RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781083|ref|YP_003065496.1| hypothetical protein CLIBASIA_04925 [Candidatus Liberibacter asiaticus str. psy62] (160 letters) >gnl|CDD|162323 TIGR01371, met_syn_B12ind, 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase. This model describes the cobalamin-independent methionine synthase. A family of uncharacterized archaeal proteins is homologous to the C-terminal region of this family. That family is excluded from this model but, along with this family, belongs to pfam model pfam01717. Length = 750 Score = 33.9 bits (78), Expect = 0.021 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 11/64 (17%) Query: 67 WSERGDIINALDQDLQDVESIEVFEYLKTRLSDLEAHRRSMSFYFAKYPKKVGPSVIDVV 126 +SE +II ++ DV SIE LS + YP +GP V D+ Sbjct: 640 YSEFNEIIESIADLDADVISIEASRSDMELLSAFKNGF--------GYPNGIGPGVYDI- 690 Query: 127 YPHS 130 HS Sbjct: 691 --HS 692 >gnl|CDD|179966 PRK05222, PRK05222, 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional. Length = 758 Score = 31.2 bits (72), Expect = 0.13 Identities = 24/71 (33%), Positives = 28/71 (39%), Gaps = 28/71 (39%) Query: 68 SERGDI---INALDQDLQDVESIEVFEYLKTR-----LSDLEAHRRSMSFYFAKYPKKVG 119 SE DI I ALD DV SIE +R L E YP ++G Sbjct: 647 SEFNDIIDAIAALD---ADVISIET-----SRSDMELLDAFEDF---------GYPNEIG 689 Query: 120 PSVIDVVYPHS 130 P V D+ HS Sbjct: 690 PGVYDI---HS 697 >gnl|CDD|185317 PRK15419, PRK15419, proline:sodium symporter PutP; Provisional. Length = 502 Score = 28.8 bits (64), Expect = 0.73 Identities = 8/20 (40%), Positives = 15/20 (75%) Query: 3 YLSVTWNDLVQVSILVFCFV 22 +L+V+W D VQ S+++F + Sbjct: 180 FLAVSWTDTVQASLMIFALI 199 >gnl|CDD|180112 PRK05478, PRK05478, isopropylmalate isomerase large subunit; Validated. Length = 466 Score = 27.4 bits (62), Expect = 1.7 Identities = 16/42 (38%), Positives = 18/42 (42%), Gaps = 10/42 (23%) Query: 96 RLSDLEAHRRSMSFYFAKYPK--KVGPSVIDVVYPHSHLVKE 135 R+ DL A A K KV P V +V P S LVK Sbjct: 351 RIEDLRA--------AAAVVKGRKVAPGVRALVVPGSGLVKA 384 >gnl|CDD|178093 PLN02475, PLN02475, 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase. Length = 766 Score = 27.0 bits (60), Expect = 2.3 Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 14/65 (21%) Query: 67 WSERGDIINALDQDLQDVESIEVFEYLKTRLSD---LEAHRRSMSFYFAKYPKKVGPSVI 123 +S DII+++ DV +IE +R SD L R KY +GP V Sbjct: 651 YSNFNDIIHSIIDMDADVITIE-----NSR-SDEKLLSVFREG-----VKYGAGIGPGVY 699 Query: 124 DVVYP 128 D+ P Sbjct: 700 DIHSP 704 >gnl|CDD|162712 TIGR02121, Na_Pro_sym, sodium/proline symporter. This family consists of the sodium/proline symporter (proline permease) from a number of Gram-negative and Gram-positive bacteria and from the archaeal genus Methanosarcina. Using the related pantothenate permease as an outgroup, candidate sequences from Bifidobacterium longum and several from archaea are found to be outside the clade defined by known proline permeases. These sequences, scoring between 570 and -40, define the range between trusted and noise cutoff scores. Length = 487 Score = 26.6 bits (59), Expect = 3.1 Identities = 8/20 (40%), Positives = 13/20 (65%) Query: 3 YLSVTWNDLVQVSILVFCFV 22 +L+V+W D VQ ++ F V Sbjct: 176 FLAVSWTDFVQGLLMFFALV 195 >gnl|CDD|152883 pfam12449, DUF3684, Protein of unknown function (DUF3684). This domain family is found in eukaryotes, and is typically between 1072 and 1090 amino acids in length. Length = 1082 Score = 26.1 bits (58), Expect = 4.4 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 6/54 (11%) Query: 85 ESIEVFEYLKTRLSDLEAHR----RSMSF--YFAKYPKKVGPSVIDVVYPHSHL 132 ++ ++FEYL +R+++L + + F + + G SV V +L Sbjct: 829 DARKLFEYLASRVAELSPNDLARLGQAAIVPVFRRAGLEKGSSVRYVAPSQCYL 882 >gnl|CDD|182159 PRK09946, PRK09946, hypothetical protein; Provisional. Length = 270 Score = 25.9 bits (57), Expect = 5.3 Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%) Query: 21 FVSHFVQRKSFADVHEAL--ERY 41 F+ HF + S+AD+H AL E Y Sbjct: 21 FLRHFPRGGSYADIHHALIEEGY 43 >gnl|CDD|185388 PRK15491, PRK15491, replication factor A; Provisional. Length = 374 Score = 25.6 bits (56), Expect = 5.6 Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 2/45 (4%) Query: 59 SSSVRRTYWSERGDIINALDQDLQDVESIEVFEYLKTRLSDLEAH 103 + S+R T W + D+I D ++ S+ + Y K S +E + Sbjct: 104 TGSIRLTLWDDLADLIKTGDIEVGK--SLNISGYAKEGYSGIEVN 146 >gnl|CDD|169939 PRK09517, PRK09517, multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase; Provisional. Length = 755 Score = 25.7 bits (56), Expect = 6.2 Identities = 11/22 (50%), Positives = 12/22 (54%) Query: 32 ADVHEALERYKKVARVVGPHIP 53 AD EAL R VV P+IP Sbjct: 357 ADATEALRRLAVHVDVVTPNIP 378 >gnl|CDD|152889 pfam12455, Dynactin, Dynein associated protein. This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with pfam01302. There is a single completely conserved residue E that may be functionally important. Dynactin has been associated with Dynein, a kinesin protein which is involved in organelle transport, mitotic spindle assembly and chromosome segregation. Dynactin anchors Dynein to specific subcellular structures. Length = 274 Score = 25.3 bits (56), Expect = 6.5 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 19/71 (26%) Query: 86 SIEVFEYLKTRLSDLEAHRRSMSFYFAKYPKKVGPSVIDVVYPHSHLVKEDKVDEKNSSS 145 S+E+F + +LE R++ F+ I+ L+K+D++DE + Sbjct: 146 SVELFLKIGGLYPELEPVERTLDFW------------IE-------LLKKDELDENECAD 186 Query: 146 ELKVDLNKLNA 156 EL+ + + Sbjct: 187 ELQRSIAYFDH 197 >gnl|CDD|183009 PRK11169, PRK11169, leucine-responsive transcriptional regulator; Provisional. Length = 164 Score = 25.5 bits (56), Expect = 7.3 Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 5/39 (12%) Query: 72 DIINALDQDLQDVESIEV----FEYL-KTRLSDLEAHRR 105 + NA Q L++++ + F+YL KTR+ D+ A+R+ Sbjct: 91 EQFNAAVQKLEEIQECHLVSGDFDYLLKTRVPDMSAYRK 129 >gnl|CDD|184978 PRK15017, PRK15017, cytochrome o ubiquinol oxidase subunit I; Provisional. Length = 663 Score = 25.3 bits (55), Expect = 8.2 Identities = 11/38 (28%), Positives = 19/38 (50%) Query: 19 FCFVSHFVQRKSFADVHEALERYKKVARVVGPHIPNSN 56 F V H +R +F ++ E E YK+ H+P ++ Sbjct: 552 FAVVPHVHERDAFWEMKEKGEAYKQPDHYEEIHMPKNS 589 >gnl|CDD|178540 PLN02954, PLN02954, phosphoserine phosphatase. Length = 224 Score = 25.0 bits (55), Expect = 10.0 Identities = 10/41 (24%), Positives = 19/41 (46%) Query: 86 SIEVFEYLKTRLSDLEAHRRSMSFYFAKYPKKVGPSVIDVV 126 S+ E L RLS + + + K P ++ P + ++V Sbjct: 53 SVPFEEALAARLSLFKPSLSQVEEFLEKRPPRLSPGIPELV 93 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 0.318 0.133 0.386 Gapped Lambda K H 0.267 0.0757 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,531,531 Number of extensions: 149103 Number of successful extensions: 350 Number of sequences better than 10.0: 1 Number of HSP's gapped: 347 Number of HSP's successfully gapped: 25 Length of query: 160 Length of database: 5,994,473 Length adjustment: 86 Effective length of query: 74 Effective length of database: 4,136,185 Effective search space: 306077690 Effective search space used: 306077690 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: 53 (24.1 bits)