RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9959
(330 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 37.8 bits (88), Expect = 2e-04
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 199 SLQNHINTHTGVKPHKCKYCESRFTT 224
+L+ H+ THTG KP+KC C F++
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 35.1 bits (81), Expect = 0.002
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 172 LARHLKSHSEERPHKCSVCERGFKT 196
L RH+++H+ E+P+KC VC + F +
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 31.6 bits (72), Expect = 0.029
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 297 HLESHMLIHTDQKPYLCDHCD 317
+L HM HT +KPY C C
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCG 21
Score = 27.7 bits (62), Expect = 0.60
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 13/38 (34%)
Query: 257 MRNHMRSHTGERPYQLHCKSHEGEKCWKCELCPYASSS 294
+R HMR+HTGE+PY KC +C + SS
Sbjct: 2 LRRHMRTHTGEKPY-------------KCPVCGKSFSS 26
Score = 27.4 bits (61), Expect = 0.84
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 227 ELVRHVRYKHTHEKPHKCSICDYA 250
L RH+R HT EKP+KC +C +
Sbjct: 1 NLRRHMR-THTGEKPYKCPVCGKS 23
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 38.6 bits (90), Expect = 0.004
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 82 EEEDLTVYDFEEVD--EVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVD 139
EEE + EE D E++ + A S ++D + E+ DE D E+P+ E
Sbjct: 1 EEEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEISKR 60
Query: 140 EKPKLSKLNKKQ 151
EK +L +L K++
Sbjct: 61 EKARLKELKKQK 72
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 38.1 bits (88), Expect = 0.005
Identities = 25/115 (21%), Positives = 38/115 (33%), Gaps = 8/115 (6%)
Query: 158 MCNYCNYTSPKRYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGV------- 210
+ SPK L S + S R AS Q+ +
Sbjct: 228 PLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFS 287
Query: 211 KPHKCKYCESRFTTSGELVRHVRYKHTHEKPHKCSICDYA-SVELSKMRNHMRSH 264
P K K C F+ S L RH+R + + K C Y+ +L + ++ H
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRH 342
Score = 35.8 bits (82), Expect = 0.024
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 183 RPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKY--CESRFTTSGELVRHVRYKHTH 238
RP C C F + L HI +HTG KP +C Y C+ F+ EL RH+R H +
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89
Score = 33.9 bits (77), Expect = 0.12
Identities = 43/169 (25%), Positives = 63/169 (37%), Gaps = 15/169 (8%)
Query: 157 HMCNYCNYTSPKRYLLARHLKS--HSEE--RPHKC--SVCERGFKTIASLQNHINTHTGV 210
CN + + L RHL+S HS E +P C S+C + F +L+ HI HT +
Sbjct: 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349
Query: 211 KPHKCKYCESRFTTSGELVRHVRYKHTHEKPHKCSICDYASVELSKMRNHMRSHTGERPY 270
P K K S + L+ + + + + ++ S +RN R
Sbjct: 350 SPAKEKLLNSS-SKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHI 408
Query: 271 QLHC-KSHEGEKCWKCELCPYASSSQRH--LESHMLIHTDQKPYLCDHC 316
H K C + S RH L H IHT+ P LC
Sbjct: 409 ITHLSFRPYNCKNPPC-----SKSFNRHYNLIPHKKIHTNHAPLLCSIL 452
Score = 27.7 bits (61), Expect = 8.6
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 157 HMCNYCNYTSPKRYLLARHLKSHSEERPHKCSVCERG--FKTIASLQNHINTHTGVKPH 213
C C + + L RH++SH+ E+P +CS F L H+ TH
Sbjct: 34 DSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSD 92
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 32.6 bits (75), Expect = 0.012
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 184 PHKCSVCERGFKTIASLQNHINTHTGVKPHK 214
C C++ FK+ +L+NH+ + K HK
Sbjct: 1 QFYCVACDKYFKSENALENHLKS----KKHK 27
>gnl|CDD|236940 PRK11633, PRK11633, cell division protein DedD; Provisional.
Length = 226
Score = 36.1 bits (84), Expect = 0.013
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 2/81 (2%)
Query: 4 GPQQLIDLNSSEYQTVTIVPSEGSTGEVSYVLIVQQNETEPGQISVEQDINPDPEHVEMK 63
G + D+ + Q + P EG+ V +P ++ + +PE ++
Sbjct: 48 GDRDEPDMMPAATQALPTQPPEGAAEAVR-AGDAAAPSLDPATVAPP-NTPVEPEPAPVE 105
Query: 64 KPQPRPKPKPLSKKLTKSEEE 84
P+P+P KP K + + E
Sbjct: 106 PPKPKPVEKPKPKPKPQQKVE 126
>gnl|CDD|236768 PRK10819, PRK10819, transport protein TonB; Provisional.
Length = 246
Score = 35.4 bits (82), Expect = 0.027
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 37 VQQNETEPGQISVEQDINPDPEHVEMKKPQPRPKPKPLSKKLTKSEE 83
V + E EP I P KP+P+PKPKP K + K EE
Sbjct: 71 VVEPEPEPEPIPEPPKEAPVVIPKPEPKPKPKPKPKP--KPVKKVEE 115
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 34.1 bits (78), Expect = 0.032
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 184 PHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCESRFTTSGELVRHVRYKH 236
P+ C +C F + SL+ HI K C C F + + HV KH
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDHVCKKH 123
Score = 27.5 bits (61), Expect = 4.9
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 210 VKPHKCKYCESRFTTSGELVRHVRYKHTHEKPHKCSIC 247
V P+ C C F++S L +H+RY H K C +C
Sbjct: 71 VSPYVCPLCLMPFSSSVSLKQHIRYT-EHSK--VCPVC 105
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 35.4 bits (81), Expect = 0.042
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 195 KTIASLQNHINTHTGVKPH-KCKYCESRFTTSGELVRHVRYKHTHEKPHKCSICD 248
T+ +N G K H C +C+ F EL RH R +H C ICD
Sbjct: 202 STLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH-----EACHICD 251
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 35.0 bits (81), Expect = 0.058
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 63 KKPQPRPKPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEED 111
R +P KK S E+D D EVD+ + E+ E++D
Sbjct: 1346 ASQSSRLLRRPRKKKSDSSSEDD----DDSEVDDSED--EDDEDDEDDD 1388
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 33.5 bits (76), Expect = 0.15
Identities = 29/125 (23%), Positives = 51/125 (40%), Gaps = 13/125 (10%)
Query: 14 SEYQTVTIVPSEGSTGEVSYVLIVQQNETEPGQISVEQDINPDPEHVEMKKPQPRPKPKP 73
+ V + + E++ V VQ E VE + P+PE +P+P P+P+P
Sbjct: 375 NGQAEVGLNSQAQTAQEITPVSAVQPVEVISQPAMVEPEPEPEPEPEPEPEPEPEPEPEP 434
Query: 74 -LSKKLTKSEEEDLTVYDFEE----------VDEVDPIGEEA--PSSEEEDLTVYDFEEV 120
+ +DL V+D V E + EE P E++ + V +V
Sbjct: 435 EPEPEPEPQPNQDLMVFDPNHHELIGLESAVVQETVSVLEEDFIPVPEQKLVQVQAETQV 494
Query: 121 DEVDP 125
+++P
Sbjct: 495 KQIEP 499
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 33.0 bits (76), Expect = 0.19
Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 3/83 (3%)
Query: 59 HVEMKKPQPRPKPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFE 118
E+ + K L K + +D+ V + + D+ D ++ +++D+ D +
Sbjct: 97 KDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDD---DDDDDLDDDDIDDDDDD 153
Query: 119 EVDEVDPIGEEAPSTIEEDVDEK 141
E D+ D ++ EE + K
Sbjct: 154 EDDDEDDDDDDVDDEDEEKKEAK 176
Score = 31.5 bits (72), Expect = 0.65
Identities = 17/85 (20%), Positives = 28/85 (32%), Gaps = 6/85 (7%)
Query: 63 KKPQPRPKPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDE 122
KK K + D ++ D++D + +E+D D ++VD+
Sbjct: 108 KKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDD 167
Query: 123 VDPIGEEAPSTIEEDVDEKPKLSKL 147
D EE E EK
Sbjct: 168 ED---EEK---KEAKELEKLSDDDD 186
Score = 30.3 bits (69), Expect = 1.6
Identities = 9/72 (12%), Positives = 26/72 (36%), Gaps = 4/72 (5%)
Query: 72 KPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAP 131
+++D+ D +E D+ D ++ +EE + E++ + D +
Sbjct: 133 DDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDE- 191
Query: 132 STIEEDVDEKPK 143
++ +
Sbjct: 192 ---DDSEALRQA 200
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.0 bits (65), Expect = 0.26
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 185 HKCSVCERGFKTIASLQNHINTH 207
++C C + FK+ ++L+ H+ TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.51
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 242 HKCSICDYASVELSKMRNHMRSH 264
++C C S +R HMR+H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.8 bits (62), Expect = 0.57
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 283 WKCELCPYASSSQRHLESHMLIH 305
++C C S+ L HM H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.8 bits (62), Expect = 0.68
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 157 HMCNYCNYTSPKRYLLARHLKSH 179
+ C C + L H+++H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 3.0
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 213 HKCKYCESRFTTSGELVRHVR 233
++C C F + L H+R
Sbjct: 1 YRCPECGKVFKSKSALREHMR 21
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 31.8 bits (72), Expect = 0.44
Identities = 28/125 (22%), Positives = 42/125 (33%), Gaps = 18/125 (14%)
Query: 34 VLIVQQNETEPGQI------SVEQDINPDPEHVEMKKPQPRPKPKPLSKKLTKSEEEDLT 87
L NE G I EQD P +E R K + E +
Sbjct: 276 PLPGDYNERRGGIILDISLNEFEQDAVPLLVDLERNGN--RIKELADFGDYYEDIFEVVE 333
Query: 88 VYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPKLSKL 147
V + +E D V EE+ E ED EV+ + + EE +V +L
Sbjct: 334 VVEKQEGDVVT---EESTDEESED-------EVEIDESVIEEVAEMELLEVQVDDLAERL 383
Query: 148 NKKQV 152
+ ++
Sbjct: 384 AETEI 388
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 28.0 bits (62), Expect = 0.49
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 213 HKCKYCESRFTTSGELVRHVRYKH 236
KC C F++ L RH+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 27.2 bits (60), Expect = 0.96
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 185 HKCSVCERGFKTIASLQNHINTH 207
KC +C + F + +L+ H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 26.1 bits (57), Expect = 2.5
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 283 WKCELCPYASSSQRHLESHMLIH 305
+KC LC + SS+ L+ H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.7 bits (56), Expect = 3.6
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 157 HMCNYCNYTSPKRYLLARHLKSH 179
C C + + L RHL+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 25.3 bits (55), Expect = 4.9
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 242 HKCSICDYASVELSKMRNHMRSH 264
KC +C + ++ H+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 31.6 bits (71), Expect = 0.62
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 1/76 (1%)
Query: 76 KKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIE 135
KL ++ED +E D+ + + E S + E F E E D EE E
Sbjct: 726 PKLDAIDDEDAKSEGSQESDQEEGLDEIFYSFDGEQDNSDSFAESSEEDESSEEEKEE-E 784
Query: 136 EDVDEKPKLSKLNKKQ 151
E+ + K +K +++
Sbjct: 785 ENKEVSAKRAKKKQRK 800
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 27.7 bits (62), Expect = 0.68
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 186 KCSVCERGFKTIASLQNHINTH 207
KC C + F ++L+ H+ TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.2 bits (58), Expect = 2.6
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 158 MCNYCNYTSPKRYLLARHLKSH 179
C C + ++ L RHL++H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 2.7
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 284 KCELCPYASSSQRHLESHMLIH 305
KC C + S + +L+ H+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 3.6
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 214 KCKYCESRFTTSGELVRHVR 233
KC C F+ L RH+R
Sbjct: 1 KCPDCGKSFSRKSNLKRHLR 20
Score = 24.6 bits (54), Expect = 8.3
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 243 KCSICDYASVELSKMRNHMRSH 264
KC C + S ++ H+R+H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 30.5 bits (69), Expect = 0.87
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 70 KPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGE 128
K L KKL + E ED+ +E DE D EE E+ED D ++ D+ D E
Sbjct: 152 KLSMLEKKLKELEAEDV-----DEEDEKDEEEEEEEEEEDED--FDDDDDDDDDDYNAE 203
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 30.9 bits (70), Expect = 0.92
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 69 PKPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGE 128
P + +K K EEE+ T EEVDE + E+ +++ T ++E +++ PI
Sbjct: 36 PDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTKPIWT 95
Query: 129 EAPSTIEED 137
P + ++
Sbjct: 96 RNPKDVTKE 104
>gnl|CDD|149172 pfam07948, Nairovirus_M, Nairovirus M polyprotein-like. The
sequences in this family are similar to the Dugbe virus
M polyprotein precursor, which includes glycoproteins G1
and G2. Both are thought to be inserted in the membrane
of the Golgi complex of the infected host cell, and G1
is known to have a role in infection of vertebrate
hosts.
Length = 645
Score = 30.9 bits (70), Expect = 1.1
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 172 LARHLKSHSEERPHKCSVCERGFKTIASLQNH-INTHTGVKPHKCKYCESRFTTSGELVR 230
L + LK + E +P C+ CE+ + H +N + C YC SR T+ G LVR
Sbjct: 482 LGKKLKQYRELKPQTCTKCEQTPVNAIDAEMHDLNCSYNI----CPYCASRLTSEG-LVR 536
Query: 231 HV 232
HV
Sbjct: 537 HV 538
>gnl|CDD|131541 TIGR02488, flgG_G_neg, flagellar basal-body rod protein FlgG,
Gram-negative bacteria. This family consists of the
FlgG protein of the flagellar apparatus in the
Proteobacteria and spirochetes [Cellular processes,
Chemotaxis and motility].
Length = 259
Score = 30.0 bits (68), Expect = 1.6
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 6/34 (17%)
Query: 26 GSTGEVSYVLIVQQNETEP---GQISVEQDINPD 56
GS GEVS + Q +TEP GQI++ INP
Sbjct: 150 GSDGEVS---VRQGGQTEPQEVGQITLATFINPA 180
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 28.4 bits (64), Expect = 1.7
Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 15/78 (19%)
Query: 63 KKPQPRPKPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDE 122
K P + +KK E+ED V D ++ D+ D + D+
Sbjct: 42 KSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLD---------------DD 86
Query: 123 VDPIGEEAPSTIEEDVDE 140
+ ++ +E+D DE
Sbjct: 87 DVDLDDDDDDFLEDDDDE 104
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 30.1 bits (67), Expect = 1.8
Identities = 22/118 (18%), Positives = 44/118 (37%)
Query: 30 EVSYVLIVQQNETEPGQISVEQDINPDPEHVEMKKPQPRPKPKPLSKKLTKSEEEDLTVY 89
VS VL ++ ++S ++ +P + + K + EEDL V
Sbjct: 221 SVSVVLKDEKELARQERVSSWENFKEEPGEPLSRPALKKEKQGAEEEGEEGMSEEDLDVG 280
Query: 90 DFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPKLSKL 147
E ++ G++ EE + EEV P +++ +E + ++L
Sbjct: 281 AAEIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERHTEL 338
>gnl|CDD|221137 pfam11571, Med27, Mediator complex subunit 27. Mediator is a large
complex of up to 33 proteins that is conserved from
plants to fungi to humans - the number and
representation of individual subunits varying with
species {1-2]. It is arranged into four different
sections, a core, a head, a tail and a kinase-activity
part, and the number of subunits within each of these is
what varies with species. Overall, Mediator regulates
the transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Mediator exists in
two major forms in human cells: a smaller form that
interacts strongly with pol II and activates
transcription, and a large form that does not interact
strongly with pol II and does not directly activate
transcription. The ubiquitous expression of Med27 mRNA
suggests a universal requirement for Med27 in
transcriptional initiation. Loss of Crsp34/Med27
decreases amacrine cell number, but increases the number
of rod photoreceptor cells.
Length = 91
Score = 28.1 bits (63), Expect = 1.9
Identities = 13/55 (23%), Positives = 22/55 (40%)
Query: 166 SPKRYLLARHLKSHSEERPHKCSVCERGFKTIASLQNHINTHTGVKPHKCKYCES 220
+P RY + R L +EE +ASL + I+++ + C C
Sbjct: 9 APSRYKVFRKLTDSAEEAILHFLNSRPPPWALASLLDWISSYVDLFSTPCAKCGK 63
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 30.0 bits (68), Expect = 2.3
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 86 LTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPKL 144
LT Y + ++E++P+ E P E EE +EVDP ++ I+++ + L
Sbjct: 817 LTTYKVKTINELEPLPYEEPEEETA-------EEPEEVDPEDVKSEDDIDDEDTGQLGL 868
>gnl|CDD|236460 PRK09300, PRK09300, tRNA splicing endonuclease; Reviewed.
Length = 330
Score = 29.6 bits (67), Expect = 2.6
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 17/61 (27%)
Query: 81 SEEEDLTVYDFEEVDE-----VDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIE 135
SE + L D E + VD EE ++T Y EV +DP G +
Sbjct: 117 SERDPLPFSDLIERKQLVLAVVD---------EESEITYY---EVKRIDPKGRMEEDPPD 164
Query: 136 E 136
+
Sbjct: 165 K 165
>gnl|CDD|218986 pfam06317, Arena_RNA_pol, Arenavirus RNA polymerase. This family
consists of several Arenavirus RNA polymerase proteins
(EC:2.7.7.48).
Length = 2206
Score = 29.6 bits (67), Expect = 2.6
Identities = 14/46 (30%), Positives = 16/46 (34%), Gaps = 6/46 (13%)
Query: 191 ERGFKTIASLQNHINTHTGVKPHKCK------YCESRFTTSGELVR 230
GF I S+ + I T VK CK YC E R
Sbjct: 1628 NGGFLYIKSILSKIMTCDHVKCEICKPGPGVWYCRKALEEVSEFSR 1673
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 27.4 bits (61), Expect = 2.8
Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 18/65 (27%)
Query: 243 KCSICDYASVELSKMRNHMRSHTGERPYQLHCKSHEGEKCWKCELCPYASSSQRHLESHM 302
KC IC + +V L ++ H R ++H K CP + S R L H
Sbjct: 3 KCPICGFTTVTLFALKQHAR------------RNHTLTK------CPVCNKSYRRLNQHF 44
Query: 303 LIHTD 307
D
Sbjct: 45 YSQYD 49
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 29.4 bits (66), Expect = 3.1
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 2/103 (1%)
Query: 50 EQDINPDPEHVEMKKPQPRPKPKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEE 109
E + + E K+ L + E+ED E D + E+ +
Sbjct: 237 ESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKRK 296
Query: 110 EDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPKLSKLNKKQV 152
+ + E+ DE I E+P EE + +P L KK+
Sbjct: 297 RLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPP--LPKKEE 337
>gnl|CDD|221203 pfam11748, DUF3306, Protein of unknown function (DUF3306). This
family of proteobacterial species proteins has no known
function.
Length = 115
Score = 28.0 bits (63), Expect = 3.2
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 4/72 (5%)
Query: 75 SKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTI 134
+KL EE + E + AP+ EEE+ + EE+ E + P T+
Sbjct: 8 RRKLAVRAEEPAEPAETAEEEAAAA--APAPAPEEEEEAELEDEELLEELDL--PDPDTL 63
Query: 135 EEDVDEKPKLSK 146
D L+K
Sbjct: 64 TPGSDFSAFLAK 75
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit
[Transcription].
Length = 175
Score = 28.2 bits (63), Expect = 3.9
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 80 KSEEEDLTVYDFEEV--DEVDPI--GEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIE 135
+ +D V FEE DE+D EE E + L + +E ++ D I E E
Sbjct: 99 DIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDDDEIVEILIEDDE 158
Query: 136 EDVDE 140
D DE
Sbjct: 159 VDEDE 163
>gnl|CDD|112355 pfam03532, OMS28_porin, OMS28 porin.
Length = 253
Score = 28.6 bits (63), Expect = 3.9
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 103 EAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPK-------LSKLNKKQVVA 154
++P+++E +LT +F +VDEV + ++E V E K L+ NK QV+A
Sbjct: 165 KSPNNKELELTKEEFAKVDEVKETLMASERALDETVQEAQKVLNMVNGLNPSNKDQVLA 223
>gnl|CDD|133049 cd06427, CESA_like_2, CESA_like_2 is a member of the cellulose
synthase superfamily. The cellulose synthase (CESA)
superfamily includes a wide variety of
glycosyltransferase family 2 enzymes that share the
common characteristic of catalyzing the elongation of
polysaccharide chains. The members include cellulose
synthase catalytic subunit, chitin synthase, Glucan
Biosynthesis protein and other families of CESA-like
proteins. Cellulose synthase catalyzes the
polymerization reaction of cellulose, an aggregate of
unbranched polymers of beta-1,4-linked glucose residues
in plants, most algae, some bacteria and fungi, and
even some animals. In bacteria, algae and lower
eukaryotes, there is a second unrelated type of
cellulose synthase (Type II), which produces acylated
cellulose, a derivative of cellulose. Chitin synthase
catalyzes the incorporation of GlcNAc from substrate
UDP-GlcNAc into chitin, which is a linear homopolymer
of beta-(1,4)-linked GlcNAc residues and Glucan
Biosynthesis protein catalyzes the elongation of
beta-1,2 polyglucose chains of glucan.
Length = 241
Score = 28.4 bits (64), Expect = 4.8
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 57 PEHVEMKKP---QPRPKPKPLSKKLTKSEEEDLTVYDFEEVDEVDP 99
P + QPR KPK + L + E + +YD E D DP
Sbjct: 56 PSIFRVVVVPPSQPRTKPKACNYALAFARGEYVVIYDAE--DAPDP 99
>gnl|CDD|150343 pfam09645, F-112, F-112 protein. F-112 protein is of 70-110
residues and is found in viruses. Its winged-helix
structure suggests a DNA-binding function.
Length = 71
Score = 26.6 bits (58), Expect = 5.2
Identities = 13/53 (24%), Positives = 23/53 (43%)
Query: 145 SKLNKKQVVAPAHMCNYCNYTSPKRYLLARHLKSHSEERPHKCSVCERGFKTI 197
L +K + + + P Y + R LK+ E+ P +C ++G KT
Sbjct: 14 KILEEKGEITAEDIIAIFEISPPSAYAIFRALKAICEQHPDECEAIKKGRKTT 66
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 28.2 bits (63), Expect = 5.6
Identities = 21/69 (30%), Positives = 32/69 (46%)
Query: 82 EEEDLTVYDFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEK 141
E +D + EE + +E +EEDL + E+ + ++ E IEE DE
Sbjct: 4 ECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDEN 63
Query: 142 PKLSKLNKK 150
KL + NKK
Sbjct: 64 NKLKEENKK 72
>gnl|CDD|227222 COG4885, COG4885, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 312
Score = 28.0 bits (62), Expect = 6.5
Identities = 10/38 (26%), Positives = 14/38 (36%)
Query: 71 PKPLSKKLTKSEEEDLTVYDFEEVDEVDPIGEEAPSSE 108
P K T +E D FE DE + + + S
Sbjct: 247 PTKKLSKGTVEKEVDFQAEKFETADEPEYVPDPEQSKS 284
>gnl|CDD|215187 PLN02328, PLN02328, lysine-specific histone demethylase 1
homolog.
Length = 808
Score = 28.4 bits (63), Expect = 6.8
Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 8/67 (11%)
Query: 22 VPSEGSTGEVSYVLIVQQNET---EPGQISVEQDINPDPEHVEMKKPQPRPKPKPLSKKL 78
V SE S+ E L Q+E GQ S E +P P P L +
Sbjct: 18 VVSEASSPETDLSLSPSQSEQNIENDGQNSPETQSPLTEL-----QPSPLPPNTTLDAPV 72
Query: 79 TKSEEED 85
+ S+ ++
Sbjct: 73 SDSQGDE 79
>gnl|CDD|163534 TIGR03822, AblA_like_2, lysine-2,3-aminomutase-related protein.
Members of this protein form a distinctive clade,
homologous to lysine-2,3-aminomutase (of Bacillus,
Clostridium, and methanogenic archaea) and likely
similar in function. Members of this family are found in
Rhodopseudomonas, Caulobacter crescentus,
Bradyrhizobium, etc.
Length = 321
Score = 27.8 bits (62), Expect = 9.1
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 13/72 (18%)
Query: 95 DEVDPIGEE-APSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPKLSKLNKKQVV 153
D DPI + P E L E D PIG++A S + V P + ++
Sbjct: 44 DPDDPIARQFVPDPAE--LVTAPEERAD---PIGDDAHSPVPGIVHRYP------DRVLL 92
Query: 154 APAHMCN-YCNY 164
P H+C YC +
Sbjct: 93 KPVHVCPVYCRF 104
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 27.9 bits (62), Expect = 9.4
Identities = 17/117 (14%), Positives = 41/117 (35%), Gaps = 7/117 (5%)
Query: 30 EVSYVLIVQQNETEPGQISVEQDINPDPEHVEMKKPQPRPKPKPLSKKLTKSEEEDLTVY 89
E+ I+ N + +E I P+ K +KK+ EE +
Sbjct: 354 EIYLYKIINANPDKLENKKIEISIKPE-------KKTINNSQIITTKKINIVEESNKNSV 406
Query: 90 DFEEVDEVDPIGEEAPSSEEEDLTVYDFEEVDEVDPIGEEAPSTIEEDVDEKPKLSK 146
F+ + + + ++ EE+ E + + + +++ + +L+K
Sbjct: 407 HFDTLYKTKIFYHKKKINQNNKEQDIKKEELLEKEFVKKSEKIPKNDELLDNLELAK 463
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
0.314 0.131 0.395
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,175,725
Number of extensions: 1496893
Number of successful extensions: 1653
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1542
Number of HSP's successfully gapped: 146
Length of query: 330
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 233
Effective length of database: 6,635,264
Effective search space: 1546016512
Effective search space used: 1546016512
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: 59 (26.5 bits)