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)