RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781148|ref|YP_003065561.1| hypothetical protein CLIBASIA_05275 [Candidatus Liberibacter asiaticus str. psy62] (69 letters) >gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model. Length = 421 Score = 38.9 bits (91), Expect = 3e-04 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%) Query: 21 IGLEQEILGSLLLK-GNLQPIISFLDAQHFIDPIHSEVFRAITR 63 I EQ +LG LLL ++ +++ L +HF H +F A+ Sbjct: 2 IEAEQAVLGGLLLDNDFIERVMAILKPEHFYSQDHRIIFEAMLD 45 >gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of > 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites. Length = 434 Score = 35.5 bits (83), Expect = 0.003 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%) Query: 21 IGLEQEILGSLLLKGNLQP-IISFLDAQHFIDPIHSEVFRAITR 63 I EQ +LG++LL + L + F P H +F+AI Sbjct: 6 IEAEQAVLGAILLDNEAIDDVAEILKPEDFYRPAHQLIFQAILD 49 >gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional. Length = 497 Score = 33.7 bits (78), Expect = 0.010 Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%) Query: 24 EQEILGSLLLKGNLQPIIS-FLDAQHFIDPIHSEVFRAITR 63 EQ +LG++L+ +S FL +HF +P+H ++ AI + Sbjct: 28 EQALLGAILINNRALDRVSDFLKPEHFFEPLHQRIYEAIAK 68 >gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated. Length = 886 Score = 30.9 bits (70), Expect = 0.083 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%) Query: 21 IGLEQEILGSLLL-KGNLQPIISFLDAQHFIDPIHSEVFRAITR 63 + EQ +LG +LL K + ++ L F P H ++ AI Sbjct: 28 LAAEQSVLGGMLLSKEAIARVLERLRPGAFYRPAHQNIYDAILD 71 >gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional. Length = 428 Score = 29.9 bits (67), Expect = 0.15 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%) Query: 24 EQEILGSLLLKGNLQPIISFLDAQHFIDPIHSEVFRAITRKTTNE 68 E+ +LGSLLL G L L Q+F P+H +F+ + RK +E Sbjct: 9 EKTVLGSLLLDGELIKECR-LTEQYFSMPVHKSIFQLM-RKMEDE 51 >gnl|CDD|177919 PLN02280, PLN02280, IAA-amino acid hydrolase. Length = 478 Score = 26.5 bits (58), Expect = 1.5 Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 2/27 (7%) Query: 4 DFSKKYYSRNNNSIYYFIGLEQEILGS 30 DFS +YS+ + +Y+IG+ E LGS Sbjct: 419 DFS--FYSQVVPAAFYYIGIRNETLGS 443 >gnl|CDD|183174 PRK11521, PRK11521, hypothetical protein; Provisional. Length = 124 Score = 24.7 bits (54), Expect = 5.6 Identities = 11/18 (61%), Positives = 12/18 (66%) Query: 27 ILGSLLLKGNLQPIISFL 44 ILGSLLL+G Q SF Sbjct: 7 ILGSLLLQGMNQQQRSFA 24 >gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated. Length = 819 Score = 23.9 bits (52), Expect = 8.8 Identities = 10/25 (40%), Positives = 14/25 (56%) Query: 10 YSRNNNSIYYFIGLEQEILGSLLLK 34 S+N I + +G E+ IL LL K Sbjct: 417 LSKNFFCITHEVGAEEIILYFLLKK 441 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 0.323 0.140 0.403 Gapped Lambda K H 0.267 0.0684 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,096,379 Number of extensions: 54733 Number of successful extensions: 117 Number of sequences better than 10.0: 1 Number of HSP's gapped: 113 Number of HSP's successfully gapped: 17 Length of query: 69 Length of database: 5,994,473 Length adjustment: 40 Effective length of query: 29 Effective length of database: 5,130,153 Effective search space: 148774437 Effective search space used: 148774437 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.1 bits)