RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10506
(435 letters)
>gnl|CDD|218289 pfam04845, PurA, PurA ssDNA and RNA-binding protein. This family
represents most of the length of the protein.
Length = 218
Score = 282 bits (722), Expect = 4e-94
Identities = 128/271 (47%), Positives = 161/271 (59%), Gaps = 57/271 (21%)
Query: 112 EQELATKMLQIQSKRFYLDVKQNRRGRFIKVAEVGADGRRSQIFLALSVAEQFRGHLSAF 171
EQELA+K L IQ+KRFYLDVKQN RGRFIK+AEVGA GR+S+I L++SVA +FR +LS F
Sbjct: 1 EQELASKRLDIQNKRFYLDVKQNARGRFIKIAEVGAGGRKSRITLSMSVAAEFRDYLSKF 60
Query: 172 SDYYASLGPPNPDTV--PDDGKLKSEVMVKDNRRYYLDLKENTRGRFLRVSQTIPRGGPR 229
++YA LGP N + + LKSE +V+DNR+YYLDLKEN RGRFLR++QT+ RGG
Sbjct: 61 IEHYAQLGPQNGEHLPEDGRSALKSEFLVRDNRKYYLDLKENQRGRFLRIAQTVMRGGS- 119
Query: 230 SQIAIPAQGMIEFRDALTDLLEEFGTEDGGYKVLSLVPHQVSQTIPRGGPRSQIAIPAQG 289
G R QIA+PAQG
Sbjct: 120 ------------------------------------------------GQRQQIALPAQG 131
Query: 290 MIEFRDALTDLLEEFGTEDGG-YKGELPEGRHMRVENKNFYFDIGQNNRGIYMRVSEVSQ 348
MIEFRDALTDL+E++G D ELPEG + V+NK FYFD+G N RG++MR+SEV
Sbjct: 132 MIEFRDALTDLIEDYGEGDEEDEPAELPEGTSLTVDNKRFYFDVGSNKRGVFMRISEV-- 189
Query: 349 TIPRGGPRSQIAIPAQGMIEFRDALTDLLEE 379
+ R+ I +P + FRD EE
Sbjct: 190 ---KPNYRNSITVPEKAWTRFRDIFCKYSEE 217
Score = 160 bits (407), Expect = 6e-47
Identities = 75/222 (33%), Positives = 114/222 (51%), Gaps = 47/222 (21%)
Query: 201 NRRYYLDLKENTRGRFLRVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEEFGTEDGGY 260
N+R+YLD+K+N RGRF+++++ + GG +S+I + EFRD L+ +E Y
Sbjct: 13 NKRFYLDVKQNARGRFIKIAE-VGAGGRKSRITLSMSVAAEFRDYLSKFIEH-------Y 64
Query: 261 KVLSLVPHQVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEEFGTEDGGYKGELPEGRH 320
L + R +S+
Sbjct: 65 AQLGPQNGEHLPEDGRSALKSEF------------------------------------- 87
Query: 321 MRVENKNFYFDIGQNNRGIYMRVSEVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEEF 380
+ +N+ +Y D+ +N RG ++R+++ G R QIA+PAQGMIEFRDALTDL+E++
Sbjct: 88 LVRDNRKYYLDLKENQRGRFLRIAQTVMRGGSG-QRQQIALPAQGMIEFRDALTDLIEDY 146
Query: 381 GTEDGG-YKGELPEGRHMRVENKNFYFDIGQNNRGIYMRVSE 421
G D ELPEG + V+NK FYFD+G N RG++MR+SE
Sbjct: 147 GEGDEEDEPAELPEGTSLTVDNKRFYFDVGSNKRGVFMRISE 188
Score = 97.9 bits (244), Expect = 1e-23
Identities = 63/229 (27%), Positives = 109/229 (47%), Gaps = 28/229 (12%)
Query: 28 NRRYYLDLKENTRGRFLRTADVNLLIIYEQDKQGQQQQEQELATKMLQIQSKRFYLDVKQ 87
N+R+YLD+K+N RGRF++ A+V G ++ + M R YL
Sbjct: 13 NKRFYLDVKQNARGRFIKIAEV-----------GAGGRKSRITLSMSVAAEFRDYL---- 57
Query: 88 NRRGRFIK-VNNIPIAICLNCQQQQEQELATKMLQIQSKRFYLDVKQNRRGRFIKVAEV- 145
+FI+ + + + L ++ L ++++YLD+K+N+RGRF+++A+
Sbjct: 58 ---SKFIEHYAQLGPQNGEHLPEDGRSALKSEFLVRDNRKYYLDLKENQRGRFLRIAQTV 114
Query: 146 --GADGRRSQIFLALSVAEQFRGHLSAFSDYYASLGPPNPDTVPDDGKLKSEVMVKDNRR 203
G G+R QI L +FR A +D G + + P + + + DN+R
Sbjct: 115 MRGGSGQRQQIALPAQGMIEFR---DALTDLIEDYGEGDEEDEPAELP-EGTSLTVDNKR 170
Query: 204 YYLDLKENTRGRFLRVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEE 252
+Y D+ N RG F+R+S+ + R+ I +P + FRD EE
Sbjct: 171 FYFDVGSNKRGVFMRISEV--KPNYRNSITVPEKAWTRFRDIFCKYSEE 217
Score = 75.2 bits (185), Expect = 1e-15
Identities = 42/125 (33%), Positives = 58/125 (46%), Gaps = 34/125 (27%)
Query: 6 GPPNPDTV--PDDGKLKSEVMVKDNRRYYLDLKENTRGRFLRTADVNLLIIYEQDKQGQQ 63
GP N + + LKSE +V+DNR+YYLDLKEN RGRFLR A ++ Q QQ
Sbjct: 68 GPQNGEHLPEDGRSALKSEFLVRDNRKYYLDLKENQRGRFLRIAQ---TVMRGGSGQRQQ 124
Query: 64 ----------------------------QQEQELA-TKMLQIQSKRFYLDVKQNRRGRFI 94
+ EL L + +KRFY DV N+RG F+
Sbjct: 125 IALPAQGMIEFRDALTDLIEDYGEGDEEDEPAELPEGTSLTVDNKRFYFDVGSNKRGVFM 184
Query: 95 KVNNI 99
+++ +
Sbjct: 185 RISEV 189
Score = 55.6 bits (134), Expect = 7e-09
Identities = 30/113 (26%), Positives = 56/113 (49%), Gaps = 21/113 (18%)
Query: 321 MRVENKNFYFDIGQNNRGIYMRVSEVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLLEEF 380
+ ++NK FY D+ QN RG +++++EV GG +S+I + EFRD L+ +E +
Sbjct: 9 LDIQNKRFYLDVKQNARGRFIKIAEVGA----GGRKSRITLSMSVAAEFRDYLSKFIEHY 64
Query: 381 GT------------EDGGYKGELPEGRHMRVENKNFYFDIGQNNRGIYMRVSE 421
K E + +N+ +Y D+ +N RG ++R+++
Sbjct: 65 AQLGPQNGEHLPEDGRSALKSEF-----LVRDNRKYYLDLKENQRGRFLRIAQ 112
>gnl|CDD|197840 smart00712, PUR, DNA/RNA-binding repeats in PUR-alpha/beta/gamma
and in hypothetical proteins from spirochetes and the
Bacteroides-Cytophaga-Flexibacter bacteria.
Length = 63
Score = 92.7 bits (231), Expect = 1e-23
Identities = 29/63 (46%), Positives = 43/63 (68%)
Query: 114 ELATKMLQIQSKRFYLDVKQNRRGRFIKVAEVGADGRRSQIFLALSVAEQFRGHLSAFSD 173
ELA+K L +++KRFY DVK+NRRGRF++++EV +G RS I + A +FR L+ +
Sbjct: 1 ELASKKLTVENKRFYFDVKENRRGRFLRISEVKNNGGRSSITVPEQGAAEFRDALTKLIE 60
Query: 174 YYA 176
Y
Sbjct: 61 KYG 63
Score = 92.7 bits (231), Expect = 2e-23
Identities = 34/64 (53%), Positives = 47/64 (73%), Gaps = 1/64 (1%)
Query: 191 KLKSEVMVKDNRRYYLDLKENTRGRFLRVSQTIPRGGPRSQIAIPAQGMIEFRDALTDLL 250
+L S+ + +N+R+Y D+KEN RGRFLR+S+ GG RS I +P QG EFRDALT L+
Sbjct: 1 ELASKKLTVENKRFYFDVKENRRGRFLRISEVKNNGG-RSSITVPEQGAAEFRDALTKLI 59
Query: 251 EEFG 254
E++G
Sbjct: 60 EKYG 63
Score = 86.5 bits (215), Expect = 3e-21
Identities = 32/67 (47%), Positives = 43/67 (64%), Gaps = 4/67 (5%)
Query: 315 LPEGRHMRVENKNFYFDIGQNNRGIYMRVSEVSQTIPRGGPRSQIAIPAQGMIEFRDALT 374
+ + VENK FYFD+ +N RG ++R+SEV G RS I +P QG EFRDALT
Sbjct: 1 ELASKKLTVENKRFYFDVKENRRGRFLRISEVK----NNGGRSSITVPEQGAAEFRDALT 56
Query: 375 DLLEEFG 381
L+E++G
Sbjct: 57 KLIEKYG 63
Score = 52.2 bits (126), Expect = 4e-09
Identities = 16/32 (50%), Positives = 25/32 (78%)
Query: 18 KLKSEVMVKDNRRYYLDLKENTRGRFLRTADV 49
+L S+ + +N+R+Y D+KEN RGRFLR ++V
Sbjct: 1 ELASKKLTVENKRFYFDVKENRRGRFLRISEV 32
Score = 51.5 bits (124), Expect = 8e-09
Identities = 14/31 (45%), Positives = 21/31 (67%)
Query: 391 LPEGRHMRVENKNFYFDIGQNNRGIYMRVSE 421
+ + VENK FYFD+ +N RG ++R+SE
Sbjct: 1 ELASKKLTVENKRFYFDVKENRRGRFLRISE 31
>gnl|CDD|221439 pfam12143, PPO1_KFDV, Protein of unknown function (DUF_B2219).
This domain family is found in eukaryotes, and is
typically between 138 and 152 amino acids in length. and
the family is found in association with pfam00264. Many
members are plant or plastid polyphenol oxidases, and
there is a highly conserved sequence motif: KFDV, from
which the name derives. This is the C-terminal domain of
these oxidases.
Length = 131
Score = 30.3 bits (69), Expect = 0.69
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 242 FRDALTDLLEEFGTEDGGYKVLSLVP 267
R +TDLLE+ G ED V++LVP
Sbjct: 90 LRLGITDLLEDLGAEDDDSVVVTLVP 115
>gnl|CDD|222632 pfam14260, zf-C4pol, C4-type zinc-finger of DNA polymerase delta.
In fission yeast this zinc-finger domain appears is the
region of Pol3 that binds directly to the B-subunit,
Cdc1. Pol delta is a hetero-tetrameric enzyme comprising
four evolutionarily well-conserved proteins: the
catalytic subunit Pol3 and three smaller subunits Cdc1,
Cdc27 and Cdm1.
Length = 73
Score = 28.5 bits (64), Expect = 1.1
Identities = 7/35 (20%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 95 KVNNIPIAICLNCQQQQEQELATKMLQIQS--KRF 127
K+ +C NC + + L + +++ +RF
Sbjct: 7 KLKEGESPLCKNCLRNPQASLYKLLSRLRELERRF 41
>gnl|CDD|224297 COG1379, COG1379, PHP family phosphoesterase with a Zn ribbon
[General function prediction only].
Length = 403
Score = 30.5 bits (69), Expect = 2.0
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 135 RRGRFIKVAEVGADGRRSQ--IFLALSVAEQFRGHLSAFSDYYASLGPP 181
+ RFI AEV R I +LS AE+ LS +S + G P
Sbjct: 67 KGVRFILTAEVEDSRRVHHLLILPSLSAAEELSEWLSKYSKNIETEGRP 115
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 29.3 bits (66), Expect = 3.9
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 219 VSQTIPRGGPRSQIAIPAQGM-IEFRDALTDLLEEFGTEDGGYKVLSLVPHQVSQTIP 275
V QT GG + + PA+ M +AL LEE G VL L+ HQ S+ +P
Sbjct: 98 VVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEE----PSGDTVLLLISHQPSRLLP 151
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 28.9 bits (65), Expect = 7.2
Identities = 20/148 (13%), Positives = 55/148 (37%), Gaps = 4/148 (2%)
Query: 56 EQDKQGQQQQEQELATKMLQIQSKRFYLDVKQNRRGRFIKVNNIPIAICLNCQQQQEQEL 115
EQ +++ L ++ ++Q +R L + + I+ N +++ +EL
Sbjct: 818 EQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKE----ELEEELEEL 873
Query: 116 ATKMLQIQSKRFYLDVKQNRRGRFIKVAEVGADGRRSQIFLALSVAEQFRGHLSAFSDYY 175
+ ++S+ L +++ ++ E + +QI + + L A +
Sbjct: 874 EAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEEL 933
Query: 176 ASLGPPNPDTVPDDGKLKSEVMVKDNRR 203
+ + P + + S V+ +
Sbjct: 934 SEIEDPKGEDEEIPEEELSLEDVQAELQ 961
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 28.8 bits (64), Expect = 7.9
Identities = 28/138 (20%), Positives = 50/138 (36%), Gaps = 15/138 (10%)
Query: 55 YEQDKQGQQQQEQELATKMLQIQSKRFYLDVKQN--RRGRFIK-VNNIPIAICLNCQQQQ 111
YE+ + Q QE A K++Q+ K ++ + IK ++ I + + Q
Sbjct: 854 YEECSKQLAQLTQEQA-KIIQLSDKLNGINQIKIQFDGDALIKFLHEITLYANVRLANQS 912
Query: 112 EQELATKMLQIQSKRFYLDVKQNRRGRFIKVAEVGADGRRSQIFLALSVAEQFRGHLS-- 169
E + + +G + VA+ R LS E F LS
Sbjct: 913 EGRFHGRYA------DSHVNARKYQGLALLVADAYTGSVRP--SATLSGGETFLASLSLA 964
Query: 170 -AFSDYYASLGPPNPDTV 186
A +D ++ G D++
Sbjct: 965 LALADLLSTSGGTVLDSL 982
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
0.319 0.139 0.402
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,940,888
Number of extensions: 2277576
Number of successful extensions: 2098
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2074
Number of HSP's successfully gapped: 32
Length of query: 435
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 335
Effective length of database: 6,502,202
Effective search space: 2178237670
Effective search space used: 2178237670
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 (21.7 bits)
S2: 60 (26.8 bits)