RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3603
(264 letters)
>gnl|CDD|239937 cd04491, SoSSB_OBF, SoSSB_OBF: A subfamily of OB folds similar to
the OB fold of the crenarchaeote Sulfolobus solfataricus
single-stranded (ss) DNA-binding protein (SSoSSB).
SSoSSB has a single OB fold, and it physically and
functionally interacts with RNA polymerase. In vitro,
SSoSSB can substitute for the basal transcription factor
TBP, stimulating transcription from promoters under
conditions in which TBP is limiting, and supporting
transcription when TBP is absent. SSoSSB selectively
melts the duplex DNA of promoter sequences. It also
relieves transcriptional repression by the chromatin
Alba. In addition, SSoSSB activates reverse gyrase
activity, which involves DNA binding, DNA cleavage,
strand passage and ligation. SSoSSB stimulates all these
steps in the presence of the chromatin protein, Sul7d.
SSoSSB antagonizes the inhibitory effect of Sul7d on
reverse gyrase supercoiling activity. It also physically
and functionally interacts with Mini-chromosome
Maintenance (MCM), stimulating the DNA helicase activity
of MCM.
Length = 82
Score = 74.2 bits (183), Expect = 3e-17
Identities = 28/82 (34%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 46 NVTCIVLDISPRVTL---KENREVRTLKVADSTACINLSLWDEPGAL-LHPGDIVRLTKC 101
+V VL IS +V++ V D T I +LWDE A L PGD+VR+
Sbjct: 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENA 60
Query: 102 YAQIWRNCLTLYSSKSGLIEKI 123
Y + + L L K+ IEK+
Sbjct: 61 YVREFNGRLELSVGKNSEIEKL 82
>gnl|CDD|180574 PRK06461, PRK06461, single-stranded DNA-binding protein; Reviewed.
Length = 129
Score = 54.7 bits (132), Expect = 1e-09
Identities = 30/112 (26%), Positives = 50/112 (44%), Gaps = 5/112 (4%)
Query: 29 EAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLK---VADSTACINLSLWDE 85
M IKDL G++ VNVT VL++ ++ RT+ V D T + L+LW E
Sbjct: 1 MEMITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGE 60
Query: 86 PGALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMS 137
L G++V + + ++R + L K G I + + E ++
Sbjct: 61 QAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD--EEVPEAEEIP 110
>gnl|CDD|237078 PRK12366, PRK12366, replication factor A; Reviewed.
Length = 637
Score = 56.2 bits (136), Expect = 5e-09
Identities = 29/111 (26%), Positives = 56/111 (50%), Gaps = 7/111 (6%)
Query: 23 EINRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENR----EVRTLKVADSTACI 78
E +++E D I D+ G NV +T +++IS T ++ + +AD+T I
Sbjct: 54 EYGQEEEEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTI 113
Query: 79 NLSLWDEPGALLHP---GDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEF 126
L+LW++ LL GD++++ ++ W N + L S I+K+ ++
Sbjct: 114 RLTLWNDNAKLLKGLKEGDVIKIENARSRKWNNDVELNSGSETRIDKLEKY 164
Score = 37.7 bits (88), Expect = 0.005
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 44 NVNVTCIVLDISPRVTLKE----NREVRTLKVADSTACINLSLWDEPGAL-LHPGDIVRL 98
++ V V++ P + +VR +++AD T I L+LWD+ + + GD +++
Sbjct: 410 DITVIARVVEDYPVNEFERSDGSKGKVRNIELADGTGSIRLTLWDDDAEIEIKEGDAIKI 469
Query: 99 TKCYAQIWRNCLTLYSSKSGLIEK 122
Y + + L L + G IE
Sbjct: 470 LHPYVKENGDYLDLSIGRYGRIEI 493
Score = 33.1 bits (76), Expect = 0.16
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 45 VNVTCIVLDISPRVTLK---ENREVRTLKVADSTACINLSLWDEPGALL---HPGDIVRL 98
V+V ++ IS + ++ EV+ +++AD T + +S W E +L GD V++
Sbjct: 294 VDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILENLKEGDAVKI 353
Query: 99 TKC 101
C
Sbjct: 354 ENC 356
>gnl|CDD|180890 PRK07218, PRK07218, replication factor A; Provisional.
Length = 423
Score = 48.5 bits (116), Expect = 2e-06
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPR-VTLKENREV-RTLKVADSTACINLSLWDEPGALLHP 92
IK+L KNV VT VL I R + + + V +AD T I+ + W + G L P
Sbjct: 61 IKELSTDDKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDFG--LSP 118
Query: 93 GDIVRLTKCYAQIWRN 108
GD V + + W
Sbjct: 119 GDTVTIGNAGVREWDG 134
Score = 41.9 bits (99), Expect = 2e-04
Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 37 DLHVGIKNVNVTCIVLDISPRVTLKENREVRTLK--VADSTACINLSLWDEPGALLHPGD 94
DL G + VNV VL++ R + E L +AD T + + WD P + G
Sbjct: 167 DLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWD-PLPEIEIGA 225
Query: 95 IVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125
+R+ Y + +R ++ S+ +E +
Sbjct: 226 SIRIEDAYVREFRGVPSVNVSEFTTVEALDR 256
>gnl|CDD|180887 PRK07211, PRK07211, replication factor A; Reviewed.
Length = 485
Score = 41.3 bits (97), Expect = 3e-04
Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 9/99 (9%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPRVTL-----KENREVRTLKVADSTACINLSLWDEPGAL 89
++DL +G+ +V + +VLD T E R V L V D T + ++LWD+ L
Sbjct: 164 VEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGR-VSNLTVGDETGRVRVTLWDDRADL 222
Query: 90 ---LHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125
L G+ V + Y + L L+ G +E++ E
Sbjct: 223 AEELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDE 261
Score = 31.3 bits (71), Expect = 0.53
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPRVTLKENRE-----VRTLKVADSTACINLSLWDEPGAL 89
I D+ G+ V VL I T + + E V ++VAD T + ++ WDE
Sbjct: 56 IADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDEQAVA 115
Query: 90 ----LHPGDIVRL 98
L G ++R+
Sbjct: 116 AEEELEVGQVLRI 128
>gnl|CDD|185388 PRK15491, PRK15491, replication factor A; Provisional.
Length = 374
Score = 40.6 bits (95), Expect = 5e-04
Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 33 VYIKDLHVGIKNVNVTCIVLDISPRVTLKENR----EVRTLKVADSTACINLSLWDEPGA 88
I D++ NVN T V+ I N V + VAD T I L+LWD+
Sbjct: 58 TKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLAD 117
Query: 89 LLHPGDI 95
L+ GDI
Sbjct: 118 LIKTGDI 124
Score = 36.4 bits (84), Expect = 0.012
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 34 YIKDLHVGIKNVNVTCIVLDISPRVTLKENR----EVRTLKVADSTACINLSLWDEPGAL 89
IKD G ++N+ VLDIS T ++ VR + + D T I ++LWD L
Sbjct: 171 DIKD---GDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTDL 227
Query: 90 ---LHPGDIVRLTKCYAQ 104
L GD V + YA+
Sbjct: 228 ADKLENGDSVEIINGYAR 245
>gnl|CDD|173162 PRK14699, PRK14699, replication factor A; Provisional.
Length = 484
Score = 40.0 bits (93), Expect = 0.001
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 8/98 (8%)
Query: 14 NHGMRAERKEINRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENR----EVRTL 69
N+G+ E +E A IKD+ G+ ++N+T VL+IS T + +V L
Sbjct: 149 NNGVLTESEE-EIDVAANSQKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNL 207
Query: 70 KVADSTACINLSLWDEPGALLHP---GDIVRLTKCYAQ 104
+ D T + ++LWD+ L+ GD V L YA+
Sbjct: 208 LLGDETGTLRVTLWDDKTDFLNQIEYGDTVELINAYAR 245
Score = 36.1 bits (83), Expect = 0.014
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 16 GMRAERKEINRKKEAMDVY--IKDLHVGIKNVNVTCIVLDISPRVTLKENR----EVRTL 69
G R+ ++ +K E + + I+D+ + N+N++ VLDIS T ++ V L
Sbjct: 258 GNRSIIRKSEKKVEYEEEFTPIEDIKADMNNINISGRVLDISEVRTFEKKDGSPGRVGNL 317
Query: 70 KVADSTACINLSLWDE 85
+ DST I L+LWDE
Sbjct: 318 LLGDSTGKIRLTLWDE 333
>gnl|CDD|224515 COG1599, RFA1, Single-stranded DNA-binding replication protein A
(RPA), large (70 kD) subunit and related ssDNA-binding
proteins [DNA replication, recombination, and repair].
Length = 407
Score = 37.9 bits (88), Expect = 0.004
Identities = 28/126 (22%), Positives = 45/126 (35%), Gaps = 7/126 (5%)
Query: 17 MRAERKEIN-RKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENRE----VRTLKV 71
+ A+ I D+ VNVT VL I + T R + + V
Sbjct: 33 LIAKELGDYLVLAMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLV 92
Query: 72 ADSTACINLS-LW-DEPGALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMV 129
D T + LW L PGD++R+ Y ++R L + G + + +
Sbjct: 93 GDETGSVKTVTLWNIAALEKLEPGDVIRIRNAYTSLYRGGKRLSVGRVGSVADVDDEEDE 152
Query: 130 FNENLD 135
E+ D
Sbjct: 153 ARESED 158
>gnl|CDD|169427 PRK08402, PRK08402, replication factor A; Reviewed.
Length = 355
Score = 37.1 bits (86), Expect = 0.007
Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 13/108 (12%)
Query: 4 KKLAGSHPEKNHG---MRAERKEIN--RKKEAMDVYIKDLHVGIKNVNVTCIVL-DISPR 57
+++ H + AE +N ++EA ++I DL G++ VN+ VL PR
Sbjct: 29 REIMKEEGISEHAAALLLAEELGVNLEGEEEAPLMHISDLVPGMRGVNIVGRVLRKYPPR 88
Query: 58 VTLKEN---REVRTLKVADSTACINLSLWDEPGAL----LHPGDIVRL 98
K++ V +L + D T + LWD A ++ GD++++
Sbjct: 89 EYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAKYYNKINVGDVIKV 136
>gnl|CDD|235790 PRK06386, PRK06386, replication factor A; Reviewed.
Length = 358
Score = 36.8 bits (85), Expect = 0.007
Identities = 26/108 (24%), Positives = 52/108 (48%), Gaps = 6/108 (5%)
Query: 35 IKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLK---VADSTACINLSLWDEPGALLH 91
I D++ +NV++ VL ++ R T+K +R + D T + + W+ P A+
Sbjct: 5 ISDINAARQNVDLKVKVLSLNKR-TIKNDRGETIYYYGIIGDETGTVPFTAWEFPDAV-K 62
Query: 92 PGDIVRLTKCYAQIWRNCLTLY-SSKSGLIEKIGEFCMVFNENLDMSI 138
GD++ + CY++ + + +Y S+S ++ K E V + I
Sbjct: 63 SGDVIEIKYCYSKEYNGKIRIYFDSRSEVMLKPDENIEVKRTYKLVKI 110
>gnl|CDD|240434 PTZ00484, PTZ00484, GTP cyclohydrolase I; Provisional.
Length = 259
Score = 29.1 bits (65), Expect = 1.9
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 147 APQSANGNSNPGNMNNSGNNKGNMRPNPIDRDVNRYSNNPDKGSSSSTQN 196
AP + S GN N ++ N R ID D N + D Q+
Sbjct: 5 APGLSLQKSENGNEENGDISR-NCRDGDIDNDANLSLLDEDASLGKGRQS 53
>gnl|CDD|225259 COG2385, SpoIID, Sporulation protein and related proteins [Cell
division and chromosome partitioning].
Length = 397
Score = 28.9 bits (65), Expect = 2.5
Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 2/65 (3%)
Query: 139 PIPNLPVNAPQSANGNSNPGNMNNSGNNKGNMRPNP--IDRDVNRYSNNPDKGSSSSTQN 196
L + + A+G + G N + K PNP R S S+ +N
Sbjct: 77 GRSILLLPSLGVASGQKSKGTTTNVTSEKSAYLPNPSPDGRITLGTSYFGGGVYRSAVKN 136
Query: 197 TWVTW 201
V
Sbjct: 137 GIVNS 141
>gnl|CDD|224960 COG2049, DUR1, Allophanate hydrolase subunit 1 [Amino acid
transport and metabolism].
Length = 223
Score = 28.4 bits (64), Expect = 3.2
Identities = 13/21 (61%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 80 LSLWD---EPGALLHPGDIVR 97
L L+D EP ALL PGD VR
Sbjct: 187 LPLFDPDREPPALLRPGDQVR 207
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 28.4 bits (63), Expect = 4.3
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 143 LPVNAPQSANGNSNPGNMNNSGNNK-GNMRPNPIDRDVNRYSNNPDKGSSSSTQ 195
P N NG+SN N + S +N G+ R + NR ++P K +++
Sbjct: 311 DPKNIIHRNNGSSNSNNDDTSSSNHLGSNRIS------NRNPSSPYKKQTTTKH 358
>gnl|CDD|222228 pfam13567, DUF4131, Domain of unknown function (DUF4131). This
domain is frequently found to the N-terminus of the
Competence domain, pfam03772.
Length = 173
Score = 27.3 bits (61), Expect = 6.0
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 78 INLSLWDEPGALLHPGDIVRLT 99
+ + + + L PGD +R+T
Sbjct: 114 VLVYVRKDSLPKLRPGDRIRVT 135
>gnl|CDD|221575 pfam12437, GSIII_N, Glutamine synthetase type III N terminal. This
domain family is found in bacteria and eukaryotes, and
is approximately 160 amino acids in length. The family
is found in association with pfam00120. This family is
the N terminal region of glutamine synthetase type III
which is one of the enzymes responsible for generation
of glutamine through conversion glutamate to glutamine
by the incorporation of ammonia (NH3).
Length = 162
Score = 27.1 bits (61), Expect = 6.3
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 4/18 (22%)
Query: 238 TSHSHWFR----LTAEKH 251
T ++HWF+ LTAEKH
Sbjct: 61 THYTHWFQPLTGLTAEKH 78
>gnl|CDD|215003 smart01060, Catalase, Catalases are antioxidant enzymes that
catalyse the conversion of hydrogen peroxide to water
and molecular oxygen, serving to protect cells from its
toxic effects. Hydrogen peroxide is produced as a
consequence of oxidative cellular metabolism and can be
converted to the highly reactive hydroxyl radical via
transition metals, this radical being able to damage a
wide variety of molecules within a cell, leading to
oxidative stress and cell death. Catalases act to
neutralise hydrogen peroxide toxicity, and are produced
by all aerobic organisms ranging from bacteria to man.
Most catalases are mono-functional, haem-containing
enzymes, although there are also bifunctional
haem-containing peroxidase/catalases that are closely
related to plant peroxidases, and non-haem,
manganese-containing catalases that are found in
bacteria.
Length = 373
Score = 27.8 bits (63), Expect = 6.7
Identities = 15/37 (40%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 141 PN---LPVNAPQSANGNSN-PGNMNNSGNNKGNMRPN 173
PN LPVN P+ N G M GN G PN
Sbjct: 338 PNYHQLPVNRPRCPVHNYQRDGAMRVDGNQGG--DPN 372
>gnl|CDD|226477 COG3968, COG3968, Uncharacterized protein related to glutamine
synthetase [General function prediction only].
Length = 724
Score = 28.0 bits (62), Expect = 6.8
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 238 TSHSHWFR----LTAEKHSGEIRP 257
T ++HWF+ LTAEKH I P
Sbjct: 86 THYTHWFQPLTGLTAEKHDAFIDP 109
>gnl|CDD|163712 cd08156, catalase_clade_3, Clade 3 of the heme-binding enzyme
catalase. Catalase is a ubiquitous enzyme found in both
prokaryotes and eukaryotes, which is involved in the
protection of cells from the toxic effects of peroxides.
It catalyzes the conversion of hydrogen peroxide to
water and molecular oxygen. Catalases also utilize
hydrogen peroxide to oxidize various substrates such as
alcohol or phenols. Clade 3 catalases are the most
abundant subfamily and are found in all three kingdoms
of life; they have a relatively small subunit size of 43
to 75 kDa, and bind a protoheme IX (heme b) group buried
deep inside the structure. Clade 3 catalases also bind
NADPH as a second redox-active cofactor. They form
tetramers, and in eukaryotic cells, catalases are
located in peroxisomes.
Length = 429
Score = 27.5 bits (62), Expect = 7.5
Identities = 19/64 (29%), Positives = 23/64 (35%), Gaps = 19/64 (29%)
Query: 143 LPVNAPQS-ANGNSNPGNMNNSGNNKG--NMRPN----------------PIDRDVNRYS 183
LPVN P+ N G M GN G N PN P+ D +RY+
Sbjct: 306 LPVNRPKCPVNNYQRDGAMRVDGNGGGAPNYEPNSFGGPPEDPEYAEPPLPVSGDADRYN 365
Query: 184 NNPD 187
D
Sbjct: 366 YRDD 369
>gnl|CDD|150132 pfam09356, Phage_BR0599, Phage conserved hypothetical protein
BR0599. This entry describes a family of proteins
found almost exclusively in phage or in prophage
regions of bacterial genomes, including the phage-like
Rhodobacter capsulatus gene transfer agent, which
packages DNA. An apparent exception is Wolbachia
pipientis wMel, a bacterial endosymbiont of the fruit
fly, which has several candidate phage-related genes
physically separate from obvious prophage regions.
Length = 80
Score = 26.0 bits (58), Expect = 7.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 80 LSLWDEPGALLHPGDIVRLT 99
L+LW+ A + GD VRLT
Sbjct: 31 LTLWEPLPAPIAVGDAVRLT 50
>gnl|CDD|219569 pfam07777, MFMR, G-box binding protein MFMR. This region is found
to the N-terminus of the pfam00170 transcription factor
domain. It is between 150 and 200 amino acids in length.
The N-terminal half is rather rich in proline residues
and has been termed the PRD (proline rich domain),
whereas the C-terminal half is more polar and has been
called the MFMR (multifunctional mosaic region). It has
been suggested that this family is composed of three
sub-families called A, B and C, classified according to
motif composition. It has been suggested that some of
these motifs may be involved in mediating
protein-protein interactions. The MFMR region contains a
nuclear localisation signal in bZIP opaque and GBF-2.
The MFMR also contains a transregulatory activity in
TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention
signals.
Length = 189
Score = 27.1 bits (60), Expect = 9.0
Identities = 14/73 (19%), Positives = 22/73 (30%), Gaps = 13/73 (17%)
Query: 137 SIPI---PNLPVNAPQSANGNSNPGNMNNSGNNKGNMRPNPIDR----------DVNRYS 183
S+P P P P + S P +M + N I + ++ +
Sbjct: 92 SMPPGSHPFSPYAMPSAEVPGSTPLSMETDAKSSDNKDKGSIKKSKGSDGSLGLAMSGKN 151
Query: 184 NNPDKGSSSSTQN 196
K S SS
Sbjct: 152 GESGKASGSSANG 164
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
0.317 0.133 0.416
Gapped
Lambda K H
0.267 0.0853 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,044,555
Number of extensions: 1169029
Number of successful extensions: 915
Number of sequences better than 10.0: 1
Number of HSP's gapped: 903
Number of HSP's successfully gapped: 35
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (25.9 bits)