RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764485|ref|YP_003065139.2| hypothetical protein CLIBASIA_03065 [Candidatus Liberibacter asiaticus str. psy62] (243 letters) >gnl|CDD|35020 COG5461, COG5461, Type IV pili component [Cell motility and secretion]. Length = 224 Score = 158 bits (400), Expect = 1e-39 Identities = 79/176 (44%), Positives = 109/176 (61%), Gaps = 1/176 (0%) Query: 67 DYRDRYPILMRKVEQIVDIPLLAGRGEIKYPIHDTIRGFLEKYKNDSASVLFLLIPSPTV 126 DYR R+PI++R+VE +DIP+L G + D +RGFL++Y + SA L + IPS + Sbjct: 37 DYRTRHPIVIREVEPEIDIPILKGDSGLTASQRDRLRGFLDRYSSASADALHIQIPSGSA 96 Query: 127 SSASIRRAVKDIRKIIISSGIPVSSISERIYDADYGMDVDTIRLSYFASKPSAGKCGFWP 186 + + R K+IR+++ SG+ + I YDA D IR+SY A KCG WP Sbjct: 97 NEVTASRMAKEIRRLLAGSGVDRARIRVVNYDASSQEDGAPIRVSYVAYTARTPKCGQWP 156 Query: 187 EDMLGNAKGNRNWTNYGCAYQNNLAAQVVNPLDLFSPRMVTPPDAEQRDKSIQRYR 242 ED+L N + N+N+ N+GCA Q+NLAAQV NP DL PR +TP DAE+R I YR Sbjct: 157 EDLL-NTRDNKNYYNFGCATQSNLAAQVANPRDLLGPRAMTPIDAERRAIVIDTYR 211 >gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA processing and modification]. Length = 924 Score = 29.1 bits (65), Expect = 1.0 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 20/92 (21%) Query: 106 LEKYKNDSASVLFLLIPSPTVSSASIRRAV-----KDIRKIIISSGIPVSSISERIYDAD 160 LE + S+ F ++P + + ++AV K RKII+++ I +SI+ I D Sbjct: 433 LEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSIT--IDDVV 490 Query: 161 YGMD--------VDTIR-----LSYFASKPSA 179 Y +D D R L + SK +A Sbjct: 491 YVIDSGLVKEKSYDPERKVSCLLLSWVSKANA 522 >gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]. Length = 1042 Score = 28.8 bits (64), Expect = 1.4 Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 28/133 (21%) Query: 79 VEQIVDIPLLAGRGEI------KYPIHDTI----RGFLEKYKNDSASVLFLLIPS--PTV 126 V+Q V I L G+I + I T + + + L I S P Sbjct: 551 VKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPAD 610 Query: 127 SSASI-RRAVKDIRKIIISSGIPVSSIS--------------ERIYDADYGMDV-DTIRL 170 A I ++A +RK I+++ I +S++ ++Y+ GMD + + Sbjct: 611 LQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPI 670 Query: 171 SYFASKPSAGKCG 183 S + AG+ G Sbjct: 671 SQANADQRAGRAG 683 >gnl|CDD|107316 cd06321, PBP1_ABC_sugar_binding_like_11, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Length = 271 Score = 28.8 bits (65), Expect = 1.5 Identities = 6/17 (35%), Positives = 12/17 (70%) Query: 140 KIIISSGIPVSSISERI 156 + I +G PVS++ +R+ Sbjct: 123 NVAILNGPPVSAVLDRV 139 >gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer. Length = 203 Score = 28.4 bits (64), Expect = 2.0 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 7/46 (15%) Query: 94 IKYPIHDTIR-GFLEKYKNDSASVLFLLIPSPTVSSASIRRAVKDI 138 + P H +R LE KN + ++F+ V SA+ ++ +KD+ Sbjct: 53 VDVPGHPKLRDKLLETLKNSAKGIVFV------VDSATFQKNLKDV 92 >gnl|CDD|133040 cd04197, eIF-2B_epsilon_N, The N-terminal domain of epsilon subunit of the eIF-2B is a subfamily of glycosyltransferase 2. N-terminal domain of epsilon subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta and epsilon. Subunit epsilon shares sequence similarity with gamma subunit, and with a family of bifunctional nucleotide-binding enzymes such as ADP-glucose pyrophosphorylase, suggesting that epsilon subunit may play roles in nucleotide binding activity. In yeast, eIF2B gamma enhances the activity of eIF2B-epsilon leading to the idea that these subunits form the catalytic subcomplex. Length = 217 Score = 27.2 bits (61), Expect = 4.0 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 11/78 (14%) Query: 118 FLLIPSPTVSSASIRRAV---KDIRK--------IIISSGIPVSSISERIYDADYGMDVD 166 F+L+ VS+ ++ + K+ RK +++ P + +D Sbjct: 107 FILVSGDVVSNIDLKEILEEHKERRKKDKNAIMTMVLKEASPPHRTRRTGEEFVIAVDPK 166 Query: 167 TIRLSYFASKPSAGKCGF 184 T RL ++ P + Sbjct: 167 TSRLLHYEELPGSKYRSI 184 >gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing and modification]. Length = 674 Score = 26.4 bits (58), Expect = 6.8 Identities = 23/117 (19%), Positives = 44/117 (37%), Gaps = 26/117 (22%) Query: 88 LAGRGEIKYPIHDTIRGFLEKY-KNDSASVLFLLIP-----SPTVSSASIRRAVKDIRKI 141 L G+ EI + L + K+ L++P S A RK+ Sbjct: 265 LTGQEEI-----EAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKV 319 Query: 142 IISSGIPVSSIS--------------ERIYDADYGMDV-DTIRLSYFASKPSAGKCG 183 I+S+ I +S++ ++ Y+ G+D + +S ++ AG+ G Sbjct: 320 ILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAG 376 >gnl|CDD|37337 KOG2126, KOG2126, KOG2126, Glycosylphosphatidylinositol anchor synthesis protein [Signal transduction mechanisms]. Length = 895 Score = 26.4 bits (58), Expect = 7.1 Identities = 9/25 (36%), Positives = 13/25 (52%) Query: 24 SLISCLKTIFWKNFFLRTLMLGQLF 48 S I+ TI F R LM+ ++F Sbjct: 836 STITVTSTILVVTIFRRHLMVWKIF 860 >gnl|CDD|73401 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.. Length = 325 Score = 26.3 bits (58), Expect = 7.7 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 6/45 (13%) Query: 51 LLFYGTS---ALAYYDEGSDYR---DRYPILMRKVEQIVDIPLLA 89 L YG+S AL+Y+ E Y + Y L+R+ ++ V IP++A Sbjct: 60 FLTYGSSFAEALSYFPEYGRYNLGPEEYLELIRRAKRAVSIPVIA 104 >gnl|CDD|48641 cd03414, CbiX_SirB_C, Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both CbiX and SirB are found in a wide range of bacteria.. Length = 117 Score = 26.3 bits (58), Expect = 8.4 Identities = 15/100 (15%), Positives = 32/100 (32%), Gaps = 9/100 (9%) Query: 87 LLAGRG----EIKYPIHDTIRGFLEKYKNDSASVLFLLIPSPTVSSASIRRAVKDIRKII 142 +L GRG + + R E F P++ A R R+++ Sbjct: 4 VLVGRGSSDPDANADVAKIARLLEEGTGFARVETAFAAATRPSLPEALERLRALGARRVV 63 Query: 143 ISS-----GIPVSSISERIYDADYGMDVDTIRLSYFASKP 177 + G+ + I E++ + ++ + P Sbjct: 64 VLPYLLFTGVLMDRIEEQVAELAAEPGIEFVLAPPLGPHP 103 >gnl|CDD|34402 COG4792, EscU, Type III secretory pathway, component EscU [Intracellular trafficking and secretion]. Length = 349 Score = 26.0 bits (57), Expect = 8.9 Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 6/46 (13%) Query: 16 FKGLANMRSLISCLKTIFWKNFFLRTLMLGQLFFLLLFYGTSALAY 61 K + ++RS++ LK++ + ++L +F+ +L + Y Sbjct: 128 AKRIFSLRSVVELLKSLL------KVVVLSLIFWFMLHGYANTFLY 167 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 0.325 0.141 0.426 Gapped Lambda K H 0.267 0.0785 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,078,734 Number of extensions: 166664 Number of successful extensions: 574 Number of sequences better than 10.0: 1 Number of HSP's gapped: 573 Number of HSP's successfully gapped: 23 Length of query: 243 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 152 Effective length of database: 4,297,318 Effective search space: 653192336 Effective search space used: 653192336 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 56 (25.2 bits)