RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17506
(252 letters)
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 32.1 bits (73), Expect = 0.22
Identities = 35/154 (22%), Positives = 50/154 (32%), Gaps = 10/154 (6%)
Query: 36 SLFGQTAT---QAPATSLFGGTQQQTTTFGSGLFGSQPQATTSATSGLFGNQQQPATNTT 92
S FG+ A SL + T GS LFG + + + + P
Sbjct: 264 SSFGKVLVISFSALGGSLSLFILYKFTPLGS-LFGPDKKRRRRRWRNMGHDSRGPYNANY 322
Query: 93 GGLFGASNTT--FGQSKPAFGGFGGTTSGGGLFGQSTMFGQTNQAQPGTSSLFGGTTSAF 150
GG F + + +S F TT GG +G S + T G S
Sbjct: 323 GGQFNSRSGRTGSSESIRGFTYDSSTTYGGSSYGTSQTDSTSTYGSRSTFDSSTGGGSQS 382
Query: 151 GGAAATGTTIKFS-PVTGTDTMMRG---GSSQTI 180
GG + G + F G+ G QT+
Sbjct: 383 GGGSTYGGSSTFDGSSRGSSDSFGVSYFGPQQTV 416
Score = 28.7 bits (64), Expect = 3.3
Identities = 19/104 (18%), Positives = 36/104 (34%), Gaps = 5/104 (4%)
Query: 29 GFGATNNSLFGQTATQAPATSLFGGTQQQTTTFGSGLFGSQPQATTSATSG-LFGNQQQP 87
N+ +G + + + T S +G T+ S +G++
Sbjct: 313 DSRGPYNANYGGQFNSRSGRTGSSESIRGFTYDSSTTYGGSSYGTSQTDSTSTYGSRSTF 372
Query: 88 ATNTTGGLFGASNTTFGQSKPAFGGFGGTTSGGGLFGQSTMFGQ 131
++T GG +T+G S F G++ G + FG
Sbjct: 373 DSSTGGGSQSGGGSTYGGSS----TFDGSSRGSSDSFGVSYFGP 412
Score = 27.1 bits (60), Expect = 10.0
Identities = 21/105 (20%), Positives = 34/105 (32%), Gaps = 13/105 (12%)
Query: 2 FGSSFGQASTSSAFGQSSFGKPAFSSPGFGATNNSLFGQTATQAPATSLFGGTQQQTTTF 61
+G F S + +S G SS +G ++ Q +TS +G TF
Sbjct: 322 YGGQFNSRSGRTGSSESIRGFTYDSSTTYGGSSYGTS-----QTDSTSTYGSRS----TF 372
Query: 62 GSGLFGSQPQATTSATSGLFGNQQQPATNTTGGLFGASNTTFGQS 106
S G + S +G ++ G + FG
Sbjct: 373 DSSTGGG----SQSGGGSTYGGSSTFDGSSRGSSDSFGVSYFGPQ 413
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 31.8 bits (72), Expect = 0.40
Identities = 18/111 (16%), Positives = 41/111 (36%), Gaps = 24/111 (21%)
Query: 163 SPVTGTDTMMRGGSSQTINTRHVCITCMKEYENKSLEE------LRYEDYKANRKG---- 212
SP + + + + S + I + + + ++ + L++E Y N+
Sbjct: 620 SPSSAEEVLQKIQSGHSREGLEQIIKLLSKEKPRNFSQCVEWARLKFEKYFNNKALQLLH 679
Query: 213 --PQQGTQATGSFFGTTPQ------------PSMFGTNTSTAQPATSLFGI 249
P +TGS F ++P+ P + A+ +++GI
Sbjct: 680 CFPLDIRTSTGSPFWSSPKRPPSPLKFDLNEPLHLSFIQAAAKLYATVYGI 730
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 16 residues in 53EXO PIN domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 28.6 bits (65), Expect = 2.4
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 203 YEDYKANRKGP 213
Y +YKANR
Sbjct: 67 YPEYKANRPPM 77
>gnl|CDD|225539 COG2992, Bax, Uncharacterized FlgJ-related protein [General
function prediction only].
Length = 262
Score = 28.7 bits (64), Expect = 2.5
Identities = 13/57 (22%), Positives = 19/57 (33%), Gaps = 10/57 (17%)
Query: 7 GQASTSSAFGQSSFGKPAFSSPGFGATNNSLFGQTATQAPATSLFGGTQQQTTTFGS 63
QA+ S +G S + N+LFG T+ + G F S
Sbjct: 143 TQAAAESGWGTSKLAR----------EANNLFGMWCTKGRCGLVPLGKVHGYKKFDS 189
>gnl|CDD|133034 cd04191, Glucan_BSP_ModH, Glucan_BSP_ModH catalyzes the elongation
of beta-1,2 polyglucose chains of glucan. Periplasmic
Glucan Biosynthesis protein ModH is a
glucosyltransferase that catalyzes the elongation of
beta-1,2 polyglucose chains of glucan, requiring a
beta-glucoside as a primer and UDP-glucose as a
substrate. Glucans are composed of 5 to 10 units of
glucose forming a highly branched structure, where
beta-1,2-linked glucose constitutes a linear backbone to
which branches are attached by beta-1,6 linkages. In
Escherichia coli, glucans are located in the periplasmic
space, functioning as regulator of osmolarity. It is
synthesized at a maximum when cells are grown in a
medium with low osmolarity. It has been shown to span
the cytoplasmic membrane.
Length = 254
Score = 28.0 bits (63), Expect = 3.9
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 40 QTATQA-PATSLFGGTQQQTTTFGSGLFGSQPQATTSATSGLFGN 83
QTA + A +LF QQ F + L+G +A G GN
Sbjct: 130 QTAPKLIGAETLFARLQQ----FANRLYGPVFGRGLAAWQGGEGN 170
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 27.5 bits (61), Expect = 8.3
Identities = 22/130 (16%), Positives = 44/130 (33%), Gaps = 8/130 (6%)
Query: 10 STSSAFGQSSFGKPAFSSPGFGATNNSLFGQTATQAPATSLFGGTQQQTTTFGSGLFGSQ 69
+SS ++ SS ++ +S Q+AT++P + + + S
Sbjct: 2 RSSSTMVSAAASTSLSSSRPQLSSFSSRSPQSATRSP--------RASSIKCSASASASS 53
Query: 70 PQATTSATSGLFGNQQQPATNTTGGLFGASNTTFGQSKPAFGGFGGTTSGGGLFGQSTMF 129
++SA+ G + + G G FG GG GG G + +
Sbjct: 54 SATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWRFWLRLFAP 113
Query: 130 GQTNQAQPGT 139
+ + +
Sbjct: 114 ADAHADEEQS 123
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 27.4 bits (61), Expect = 8.7
Identities = 21/78 (26%), Positives = 26/78 (33%), Gaps = 10/78 (12%)
Query: 93 GGLFGASNTTFGQSKPAFGGFGGTTSGGGLFGQSTMFGQTNQAQPGT-SSLFGGTTSAFG 151
GG FG FGGFG G F + +F + G LFGG F
Sbjct: 80 GGGFGGR---RFDGGGGFGGFGTGGDGAE-FNLNDLFDAAGRGGGGGIGDLFGGL---FN 132
Query: 152 GAAATGTTIKFSPVTGTD 169
+ + P G D
Sbjct: 133 RGGGSARPSR--PRRGND 148
>gnl|CDD|181154 PRK07869, PRK07869, amidase; Provisional.
Length = 468
Score = 27.3 bits (61), Expect = 9.6
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 12/61 (19%)
Query: 195 NKSLEELRYEDYKANRKGPQQGTQATGSFFGTTP-----------QPSMFGTNTSTAQPA 243
N +L L Y + R + G FF P P+M G++ T +PA
Sbjct: 46 NPALNALAYAAFDRARDRAARPGSQGG-FFSGVPTFIKDNVDVAGLPTMHGSDAWTPRPA 104
Query: 244 T 244
Sbjct: 105 K 105
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.311 0.126 0.363
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,971,429
Number of extensions: 1062883
Number of successful extensions: 938
Number of sequences better than 10.0: 1
Number of HSP's gapped: 856
Number of HSP's successfully gapped: 82
Length of query: 252
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 157
Effective length of database: 6,723,972
Effective search space: 1055663604
Effective search space used: 1055663604
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 (21.8 bits)
S2: 58 (26.3 bits)