RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780183|ref|YP_003064596.1| single-strand binding protein
(ssb) [Candidatus Liberibacter asiaticus str. psy62]
(159 letters)
>gnl|CDD|109492 pfam00436, SSB, Single-strand binding protein family. This family
includes single stranded binding proteins and also the
primosomal replication protein N (PriB). PriB forms a
complex with PriA, PriC and ssDNA.
Length = 104
Score = 125 bits (317), Expect = 4e-30
Identities = 44/106 (41%), Positives = 70/106 (66%), Gaps = 2/106 (1%)
Query: 5 LNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEEL 64
+NKVIL+G L DP++R+T +G + N +A + +KD+ E E+T++ V+V+ + L
Sbjct: 1 MNKVILVGRLTRDPELRYTPNGNAVANFTLAVNRRFKDQ-NGESDEETDFIRVVVWGK-L 58
Query: 65 CRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVML 110
+YL+KGS VY+EG L+TRK++DQ G RY TEI+ ++ L
Sbjct: 59 AENAAEYLKKGSLVYVEGRLRTRKYEDQEGQKRYVTEIVADNVQFL 104
>gnl|CDD|30974 COG0629, Ssb, Single-stranded DNA-binding protein [DNA replication,
recombination, and repair].
Length = 167
Score = 123 bits (310), Expect = 2e-29
Identities = 56/168 (33%), Positives = 84/168 (50%), Gaps = 12/168 (7%)
Query: 3 ASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSE 62
+NKVIL+G L DP++R+T +G +V + A + D + ER E+T+W V+++
Sbjct: 1 MMMNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWG- 59
Query: 63 ELCRIVEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMR----SMVMLDGRRDSLQ 118
+L +YL+KGS VY+EG LQTRKW+DQ G RY TEI+ S+ ML R+
Sbjct: 60 KLAENAAEYLKKGSLVYVEGRLQTRKWEDQEGQKRYQTEIVTEIVADSVQMLGSRKSGEA 119
Query: 119 GEEQRSEQHSNNLKENVVGNRYSSPRE-------ESVFSDELDDEIPF 159
+S + E + + DD+IPF
Sbjct: 120 AGGGGGGSNSPDSPPPAQSAEAPGDDENASPFVVVNAPIEFDDDDIPF 167
>gnl|CDD|72968 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the
OB fold of ssDNA-binding protein (SSB). SSBs bind with
high affinity to ssDNA. They bind to and protect ssDNA
intermediates during DNA metabolic pathways. All
bacterial and eukaryotic SSBs studied to date
oligomerize to bring together four OB folds in their
active state. The majority (e.g. Escherichia coli SSB)
have a single OB fold per monomer, which oligomerize to
form a homotetramer. However, Deinococcus and Thermus
SSB proteins have two OB folds per monomer, which
oligomerize to form a homodimer. Mycobacterium
tuberculosis SSB varies in quaternary structure from E.
coli SSB. It forms a dimer of dimers having a unique
dimer interface, which lends the protein greater
stability. Included in this group are OB folds similar
to Escherichia coli PriB. E.coli PriB is homodimeric
with each monomer having a single OB fold. It does not
appear to form higher order oligomers. PriB is an
essential protein for the replication restart at forks
that have stalled at sites of DNA damage. It also plays
a role in the assembly of primosome during replication
initiation at the bacteriophage phiX174 origin. PriB
physically interacts with SSB and binds ssDNA with high
affinity..
Length = 100
Score = 107 bits (269), Expect = 1e-24
Identities = 42/103 (40%), Positives = 62/103 (60%), Gaps = 3/103 (2%)
Query: 8 VILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEELCRI 67
VILIG LG DP++R+T G + +A + KDR +E E+T+W V+ F + L
Sbjct: 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDR--DEEEEETDWIRVVAFGK-LAEN 57
Query: 68 VEQYLRKGSKVYIEGSLQTRKWQDQSGNNRYTTEIIMRSMVML 110
+YL+KG VY+EG L+TR W+D+ G RY TE++ + L
Sbjct: 58 AAKYLKKGDLVYVEGRLRTRSWEDKDGQKRYGTEVVADRIEFL 100
>gnl|CDD|36866 KOG1653, KOG1653, KOG1653, Single-stranded DNA-binding protein
[Replication, recombination and repair].
Length = 175
Score = 77.0 bits (189), Expect = 2e-15
Identities = 37/113 (32%), Positives = 60/113 (53%), Gaps = 3/113 (2%)
Query: 4 SLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNE--RREKTEWHSVIVFS 61
+NKVIL+G +G DP + ++GR + + T +K R+ + + T+WH V VF+
Sbjct: 54 GVNKVILVGRVGQDPLQKILRNGRPVTIFSVGTGGMFKQRLYQAGDQPQPTQWHRVSVFN 113
Query: 62 EELCRIVEQYLRKGSKVYIEGSLQTRKWQ-DQSGNNRYTTEIIMRSMVMLDGR 113
E L +YL+KGS++Y+EG ++ R D GN + II+ V
Sbjct: 114 EVLADYALKYLKKGSRIYVEGKIEYRGENDDIQGNVKRIPTIIIARDVSFLID 166
>gnl|CDD|113557 pfam04791, LMBR1, LMBR1-like membrane protein. Members of this
family are integral membrane proteins that are around
500 residues in length. LMBR1 is not involved in
preaxial polydactyly, as originally thought. Vertebrate
members of this family may play a role in limb
development. A member of this family has been shown to
be a lipocalin membrane receptor.
Length = 419
Score = 29.3 bits (66), Expect = 0.42
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 124 SEQHSNNLKENVVGNRYSSPREESVFSDELDDE 156
S L E+V R S E + EL+
Sbjct: 218 SVSLLPRLLEDVNEQRSKSATELGKLTRELNLS 250
>gnl|CDD|33020 COG3207, DIT1, Pyoverdine/dityrosine biosynthesis protein
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 330
Score = 28.5 bits (63), Expect = 0.88
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 17/66 (25%)
Query: 22 HTQDGRKIVNIRIATSDSWKDRVTNERREKTEWHSVIVFSEELCRIV-----EQYLRKGS 76
H DG K ++ + T D + T WH V V +E R V E GS
Sbjct: 259 HPADGLKFGSLMMPTEDDFL----------TPWHGVAVNTE--DRFVLMKRSEVLELGGS 306
Query: 77 KVYIEG 82
V I G
Sbjct: 307 LVQING 312
>gnl|CDD|145480 pfam02353, CMAS, Cyclopropane-fatty-acyl-phospholipid synthase.
This family consist of
Cyclopropane-fatty-acyl-phospholipid synthase or CFA
synthase EC:2.1.1.79 this enzyme catalyse the reaction:
S-adenosyl-L-methionine + phospholipid olefinic fatty
acid <=> S-adenosyl-L-homocysteine + phospholipid
cyclopropane fatty acid.
Length = 273
Score = 26.5 bits (59), Expect = 2.9
Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 36 TSDSWKDRVTNERREKTEWHSVIVFSEELCRIVEQYLRKGSKVYIEGSLQTRKW 89
T D W + + +++ ++ + SEE R+ YL + + G + ++
Sbjct: 225 TLDLWAENL-QANKDE----AIALQSEEFYRMWMLYLTGCAVAFRVGYIDVHQF 273
>gnl|CDD|37118 KOG1907, KOG1907, KOG1907, Phosphoribosylformylglycinamidine
synthase [Nucleotide transport and metabolism].
Length = 1320
Score = 25.3 bits (55), Expect = 7.3
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 43 RVTNERREKTEWHSVIVFSEELCRIVEQYLRKGS 76
RV E E+ E+H I+FS + I +Q+ RK
Sbjct: 413 RVLLENGERREYHKPIMFSGGIGTIRKQHARKEP 446
>gnl|CDD|146811 pfam04364, DNA_pol3_chi, DNA polymerase III chi subunit, HolC.
The DNA polymerase III holoenzyme (EC:2.7.7.7) is the
polymerase responsible for the replication of the
Escherichia coli chromosome. The holoenzyme is composed
of the DNA polymerase III core, the sliding clamp, and
the DnaX clamp loading complex. The DnaX complex
contains either either the tau or gamma product of gene
dnax, complexed to delta.delta' and to chi psi. Chi
forms a 1:1 heterodimer with psi. The chi psi complex
functions by increasing the affinity of tau and gamma
for delta.delta' allowing a functional clamp-loading
complex to form at physiological subunit
concentrations. Psi is responsible for the interaction
with DnaX (gamma/tau), but psi is insoluble unless it
is in a complex with chi.
Length = 136
Score = 25.2 bits (56), Expect = 8.2
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 64 LCRIVEQYLRKGSKVYI 80
CR+ E+ LR+G +V +
Sbjct: 18 ACRLAEKALRQGWRVLV 34
>gnl|CDD|30929 COG0584, UgpQ, Glycerophosphoryl diester phosphodiesterase
[Energy production and conversion].
Length = 257
Score = 25.2 bits (54), Expect = 8.7
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 2 VASLNKVILIGNLGADPDVRHTQDGRKIVNIRIATSDSWKDRVTNERRE 50
+A+ G + DV+ T+DG +V I D DR TN
Sbjct: 23 LAAFELAAEQGADYIELDVQLTKDG-VLVVIH----DETLDRTTNGLGT 66
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.314 0.131 0.371
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,864,214
Number of extensions: 86778
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 164
Number of HSP's successfully gapped: 27
Length of query: 159
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,405,363
Effective search space: 321591499
Effective search space used: 321591499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.3 bits)