RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780417|ref|YP_003064830.1| transcriptional regulator CarD family protein [Candidatus Liberibacter asiaticus str. psy62] (188 letters) >gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. Length = 926 Score = 35.4 bits (82), Expect = 0.010 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 6/67 (8%) Query: 2 TFQQKRDAMRQGF---RTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIA-FDKDKMCL 57 + + + G+++V+ HG+G ++ EV G++ ++ V+ +DK L Sbjct: 313 KKSRLKSKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDK--L 370 Query: 58 KVPVGKA 64 VPV + Sbjct: 371 YVPVEQL 377 >gnl|CDD|179244 PRK01198, PRK01198, V-type ATP synthase subunit C; Provisional. Length = 352 Score = 31.8 bits (73), Expect = 0.11 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 18/93 (19%) Query: 89 ARVKRTMWSRRA-----QEYDAKINSGDLIAIAEVVRDLHRTDSQPE-----KSYSERQL 138 ARV+ R A ++Y+ + L E++R L T+ + E YS L Sbjct: 16 ARVR----VREAKLLDREKYERLLEMKSL---EEIIRFLEETEYKEEIDELGSRYSGPDL 68 Query: 139 YESALNR-MVREIAAVNSISEPEAINLIEVNLS 170 E ALNR + + + IS L++V L Sbjct: 69 IEKALNRNLAKTYELLLEISPGRLKELVDVYLR 101 >gnl|CDD|106078 PRK13041, PRK13041, superantigen-like protein; Reviewed. Length = 231 Score = 27.3 bits (60), Expect = 2.7 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 7/100 (7%) Query: 33 IKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVK 92 IK + +FF DK+ M L K ID +RK ++ ++ GK VK Sbjct: 139 IKADHIGEYDYDFFPFKIDKEAMSL-----KEIDFKLRKYLIDNYGLYG-EMSTGKITVK 192 Query: 93 RTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKS 132 + + + E D K+ + + V D+ R + + K+ Sbjct: 193 KKYYGKYTFELDKKLQEDRMSDVINVT-DIDRIEIKVRKA 231 >gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional. Length = 1147 Score = 27.0 bits (60), Expect = 3.1 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%) Query: 15 RTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPV 61 G+ +V+ HGVG + E G+K E+ ++ + D L VPV Sbjct: 478 HPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAK-LYVPV 523 >gnl|CDD|184850 PRK14848, PRK14848, deubiquitinase SseL; Provisional. Length = 317 Score = 26.1 bits (57), Expect = 5.0 Identities = 11/25 (44%), Positives = 15/25 (60%) Query: 147 VREIAAVNSISEPEAINLIEVNLSS 171 + E A + ISE E +N IE NL + Sbjct: 232 IIEAAKIAGISENEDVNFIETNLQN 256 >gnl|CDD|172935 PRK14460, PRK14460, ribosomal RNA large subunit methyltransferase N; Provisional. Length = 354 Score = 26.2 bits (58), Expect = 5.4 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 8/58 (13%) Query: 125 TDSQPEKSYSERQLYESALNRMVREIAAVNSISEP--------EAINLIEVNLSSKSS 174 T E + RQ+++ + R+ ++ ++S+ IN EV SS Sbjct: 17 TAELGEPRFRARQIWQWLWQKGARDFDSMTNVSKALRARLAEKAVINWPEVETVQTSS 74 >gnl|CDD|148640 pfam07147, PDCD9, Mitochondrial 28S ribosomal protein S30 (PDCD9). This family consists of several eukaryotic mitochondrial 28S ribosomal protein S30 (or programmed cell death protein 9 PDCD9) sequences. The exact function of this family is unknown although it is known to be a component of the mitochondrial ribosome and a component in cellular apoptotic signaling pathways. Length = 423 Score = 25.5 bits (56), Expect = 8.4 Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 7/39 (17%) Query: 9 AMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFV 47 AM QGF GE + P IT+ G FF Sbjct: 334 AMYQGFWQGEDVTRPFTSQCVITD-------GKYFSFFC 365 >gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase; Provisional. Length = 336 Score = 25.4 bits (56), Expect = 9.6 Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 1/27 (3%) Query: 136 RQLYESALNRMVREIAAVNSISEPEAI 162 R LYES R + A+N +++ E + Sbjct: 18 RALYESG-RRAEITVVAINELADAEGM 43 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 0.129 0.348 Gapped Lambda K H 0.267 0.0631 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,902,701 Number of extensions: 177907 Number of successful extensions: 360 Number of sequences better than 10.0: 1 Number of HSP's gapped: 360 Number of HSP's successfully gapped: 24 Length of query: 188 Length of database: 5,994,473 Length adjustment: 88 Effective length of query: 100 Effective length of database: 4,092,969 Effective search space: 409296900 Effective search space used: 409296900 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: 54 (24.8 bits)