RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781150|ref|YP_003065563.1| hypothetical protein CLIBASIA_05285 [Candidatus Liberibacter asiaticus str. psy62] (33 letters) >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 = 35.1 bits (82), Expect = 0.004 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 8/31 (25%) Query: 2 DFIVAKQRNGPIESVSL--------FVDMPY 24 + I+AKQRNGP +V L F ++ Sbjct: 404 EIIIAKQRNGPTGTVKLAFQGEYTRFENLAR 434 >gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional. Length = 497 Score = 34.9 bits (81), Expect = 0.005 Identities = 10/28 (35%), Positives = 17/28 (60%) Query: 2 DFIVAKQRNGPIESVSLFVDMPYSVIKD 29 + I+AKQR+GP +V L + ++ D Sbjct: 459 EVIIAKQRHGPTGTVKLAFESEFTRFGD 486 >gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated. Length = 886 Score = 32.4 bits (74), Expect = 0.030 Identities = 12/28 (42%), Positives = 17/28 (60%) Query: 2 DFIVAKQRNGPIESVSLFVDMPYSVIKD 29 +FIVAK RNGP +V+L + S + Sbjct: 855 EFIVAKHRNGPTGTVTLAFQLHLSRFAN 882 >gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional. Length = 472 Score = 31.1 bits (71), Expect = 0.068 Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 8/28 (28%) Query: 4 IVAKQRNGPIESVSL--------FVDMP 23 I+ K RNGP +V L FVD P Sbjct: 425 IIGKNRNGPTGTVKLRFQKEFTRFVDKP 452 >gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional. Length = 505 Score = 29.0 bits (65), Expect = 0.26 Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 8/30 (26%) Query: 2 DFIVAKQRNGPIESV--------SLFVDMP 23 D I+AK R GPI++V S FVDM Sbjct: 474 DIILAKHRGGPIDTVQVAHQLHYSRFVDMA 503 >gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional. Length = 448 Score = 29.2 bits (66), Expect = 0.29 Identities = 10/15 (66%), Positives = 13/15 (86%) Query: 4 IVAKQRNGPIESVSL 18 I+AKQRNGP+ +V L Sbjct: 416 IIAKQRNGPVGTVEL 430 >gnl|CDD|181562 PRK08840, PRK08840, replicative DNA helicase; Provisional. Length = 464 Score = 28.8 bits (64), Expect = 0.37 Identities = 13/24 (54%), Positives = 15/24 (62%) Query: 2 DFIVAKQRNGPIESVSLFVDMPYS 25 + I+ KQRNGPI SV L YS Sbjct: 428 EIIIGKQRNGPIGSVRLTFQGQYS 451 >gnl|CDD|180791 PRK07004, PRK07004, replicative DNA helicase; Provisional. Length = 460 Score = 28.0 bits (62), Expect = 0.65 Identities = 10/17 (58%), Positives = 12/17 (70%) Query: 2 DFIVAKQRNGPIESVSL 18 + I+ KQRNGPI V L Sbjct: 423 EIIIGKQRNGPIGPVRL 439 >gnl|CDD|136106 PRK06904, PRK06904, replicative DNA helicase; Validated. Length = 472 Score = 27.7 bits (61), Expect = 0.75 Identities = 12/24 (50%), Positives = 14/24 (58%) Query: 2 DFIVAKQRNGPIESVSLFVDMPYS 25 + I+ KQRNGPI V L YS Sbjct: 434 EIIIGKQRNGPIGRVRLAFQGQYS 457 >gnl|CDD|180157 PRK05595, PRK05595, replicative DNA helicase; Provisional. Length = 444 Score = 27.1 bits (60), Expect = 0.93 Identities = 10/15 (66%), Positives = 12/15 (80%) Query: 4 IVAKQRNGPIESVSL 18 I+AKQRNGP +V L Sbjct: 412 IIAKQRNGPTGTVKL 426 >gnl|CDD|181193 PRK08006, PRK08006, replicative DNA helicase; Provisional. Length = 471 Score = 26.5 bits (58), Expect = 1.7 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 2 DFIVAKQRNGPIESVSL 18 + I+ KQRNGPI +V L Sbjct: 435 EIIIGKQRNGPIGTVRL 451 >gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional. Length = 428 Score = 26.5 bits (58), Expect = 1.8 Identities = 9/17 (52%), Positives = 11/17 (64%) Query: 2 DFIVAKQRNGPIESVSL 18 + VAK RNGP+ S L Sbjct: 399 EIHVAKHRNGPVGSFKL 415 >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 = 25.4 bits (56), Expect = 3.5 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 2 DFIVAKQRNGPIESVSL 18 + I+AK R+GP +V L Sbjct: 403 ELILAKNRHGPTGTVEL 419 >gnl|CDD|178450 PLN02859, PLN02859, glutamine-tRNA ligase. Length = 788 Score = 24.3 bits (53), Expect = 6.3 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%) Query: 9 RNGPI-ESVSLFVDMPYSVIKDGK 31 R+ PI ES+ LF DM +I++GK Sbjct: 379 RDRPIEESLKLFEDMRRGLIEEGK 402 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 0.320 0.138 0.421 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: 510,523 Number of extensions: 13592 Number of successful extensions: 42 Number of sequences better than 10.0: 1 Number of HSP's gapped: 42 Number of HSP's successfully gapped: 15 Length of query: 33 Length of database: 5,994,473 Length adjustment: 7 Effective length of query: 26 Effective length of database: 5,843,217 Effective search space: 151923642 Effective search space used: 151923642 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.1 bits)