RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781191|ref|YP_003065604.1| hypothetical protein CLIBASIA_05490 [Candidatus Liberibacter asiaticus str. psy62] (165 letters) >gnl|CDD|151373 pfam10926, DUF2800, Protein of unknown function (DUF2800). This is a family of uncharacterized proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins. Length = 363 Score = 108 bits (272), Expect = 7e-25 Identities = 49/146 (33%), Positives = 79/146 (54%), Gaps = 11/146 (7%) Query: 6 CRFCRAKPRCGALAVKALST----FSEHMQILSNRQLSQVMNVLPLIETWMKGVKEEALN 61 CRFC+AK C A A L+ F + L++ +L++++ L+E W K V+ AL+ Sbjct: 215 CRFCKAKATCRARAQAVLNLAKYDFEDPTLDLTDEELAELLEKADLLEKWAKDVEAYALD 274 Query: 62 VLSSGEDLPNYELKEGRKGSRTYNNDNQVEQLLMRE-LGDEA-YNRTLLSPTETEQLVKR 119 +G+++P Y+L EGR +R + ++ V L L DE Y + L+SPT+ E+L+ + Sbjct: 275 EARNGKEVPGYKLVEGR-SNRKWTDEEAVAAALKAAGLKDEDIYKKKLISPTQAEKLLGK 333 Query: 120 KKVSETTWEQLQKFITRKDGKQVIVP 145 KK E L I + GK +VP Sbjct: 334 KKFKEL----LGALIVKPPGKPTLVP 355 >gnl|CDD|150843 pfam10232, Med8, Mediator of RNA polymerase II transcription complex subunit 8. Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20. Length = 226 Score = 30.6 bits (69), Expect = 0.19 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 5/85 (5%) Query: 44 VLPLIETWMKGVKEEALNVLSSGEDLPNYELKEGRKGSRTYNNDNQVEQLLMRELGDEAY 103 P +E WMK +++A N E+ ++ N ++V L E E+ Sbjct: 99 PDPEVEEWMKQARQKAENSTKDTAAKQEVEIDILQQNKEVSNWLDKV-TKLREEWEFESS 157 Query: 104 NRT----LLSPTETEQLVKRKKVSE 124 +R +T QLV K + Sbjct: 158 HRVEIEQTSEEEDTNQLVAAVKDGK 182 >gnl|CDD|151744 pfam11303, DUF3105, Protein of unknown function (DUF3105). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. Length = 130 Score = 29.6 bits (67), Expect = 0.38 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 9/54 (16%) Query: 83 TYN---NDNQVEQLLMRELGDEAYNRTLLSPTETEQLVKRKKVSETTWEQLQKF 133 TY+ ++VE+L + L R LLSP V+ T W + + Sbjct: 55 TYDPDLPPDEVEKL--KALAAGCLPRVLLSPYPG----LDSPVALTAWGRQLEL 102 >gnl|CDD|184618 PRK14318, glmM, phosphoglucosamine mutase; Provisional. Length = 448 Score = 27.2 bits (61), Expect = 2.2 Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%) Query: 96 RELGDEAYNRTLLSPTETEQLVK 118 ELGD R LL P+ TE LV+ Sbjct: 401 AELGDTG--RVLLRPSGTEPLVR 421 >gnl|CDD|161897 TIGR00474, selA, seryl-tRNA(sec) selenium transferase. In bacteria, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes SelA. This model excludes homologs that appear to differ in function from Frankia alni, Helicobacter pylori, Methanococcus jannaschii and other archaea, and so on. Length = 454 Score = 26.8 bits (60), Expect = 2.6 Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 4/31 (12%) Query: 72 YELKEGRKGSRTYNNDNQVEQLLMRELGDEA 102 Y+L+ G++GSR + VE LL G E Sbjct: 113 YDLETGKRGSR----YSHVEGLLCELTGAED 139 >gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed. Length = 273 Score = 26.9 bits (59), Expect = 2.8 Identities = 19/95 (20%), Positives = 46/95 (48%), Gaps = 16/95 (16%) Query: 81 SRTYNNDNQVEQLLMRELGDEAYNRTLLSPTETEQLVKRKKVSETT-------WEQLQKF 133 SR + + ++ + ++LG + L+ + +V+R +++ T Q +++ Sbjct: 183 SRNVDGERELLEAFAKKLGSQ-----LIHFVPRDNIVQRAEINRKTVIDFDPESNQAKEY 237 Query: 134 ITRKDGKQ----VIVPCDLPVNHLKANISEFSVLK 164 +T Q ++VP LP+ L+A + EF +++ Sbjct: 238 LTLAHNVQNNDKLVVPTPLPMEELEAMMVEFGIVE 272 >gnl|CDD|180894 PRK07226, PRK07226, fructose-bisphosphate aldolase; Provisional. Length = 267 Score = 26.7 bits (60), Expect = 3.1 Identities = 8/18 (44%), Positives = 12/18 (66%) Query: 130 LQKFITRKDGKQVIVPCD 147 L++ R+ G+ VIVP D Sbjct: 10 LERIFNRRTGRTVIVPMD 27 >gnl|CDD|177868 PLN02222, PLN02222, phosphoinositide phospholipase C 2. Length = 581 Score = 26.5 bits (58), Expect = 3.4 Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%) Query: 26 FSEHMQILSNRQLSQVMNVLPLIETWMKGVKEEALNVL-SSGED 68 F+ H L+ QLS + +P+I+ KGV+ L++ +S +D Sbjct: 115 FTGHNSYLTGNQLSSDCSEVPIIDALKKGVRVIELDIWPNSDKD 158 >gnl|CDD|178827 PRK00053, alr, alanine racemase; Reviewed. Length = 363 Score = 26.3 bits (59), Expect = 4.0 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%) Query: 123 SETTWEQLQKFITRKDGKQVIVPCDLPVNHLKAN 156 + T +QL +F + + P+ HL AN Sbjct: 170 NSYTEQQLNRF---EAALAGLPGKGKPLRHL-AN 199 >gnl|CDD|182335 PRK10252, entF, enterobactin synthase subunit F; Provisional. Length = 1296 Score = 26.2 bits (58), Expect = 4.0 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 24/76 (31%) Query: 41 VMNVLPLIETWMKGVKEEALNVLSSGEDLP------NYELKEGRKGSRTYNNDNQVEQLL 94 V+NVLPL ++ +++ E LP +LK+ R+ R Y EQ++ Sbjct: 293 VLNVLPL-----------RVH-IAAQETLPELATRLAAQLKKMRRHQR-Y----DAEQIV 335 Query: 95 MRELGDEAYNRTLLSP 110 R+ G A + L P Sbjct: 336 -RDSGRAAGDEPLFGP 350 >gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric. This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase. Length = 1165 Score = 25.9 bits (57), Expect = 4.9 Identities = 10/26 (38%), Positives = 15/26 (57%) Query: 17 ALAVKALSTFSEHMQILSNRQLSQVM 42 A+A ALS F +H +++ RQ M Sbjct: 111 AIAAHALSIFGDHQDVMAARQTGFAM 136 >gnl|CDD|119297 pfam10777, YlaC, Extracytoplasmic function sigma factor YlaC. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis. Length = 156 Score = 25.8 bits (57), Expect = 6.0 Identities = 10/37 (27%), Positives = 17/37 (45%) Query: 101 EAYNRTLLSPTETEQLVKRKKVSETTWEQLQKFITRK 137 E YN +S ++++ V + QL+K I K Sbjct: 103 EWYNTRAVSQQLIDEILNSPNVPDEQKAQLKKIIATK 139 >gnl|CDD|166345 PLN02704, PLN02704, flavonol synthase. Length = 335 Score = 25.1 bits (55), Expect = 8.9 Identities = 11/30 (36%), Positives = 16/30 (53%) Query: 51 WMKGVKEEALNVLSSGEDLPNYELKEGRKG 80 +++GV ++ LS G L ELKE G Sbjct: 165 YLRGVADKLFKTLSLGLGLEEDELKEAVGG 194 >gnl|CDD|177331 PHA02004, PHA02004, capsid protein. Length = 332 Score = 25.2 bits (55), Expect = 9.4 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%) Query: 90 VEQLLMRELGDEAYNR--TLLSPTETEQLVKRKKV 122 VE L+ R+LGD Y+ TL+SP L++ K+ Sbjct: 182 VETLIKRDLGDAVYSEGLTLVSPRIFSLLLEHDKL 216 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 0.315 0.130 0.371 Gapped Lambda K H 0.267 0.0656 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,541,360 Number of extensions: 147800 Number of successful extensions: 346 Number of sequences better than 10.0: 1 Number of HSP's gapped: 343 Number of HSP's successfully gapped: 20 Length of query: 165 Length of database: 5,994,473 Length adjustment: 86 Effective length of query: 79 Effective length of database: 4,136,185 Effective search space: 326758615 Effective search space used: 326758615 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 (21.6 bits) S2: 53 (24.3 bits)