.5 Identities = 4/18 (22%), Positives = 11/18 (61%) Query: 2 SKTITRSDLVKSISKEFG 19 + + +L+K +++FG Sbjct: 103 TAAVKNPELIKEAAEKFG 120 >gnl|CDD|147677 pfam05648, PEX11, Peroxisomal biogenesis factor 11 (PEX11). This family consists of several peroxisomal biogenesis factor 11 (PEX11) proteins from several eukaryotic species. The PEX11 peroxisomal membrane proteins promote peroxisome division in multiple eukaryotes. Length = 225 Score = 24.1 bits (53), Expect = 8.2 Identities = 7/22 (31%), Positives = 12/22 (54%) Query: 2 SKTITRSDLVKSISKEFGLSRK 23 + D +K++ +F LSRK Sbjct: 36 GSSPELIDRLKNLESQFSLSRK 57 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.131 0.355 Gapped Lambda K H 0.267 0.0752 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,175,798 Number of extensions: 49947 Number of successful extensions: 107 Number of sequences better than 10.0: 1 Number of HSP's gapped: 107 Number of HSP's successfully gapped: 10 Length of query: 114 Length of database: 6,263,737 Length adjustment: 80 Effective length of query: 34 Effective length of database: 4,535,017 Effective search space: 154190578 Effective search space used: 154190578 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (23.4 bits)