RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781203|ref|YP_003065616.1| hypothetical protein CLIBASIA_05550 [Candidatus Liberibacter asiaticus str. psy62] (478 letters) >gnl|CDD|38804 KOG3598, KOG3598, KOG3598, Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]. Length = 2220 Score = 36.6 bits (84), Expect = 0.013 Identities = 33/185 (17%), Positives = 55/185 (29%), Gaps = 34/185 (18%) Query: 262 KHGVKSSSPGLHTSFDAYEAHTDTLAHGVDSLVRGEYPHFDQEKLQTIADNTLEDPHFKP 321 K+G++ S+ + +D +E G L + F ++ N E Sbjct: 1710 KNGLQVSTKQKKSPWDLFE--------GTKHLAPLSWKWFGTVRVDRRVKNVEEQLRLLL 1761 Query: 322 H----LPEP-----EPLPQYKEHSDRQKPSEPLAEHPHPKRKEV-----------ERELS 361 + LP P PLP E + K +E E + + E + Sbjct: 1762 YHTHVLPFPRDYYLAPLPLPPEDEEEAKKAEEEKEAAEKEEESKNAEDEKNKNTAENKKD 1821 Query: 362 EIEGAKKESSARKFFDEG------SPDHSPFKGERNQKLDPMRGADFTDAPHAKFDATTF 415 EG K +S ++ E SP + A +AP T Sbjct: 1822 TKEGEKGKSKDKEKEGEKEKCKRASPKDDVTSEKNEHHPRASDAAAALNAPETNKGMDTQ 1881 Query: 416 TESLP 420 + L Sbjct: 1882 NQKLA 1886 >gnl|CDD|34463 COG4854, COG4854, Predicted membrane protein [Function unknown]. Length = 126 Score = 34.9 bits (80), Expect = 0.054 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%) Query: 93 GAALAGKLLSFIPTPLTRLAGLALQSAPLAA----GALYAYLSHKA 134 AAL G +L + PL A AL+ A A A Y Y S +A Sbjct: 79 SAALGGAVLLALKNPLHTNAAFALEFAVCAVIVLYLAFYMYYSRRA 124 >gnl|CDD|32452 COG2271, UhpC, Sugar phosphate permease [Carbohydrate transport and metabolism]. Length = 448 Score = 32.9 bits (75), Expect = 0.18 Identities = 18/70 (25%), Positives = 22/70 (31%), Gaps = 4/70 (5%) Query: 74 VGTGAHLVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYLSHK 133 GT G L Y+ GAALAG L +I G + S L Sbjct: 380 AGTAT----GFVGLFAYLIGAALAGLPLGYIADTWGWDGGFIVLSIAALLAILLLLPVWN 435 Query: 134 AESSIHHQIE 143 AE + Sbjct: 436 AEERKIRDEK 445 >gnl|CDD|31074 COG0730, COG0730, Predicted permeases [General function prediction only]. Length = 258 Score = 30.4 bits (68), Expect = 1.2 Identities = 21/94 (22%), Positives = 26/94 (27%), Gaps = 4/94 (4%) Query: 77 GAHLVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYLSHKAES 136 L L + GA L L +P L +L L L ALY L + Sbjct: 70 NVDWKLALILLLGALIGAFLGALLALLLPAELLKLLFGLL----LLLLALYMLLGPRLAK 125 Query: 137 SIHHQIEGVDKETADALAWREAIVHTSALLAPGA 170 + A AL S L G Sbjct: 126 AEDRAARLRPLLFALALLIGFLAGFLSGLFGVGG 159 >gnl|CDD|37262 KOG2051, KOG2051, KOG2051, Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]. Length = 1128 Score = 29.6 bits (66), Expect = 2.1 Identities = 29/154 (18%), Positives = 58/154 (37%), Gaps = 16/154 (10%) Query: 327 EPLPQYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFFDEGSPDHSPF 386 E +P+ +E SD P E ++ +E S+ + R F++ D F Sbjct: 286 ELMPELEEESDEADPGEEASQMGKNGSLSIEDLWSDED-------TRAFYENL-IDLRDF 337 Query: 387 KGERNQKLDPMRGAD---FTDAPHAKFDA--TTFTESLPH-VDEQTMHRFSELKERHPVE 440 N+ + + + ++A D TT S + ++ +LKE + Sbjct: 338 VPATNEGFNKSKEVEKESNSEAAMVWDDREQTTEVSSPSNFMEGSIAEMKEDLKESKGED 397 Query: 441 AREVL--EGLQEKLQGTKEIKTKSLIKEAINCFL 472 +E L ++ L ++ S + ++CFL Sbjct: 398 EKEELGKNKQEQDLLESEGDLNTSQVVSNVDCFL 431 >gnl|CDD|31004 COG0659, SUL1, Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]. Length = 554 Score = 29.1 bits (65), Expect = 2.5 Identities = 35/160 (21%), Positives = 57/160 (35%), Gaps = 18/160 (11%) Query: 90 YIAGAALAGKLLSFIPTPLTR--LAGLAL-----QSAPLAAGALYAYLSHKAESSIHHQI 142 + G G+L+ FIP P+ AG+A+ Q L A S++ + Sbjct: 112 ILLGLLRLGRLIRFIPRPVLIGFTAGIAILIILTQLPVLLGLASKVSGFWAKVSALFTVL 171 Query: 143 EGVDKETADALAWREAIVHTSALLAPGAIASQSIAKTVASGAVLNVPFGMVERGWSSKVL 202 ++ T AI+ L P I S IA + + V P + G L Sbjct: 172 LTINLATLLLGLLTLAILLFLPRLTP-RIPSPLIALVLGTLIVWIFPLDSLRYGEIPGSL 230 Query: 203 EDHGYPDMAQHYRIFD-----MESLITDGLIGAFFGGMHS 237 P H+R+ + + +L+ L A G + S Sbjct: 231 -----PSGLPHFRLPNVSLSLLLALLPYALALALLGLLES 265 >gnl|CDD|34016 COG4294, Uve, UV damage repair endonuclease [DNA replication, recombination, and repair]. Length = 347 Score = 28.8 bits (64), Expect = 3.3 Identities = 32/152 (21%), Positives = 54/152 (35%), Gaps = 18/152 (11%) Query: 199 SKVLEDHGYPDMAQHYRIFDMESLITDGLIGAFFGGMHSKQVQNMS--LRLVNDLKEGIT 256 + + D D+A HYRI D L + GG H + + + ++ + L + + Sbjct: 146 REEVVDSSIRDLAYHYRILDGMGLAERSVWNLHLGGTHGGKKERLEQFIKNIQRLPDSVK 205 Query: 257 ERLPYKHGVKSSSP--------GLHTSFDAYEAHTDTLAHGVDSLVRGEYPHFDQEKLQT 308 RL ++ KS S L+ ++AH + G+D +L Sbjct: 206 SRLTLENDDKSYSTEELLPLCEKLNIPL-VFDAHHHNVHPGLDR-----EDSPSLMELIP 259 Query: 309 IADNTLEDPHFKP--HLPEPEPLPQYKEHSDR 338 T P + HL P + HSD Sbjct: 260 RIRETWTRPGLQQKVHLSSPASGTADRRHSDY 291 >gnl|CDD|39109 KOG3906, KOG3906, KOG3906, Tryptophan 2,3-dioxygenase [Amino acid transport and metabolism]. Length = 399 Score = 28.9 bits (64), Expect = 3.3 Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 2/70 (2%) Query: 331 QYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFFDEGSPDHSPFKGER 390 +Y++ +R +E ++L+E K + FD + G R Sbjct: 220 KYEKSVNRYLEDLAKQAADPSNTEEKAKQLAEYH--KTAEVFQSIFDPRQHEQLIRNGNR 277 Query: 391 NQKLDPMRGA 400 ++GA Sbjct: 278 RLSHRALQGA 287 >gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional. Length = 287 Score = 28.5 bits (64), Expect = 4.7 Identities = 11/22 (50%), Positives = 15/22 (68%) Query: 255 ITERLPYKHGVKSSSPGLHTSF 276 + +RL G+ SS+PGLH SF Sbjct: 43 LIDRLRKNLGLTSSNPGLHMSF 64 >gnl|CDD|37349 KOG2138, KOG2138, KOG2138, Predicted RNA binding protein, contains G-patch domain [RNA processing and modification]. Length = 883 Score = 28.1 bits (62), Expect = 5.1 Identities = 16/77 (20%), Positives = 33/77 (42%) Query: 317 PHFKPHLPEPEPLPQYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFF 376 P FKP+ E +P ++H ++ + E K + + + +G +K +K Sbjct: 788 PVFKPNASETLEVPLKEKHKKKKDKHKKKKEKRRKSEKSKKHKKHKKKGKQKNRKPKKSS 847 Query: 377 DEGSPDHSPFKGERNQK 393 S D S + ++ +K Sbjct: 848 SSESSDSSDKQSDKEKK 864 >gnl|CDD|37884 KOG2673, KOG2673, KOG2673, Uncharacterized conserved protein, contains PSP domain [Function unknown]. Length = 485 Score = 28.1 bits (62), Expect = 6.0 Identities = 13/76 (17%), Positives = 19/76 (25%) Query: 299 PHFDQEKLQTIADNTLEDPHFKPHLPEPEPLPQYKEHSDRQKPSEPLAEHPHPKRKEVER 358 E + +N + L P P K +++ EP K E Sbjct: 313 SDSGTEVDDPLTENEVASEPRPNSLDLPVPEDPGKTSDGKERLEEPELPDIFTKDVEAGH 372 Query: 359 ELSEIEGAKKESSARK 374 E RK Sbjct: 373 ASDEDSEVTSLCQKRK 388 >gnl|CDD|38255 KOG3045, KOG3045, KOG3045, Predicted RNA methylase involved in rRNA processing [RNA processing and modification]. Length = 325 Score = 28.1 bits (62), Expect = 6.0 Identities = 25/143 (17%), Positives = 46/143 (32%), Gaps = 15/143 (10%) Query: 330 PQYKEHSDRQKPSEPLAEHPHPKRKEVERELSEIEGAKKESSARKFFDEGSPDHSPFKGE 389 P K S + K + KRK+ ER+L + A+ + + + SP + Sbjct: 23 PSEKPTSSKTKEEKK-----KKKRKKGERKLKAKKAAELKENVEEPPLGSEAKSSPKENS 77 Query: 390 RNQKLDPMRGADFTDAPHAKFDATTFTESLPHVDEQTMHRFSELKERHPVEAREVLEGLQ 449 + ++ + + A A T + + R + R+ L Sbjct: 78 KKKRRNETKKKKEKPPEKAGAAAETEKTEATDLQAKMKKRLDGGRFRY----------LN 127 Query: 450 EKLQGTKEIKTKSLIKEAINCFL 472 E+L + L KE F Sbjct: 128 EQLYTGTSSEAFDLFKEDPTAFD 150 >gnl|CDD|146672 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Length = 186 Score = 27.8 bits (62), Expect = 7.5 Identities = 20/64 (31%), Positives = 29/64 (45%) Query: 80 LVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYLSHKAESSIH 139 ++ GL +A IA L G L + + L +A LAL LA G L L +S Sbjct: 12 IILGLLLIASGIALLVLFGAGLGALISTLLGIALLALGLVLLALGLLCLLLKAPVQSVRP 71 Query: 140 HQIE 143 ++E Sbjct: 72 QKLE 75 >gnl|CDD|111851 pfam03007, UPF0089, Uncharacterized protein family (UPF0089). This family of uncharacterized proteins is greatly expanded in Mycobacterium tuberculosis. The most conserved region of the proteins contains conserved histidine and aspartate residues suggesting a possible metal binding site suggestive of a protease activity (Bateman A. pers. obs.). Length = 263 Score = 27.7 bits (62), Expect = 7.8 Identities = 28/104 (26%), Positives = 37/104 (35%), Gaps = 21/104 (20%) Query: 38 VINMPARSLDKL-VAPFREETHDQPNYYRGSRTDPHSVGTGAHLVEGLTSLAPYIAGAA- 95 +N+ AR LD P R P RTD + G GL +A +AG Sbjct: 145 GLNLLARLLDLDPDPPPRPTPPQTP--PGDPRTDLRASGILVLPAAGLGRVAGGVAGVVS 202 Query: 96 LAGKLL-----------------SFIPTPLTRLAGLALQSAPLA 122 AG+LL + P++R A QS PL Sbjct: 203 TAGRLLERALIARSVALPFAAPHTPFNAPVSRARRFAAQSLPLD 246 >gnl|CDD|145649 pfam02610, Arabinose_Isome, L-arabinose isomerase. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme. Length = 359 Score = 27.6 bits (62), Expect = 8.2 Identities = 9/28 (32%), Positives = 16/28 (57%) Query: 2 YFNAVSDEDIRDNIKEWAQRPRVSPDIK 29 NAVSDED+ + E+ ++P++ Sbjct: 217 AVNAVSDEDVDALVAEYEDLYDLAPELN 244 >gnl|CDD|36921 KOG1709, KOG1709, KOG1709, Guanidinoacetate methyltransferase and related proteins [Amino acid transport and metabolism]. Length = 271 Score = 27.6 bits (61), Expect = 8.8 Identities = 24/87 (27%), Positives = 34/87 (39%), Gaps = 17/87 (19%) Query: 106 TPLTRLAGLALQSAPLAAGALYAYLSHKAESSIHHQIEGVDKETADALAWREAIVHTSAL 165 L L +A A L YLS ++ + +GV + W I+H A Sbjct: 43 LLLFALGRNESPNADGNAPYLQDYLSTAEDTLLDSLGKGV------MMRWETPIMHALA- 95 Query: 166 LAPGAIASQSIAKTVASGAVLNVPFGM 192 AI+++ G VLNV FGM Sbjct: 96 ---EAISTKG-------GRVLNVGFGM 112 >gnl|CDD|119358 cd02879, GH18_plant_chitinase_class_V, The class V plant chitinases have a glycosyl hydrolase family 18 (GH18) domain, but lack the chitin-binding domain present in other GH18 enzymes. The GH18 domain of the class V chitinases has endochitinase activity in some cases and no catalytic activity in others. Included in this family is a lectin found in black locust (Robinia pseudoacacia) bark, which binds chitin but lacks chitinase activity. Also included is a chitinase-related receptor-like kinase (CHRK1) from tobacco (Nicotiana tabacum), with an N-terminal GH18 domain and a C-terminal kinase domain, which is thought to be part of a plant signaling pathway. The GH18 domain of CHRK1 is expressed extracellularly where it binds chitin but lacks chitinase activity.. Length = 299 Score = 27.3 bits (61), Expect = 9.2 Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 1/32 (3%) Query: 408 AKFDATTFTESLPHVDEQTMHRFSE-LKERHP 438 A D +T+ + DE F+E +K ++P Sbjct: 34 ADLDPSTYEVVISPSDESEFSTFTETVKRKNP 65 >gnl|CDD|36175 KOG0957, KOG0957, KOG0957, PHD finger protein [General function prediction only]. Length = 707 Score = 27.4 bits (60), Expect = 9.7 Identities = 10/40 (25%), Positives = 14/40 (35%) Query: 319 FKPHLPEPEPLPQYKEHSDRQKPSEPLAEHPHPKRKEVER 358 F EP P P+Y E + K + + P E Sbjct: 631 FINVPKEPAPAPEYIEDTKSPKRPKLQSPCKTPINVPAEA 670 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 0.314 0.132 0.388 Gapped Lambda K H 0.267 0.0479 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,840,734 Number of extensions: 310322 Number of successful extensions: 725 Number of sequences better than 10.0: 1 Number of HSP's gapped: 725 Number of HSP's successfully gapped: 31 Length of query: 478 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 381 Effective length of database: 4,167,664 Effective search space: 1587879984 Effective search space used: 1587879984 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: 42 (22.0 bits) S2: 59 (27.1 bits)