RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6569
(164 letters)
>gnl|CDD|114912 pfam06220, zf-U1, U1 zinc finger. This family consists of
several U1 small nuclear ribonucleoprotein C (U1-C)
proteins. The U1 small nuclear ribonucleoprotein (U1
snRNP) binds to the pre-mRNA 5' splice site (ss) at
early stages of spliceosome assembly. Recruitment of U1
to a class of weak 5' ss is promoted by binding of the
protein TIA-1 to uridine-rich sequences immediately
downstream from the 5' ss. Binding of TIA-1 in the
vicinity of a 5' ss helps to stabilise U1 snRNP
recruitment, at least in part, via a direct interaction
with U1-C, thus providing one molecular mechanism for
the function of this splicing regulator. This domain is
probably a zinc-binding. It is found in multiple copies
in some members of the family.
Length = 38
Score = 82.9 bits (205), Expect = 5e-22
Identities = 33/38 (86%), Positives = 34/38 (89%)
Query: 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYY 38
MPKYYCDYCD YLTHDSPSVRK+H GRKHKDNVK YY
Sbjct: 1 MPKYYCDYCDCYLTHDSPSVRKSHNGGRKHKDNVKDYY 38
>gnl|CDD|227465 COG5136, COG5136, U1 snRNP-specific protein C [RNA processing and
modification].
Length = 188
Score = 65.9 bits (160), Expect = 6e-14
Identities = 37/98 (37%), Positives = 43/98 (43%), Gaps = 8/98 (8%)
Query: 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYY----QKWMEEQAQNLIDATTAA 56
MP+Y+C+YC+ LTHD SVRK HC G KH K YY + E A L D TA
Sbjct: 1 MPRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYYMEMAEDIAAEMASILRDIKTAG 60
Query: 57 YKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPP 94
K N A PP +L P PP
Sbjct: 61 EKVECEGNKSTSYPPFPAFPPGDFYLNLALP----EPP 94
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type
zinc fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 52.3 bits (126), Expect = 3e-10
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVK 35
+YC C+ T D SV H +G+KHK NVK
Sbjct: 1 TGGFYCKLCNVTFT-DEISVE-AHLKGKKHKKNVK 33
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 44.4 bits (105), Expect = 1e-05
Identities = 18/79 (22%), Positives = 22/79 (27%), Gaps = 2/79 (2%)
Query: 84 LMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAM 143
L P Q P GM P P PP G + A
Sbjct: 172 LPQPPQQVLPQGMP--PRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQ 229
Query: 144 GPMGPMGPMRPPMMQDHPQ 162
P+ P P +PP +Q
Sbjct: 230 PPLPPQLPQQPPPLQQPQF 248
Score = 34.7 bits (80), Expect = 0.014
Identities = 12/66 (18%), Positives = 17/66 (25%), Gaps = 2/66 (3%)
Query: 97 QQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPM 156
Q P + P ++ GM P G P P G ++P
Sbjct: 161 AQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQ--GPPEQPPGYPQPPQGHPEQVQPQQ 218
Query: 157 MQDHPQ 162
P
Sbjct: 219 FLPAPS 224
Score = 34.0 bits (78), Expect = 0.032
Identities = 22/89 (24%), Positives = 28/89 (31%), Gaps = 8/89 (8%)
Query: 75 IPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGM 134
P P L PP Q PG+ Q PP P PP P P
Sbjct: 230 PPLPPQLPQQPPPLQQPQFPGLSQQMPP---PPPQPPQ----QQQQPPQPQAQPPPQ-NQ 281
Query: 135 GGMGPMMAMGPMGPMGPMRPPMMQDHPQR 163
P + G P+ P + P + Q+
Sbjct: 282 PTPHPGLPQGQNAPLPPPQQPQLLPLVQQ 310
Score = 30.9 bits (70), Expect = 0.32
Identities = 9/78 (11%), Positives = 17/78 (21%)
Query: 85 MPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMG 144
P+ PP + P P + + + + + M
Sbjct: 128 TAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPR 187
Query: 145 PMGPMGPMRPPMMQDHPQ 162
P +PQ
Sbjct: 188 QAAFPQQGPPEQPPGYPQ 205
Score = 27.0 bits (60), Expect = 5.1
Identities = 18/95 (18%), Positives = 21/95 (22%), Gaps = 4/95 (4%)
Query: 72 GAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGM-NPGMMGMRPM 130
P + P Q PP + Q PPP P M P P
Sbjct: 212 EQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQ 271
Query: 131 MGGMG---GMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
P G P+ PP
Sbjct: 272 PQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLP 306
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 35.9 bits (84), Expect = 3e-04
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 4 YYCDYCDTYLTHDSPSVRKTHCQGRKH 30
+YC+ C+ T S S K+H +G+KH
Sbjct: 1 FYCELCNVTFT--SESQLKSHLRGKKH 25
>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 = 36.0 bits (84), Expect = 4e-04
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHK 31
++YC CD Y S + + H + +KHK
Sbjct: 1 QFYCVACDKYFK--SENALENHLKSKKHK 27
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 36.2 bits (85), Expect = 0.005
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 7/36 (19%)
Query: 101 PPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGG 136
MM M PPGM M + ++ M G +G
Sbjct: 180 AAPMMEIMGPPGMEEM-------TIQLQDMFGNLGP 208
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 35.9 bits (83), Expect = 0.006
Identities = 24/82 (29%), Positives = 27/82 (32%), Gaps = 15/82 (18%)
Query: 94 PGMQQGPPPGMMPGMM--PP--GMN-MMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMG- 147
P M+Q P M G M PP G P MM MGP + P G
Sbjct: 380 PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMM--PTPMGPGGPLRPNGL 437
Query: 148 -PMGPMRPP------MMQDHPQ 162
PM +R P Q P
Sbjct: 438 APMNAVRAPSRNAQNAAQKPPM 459
Score = 34.4 bits (79), Expect = 0.018
Identities = 20/91 (21%), Positives = 22/91 (24%), Gaps = 7/91 (7%)
Query: 77 PPSNLSSLMPPRQVGPP-----PGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPM- 130
+ S M PP P Q P P M M G G+ PM
Sbjct: 383 RQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRP-NGLAPMN 441
Query: 131 MGGMGGMGPMMAMGPMGPMGPMRPPMMQDHP 161
A M PP Q P
Sbjct: 442 AVRAPSRNAQNAAQKPPMQPVMYPPNYQSLP 472
Score = 32.5 bits (74), Expect = 0.094
Identities = 10/59 (16%), Positives = 13/59 (22%), Gaps = 2/59 (3%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMN 121
P G + +P P P R G P P +M
Sbjct: 410 NGQPLGWPRMSMMPTPMGPGG--PLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPP 466
>gnl|CDD|218067 pfam04402, SIMPL, Protein of unknown function (DUF541). Members of
this family have so far been found in bacteria and mouse
SwissProt or TrEMBL entries. However possible family
members have also been identified in translated rat
(Genbank:AW144450) and human (Genbank:AI478629) ESTs. A
mouse family member has been named SIMPL (signalling
molecule that associates with mouse pelle-like kinase).
SIMPL appears to facilitate and/or regulate complex
formation between IRAK/mPLK (IL-1 receptor-associated
kinase) and IKK (inhibitor of kappa-B kinase) containing
complexes, and thus regulate NF-kappa-B activity.
Separate experiments demonstrate that a mouse family
member (named LaXp180) binds the Listeria monocytogenes
surface protein ActA, which is a virulence factor that
induces actin polymerisation. It may also bind stathmin,
a protein involved in signal transduction and in the
regulation of microtubule dynamics. In bacteria its
function is unknown, but it is thought to be located in
the periplasm or outer membrane.
Length = 210
Score = 35.0 bits (81), Expect = 0.009
Identities = 17/105 (16%), Positives = 28/105 (26%), Gaps = 25/105 (23%)
Query: 32 DNVKFYYQKWMEEQAQN--LIDATTAAY-KAGKIANNPFGNKGGAAIPPPSNLSSLMPPR 88
++F E + ++ L +A A KA +A G
Sbjct: 114 SGIEFSLSD--EAELKDEALAEAVKDAREKAEALAE-ALG-------------------V 151
Query: 89 QVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGG 133
++G + G P MM M P+ G
Sbjct: 152 KLGKVVSINIGSQGPPPPPMMAAAAAMAAAASAAAAAAPTPIEPG 196
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 35.2 bits (81), Expect = 0.010
Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 7/66 (10%)
Query: 60 GKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMG 119
G +A G++ G PPS P P P PG +M+ G
Sbjct: 230 GPLAPLAGGDRMGPPHGPPS----RYRPAYEAAPLA---PAISSYGPAGGGPGSVLMVSG 282
Query: 120 MNPGMM 125
++ +
Sbjct: 283 LHQEKV 288
>gnl|CDD|221143 pfam11593, Med3, Mediator complex subunit 3 fungal. 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. 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 subunit
Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast
transcriptional co-repressor.
Length = 381
Score = 35.0 bits (80), Expect = 0.010
Identities = 27/130 (20%), Positives = 39/130 (30%), Gaps = 8/130 (6%)
Query: 28 RKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPFGNKGGAAIPPPS----NLSS 83
RK + K + QA A +AY P A IP P+ L+
Sbjct: 195 RKPRQTKKTGPAAAAKAQASAQAQAQASAYNQMGSLGVPQNTSMLAQIPNPTPLMQLLNG 254
Query: 84 LMPPRQVGPPPGMQQGPPPGMM--PGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMM 141
+ P + P + P + G G M N M GM P
Sbjct: 255 VSPNNAMASP--LNNMSPMRNLNQMGNQNNGGQMTPSANNGNMNNQSRENSMNQGMTPSA 312
Query: 142 AMGPMGPMGP 151
+M + + P
Sbjct: 313 SMINLNNITP 322
Score = 28.8 bits (64), Expect = 1.3
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 119 GMNPGMMGMRPMMGGMGGMGPMMAMG-PMGPMGPMRPP 155
M + P+M + G+ P AM P+ M PMR
Sbjct: 237 SMLAQIPNPTPLMQLLNGVSPNNAMASPLNNMSPMRNL 274
>gnl|CDD|234400 TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa. This
model represents the N-terminal domain or EccCa subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 661
Score = 33.8 bits (78), Expect = 0.028
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 104 MMPGMMPPGM-NMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGP 148
++P +M M M++M G PM M + +G +
Sbjct: 7 LLPVVMVVAMVGMVVMMFASGGRQRNPMFLIFPLMMLVSMLGMLAG 52
Score = 33.0 bits (76), Expect = 0.063
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 110 PPGMNMMMMGMNPGMMGMRPMM--GGMGGMGPMMAMGPM 146
++ + M M+GM MM G PM + P+
Sbjct: 2 SVLQKLLPVVMVVAMVGMVVMMFASGGRQRNPMFLIFPL 40
Score = 26.5 bits (59), Expect = 7.4
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 103 GMMPGMMPPGM---NMMMMGMNPGMMGMRPMMGGMGGMG 138
GM+ M G N M + + P MM + + GG G
Sbjct: 18 GMVVMMFASGGRQRNPMFL-IFPLMMLVSMLGMLAGGRG 55
Score = 26.5 bits (59), Expect = 8.0
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 12/46 (26%)
Query: 94 PGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGP 139
G +Q P M + P +MM + M+GM + GG GG G
Sbjct: 26 SGGRQRNP---MFLIFP-----LMMLV--SMLGM--LAGGRGGAGK 59
>gnl|CDD|227571 COG5246, PRP11, Splicing factor 3a, subunit 2 [RNA processing and
modification].
Length = 222
Score = 33.1 bits (75), Expect = 0.044
Identities = 25/103 (24%), Positives = 39/103 (37%), Gaps = 21/103 (20%)
Query: 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNV------------------KFYYQKWMEE 44
KY C C T H + H +G+KHK+N F Q+ + E
Sbjct: 53 KYVCLLCKT--KHLTEMSYVKHREGKKHKENSSRRSEEKSSLGRENQTTHDFRQQQKIIE 110
Query: 45 QAQNLIDATTAAYKAGKIANNPFGNKG-GAAIPPPSNLSSLMP 86
Q+L + +YK + G +G G + +L+ MP
Sbjct: 111 AKQSLKRSGIPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEMP 153
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 33.2 bits (76), Expect = 0.046
Identities = 11/23 (47%), Positives = 11/23 (47%)
Query: 91 GPPPGMQQGPPPGMMPGMMPPGM 113
G P GM G P GM G P G
Sbjct: 619 GMPGGMPGGMPGGMPGGAGPAGA 641
Score = 29.4 bits (66), Expect = 0.83
Identities = 12/25 (48%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 102 PGMMPGMMPPGMNMMMMGMNPGMMG 126
PG MPG MP GM G P G
Sbjct: 621 PGGMPGGMPGGM---PGGAGPAGAG 642
Score = 29.4 bits (66), Expect = 0.89
Identities = 12/38 (31%), Positives = 13/38 (34%), Gaps = 2/38 (5%)
Query: 120 MNPGMMGM-RPMMGGMGGMGPMMAMGPMGPMGPMRPPM 156
NP M M + GGM G P M P G
Sbjct: 605 CNPIMTKMYQAAGGGMPGGMPG-GMPGGMPGGAGPAGA 641
Score = 28.6 bits (64), Expect = 1.9
Identities = 13/45 (28%), Positives = 14/45 (31%), Gaps = 2/45 (4%)
Query: 107 GMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGP 151
+ P M M GM G P GGM G P A
Sbjct: 603 SVCNPIMTKMYQAAGGGMPGGMP--GGMPGGMPGGAGPAGAGASS 645
>gnl|CDD|236810 PRK10965, PRK10965, multicopper oxidase; Provisional.
Length = 523
Score = 32.3 bits (74), Expect = 0.085
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 108 MMPPGMNMMMMGMNPGMMGMRPMMG-GMGGMGPMMAMGPMGPMG 150
M P ++MM M M G + M G M M M G M M
Sbjct: 355 SMDPRLDMMGMQMLMEKYGDQAMAGMDMDHMMGHMGHGNMDHMN 398
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 31.7 bits (73), Expect = 0.13
Identities = 10/32 (31%), Positives = 11/32 (34%), Gaps = 2/32 (6%)
Query: 127 MRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQ 158
M+ MM M G G M M M M
Sbjct: 421 MKKMMKKMSGGGGKGKM--MRGMKGMMGGKFP 450
Score = 31.7 bits (73), Expect = 0.14
Identities = 9/26 (34%), Positives = 9/26 (34%), Gaps = 1/26 (3%)
Query: 114 NMM-MMGMNPGMMGMRPMMGGMGGMG 138
MM M G M M GM G
Sbjct: 423 KMMKKMSGGGGKGKMMRGMKGMMGGK 448
Score = 30.6 bits (70), Expect = 0.36
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 113 MNMMMMGMNPGMMGMRPMMGGMGGMGPMM 141
M MM M+ G G MM GM GM
Sbjct: 421 MKKMMKKMS-GGGGKGKMMRGMKGMMGGK 448
Score = 30.6 bits (70), Expect = 0.39
Identities = 11/30 (36%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 104 MMPGMMPPGMNMMMMGMNPGMMGMRPMMGG 133
MM M G MM GMMG G
Sbjct: 424 MMKKMSGGGGKGKMMRGMKGMMGG--KFPG 451
Score = 27.5 bits (62), Expect = 3.4
Identities = 10/34 (29%), Positives = 10/34 (29%), Gaps = 5/34 (14%)
Query: 113 MNMM--MMGMNPGMMGMRPMMGGMGGMGPMMAMG 144
M MM M G M GM MM
Sbjct: 418 FKQMKKMMKK---MSGGGGKGKMMRGMKGMMGGK 448
Score = 27.1 bits (61), Expect = 5.2
Identities = 13/27 (48%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 113 MNMMMMGMNPGMMGMRPMMGGMGGMGP 139
M M G G M MR M G MGG P
Sbjct: 425 MKKMSGGGGKGKM-MRGMKGMMGGKFP 450
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 31.9 bits (73), Expect = 0.14
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 7/36 (19%)
Query: 101 PPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGG 136
P M PPGM M ++ M G +GG
Sbjct: 181 GPPGFEIMGPPGMEEM-------TNNLQDMFGNLGG 209
>gnl|CDD|233432 TIGR01480, copper_res_A, copper-resistance protein, CopA family.
This model represents the CopA copper resistance protein
family. CopA is related to laccase (benzenediol:oxygen
oxidoreductase) and L-ascorbate oxidase, both
copper-containing enzymes. Most members have a typical
TAT (twin-arginine translocation) signal sequence with
an Arg-Arg pair. Twin-arginine translocation is observed
for a large number of periplasmic proteins that cross
the inner membrane with metal-containing cofactors
already bound. The combination of copper-binding sites
and TAT translocation motif suggests a mechansism of
resistance by packaging and export [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 587
Score = 31.4 bits (71), Expect = 0.22
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 114 NMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQD 159
+M M GM+ GM + MGGM GM M+M PM M
Sbjct: 370 DMGMGGMHHGMDHSKMSMGGMPGMD--MSMRAQSNA-PMDHSQMAM 412
>gnl|CDD|239075 cd02335, ZZ_ADA2, Zinc finger, ZZ type. Zinc finger present in
ADA2, a putative transcriptional adaptor, and related
proteins. The ZZ motif coordinates two zinc ions and
most likely participates in ligand binding or molecular
scaffolding.
Length = 49
Score = 28.0 bits (63), Expect = 0.45
Identities = 7/23 (30%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 4 YYCDYCDTYLTHDSPSVRKTHCQ 26
Y+CDYC +T + ++ C
Sbjct: 1 YHCDYCSKDITG-TIRIKCAECP 22
>gnl|CDD|180801 PRK07033, PRK07033, hypothetical protein; Provisional.
Length = 427
Score = 30.0 bits (68), Expect = 0.60
Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 7/60 (11%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNP 122
+++PF G +PP + G P + G G+N ++ NP
Sbjct: 3 SSDPFSAGSGGFVPPNPGDRTPAAAPAAGAPFQPRPGRGAA-------SGLNPLVAAANP 55
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 30.0 bits (67), Expect = 0.60
Identities = 28/88 (31%), Positives = 29/88 (32%), Gaps = 2/88 (2%)
Query: 71 GGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPM 130
G SS P Q G QQG G GM G + P MG P
Sbjct: 143 PGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQ-GQQGPVGQQQPPQMGQ-PG 200
Query: 131 MGGMGGMGPMMAMGPMGPMGPMRPPMMQ 158
M G GG G M G G P M Q
Sbjct: 201 MPGGGGQGQMQQQGQPGGQQQQNPQMQQ 228
Score = 30.0 bits (67), Expect = 0.67
Identities = 25/101 (24%), Positives = 33/101 (32%), Gaps = 1/101 (0%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGM-MPGMMPPGMNMMMMGMN 121
A +GG +P P N + + P GP PG M M + +
Sbjct: 57 AAQQQVLQGGQGMPDPINALQNLTGQGTRGPQMGPMGPGPGRPMGQQMGGPGTASNLLQS 116
Query: 122 PGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
+ G PM G M +G M P G M Q Q
Sbjct: 117 LNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQ 157
Score = 27.3 bits (60), Expect = 4.2
Identities = 20/91 (21%), Positives = 25/91 (27%), Gaps = 1/91 (1%)
Query: 68 GNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMG- 126
G + + N+ MP G P G M
Sbjct: 106 GPGTASNLLQSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQ 165
Query: 127 MRPMMGGMGGMGPMMAMGPMGPMGPMRPPMM 157
M P G G M G GP+G +PP M
Sbjct: 166 MGPQQGQAQGQAGGMNQGQQGPVGQQQPPQM 196
>gnl|CDD|227642 COG5337, CotH, Spore coat assembly protein [Cell envelope
biogenesis, outer membrane].
Length = 473
Score = 29.9 bits (67), Expect = 0.64
Identities = 18/62 (29%), Positives = 23/62 (37%), Gaps = 17/62 (27%)
Query: 96 MQQGPPPGMMPG-------------MMPPGMNMMMM----GMNPGMMGMRPMMGGMGGMG 138
+ GM PG +M N+ + GM P +MGM P MG GM
Sbjct: 334 IGGFGTLGMRPGGLDESEFRGSYKRLMEKTGNLQSLFTIEGMPPKIMGMYPRMGPFVGMD 393
Query: 139 PM 140
P
Sbjct: 394 PY 395
>gnl|CDD|226193 COG3667, PcoB, Uncharacterized protein involved in copper
resistance [Inorganic ion transport and metabolism].
Length = 321
Score = 29.8 bits (67), Expect = 0.66
Identities = 17/78 (21%), Positives = 20/78 (25%), Gaps = 22/78 (28%)
Query: 87 PRQVGPPPGMQQGP---PPGMMPGMMP------PGMNMMMMGMNPGMMGMRPMMGGMGGM 137
P + P + P P MPGM PG M M+ G M
Sbjct: 26 PTEAAQPHAHEHAPMDAPHPAMPGMDHHAHSKMPGPEMAAPQMDHGAM------------ 73
Query: 138 GPMMAMGPMGPMGPMRPP 155
P M P
Sbjct: 74 -PHMDHAPPPIPTQHAAE 90
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.0 bits (65), Expect = 1.3
Identities = 15/94 (15%), Positives = 26/94 (27%), Gaps = 16/94 (17%)
Query: 73 AAIPPPSNLSSLMPPRQVGPPPGMQQG--PPPGMM----PGMMPPGMNMMMMGMNPGMMG 126
AA PS S + P Q PP + + P
Sbjct: 395 AAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRPAQFKE 454
Query: 127 MRPMMGGMGGMGPMMAMGPMGP--MGPMRPPMMQ 158
+ + P+ + +GP + P++ Q
Sbjct: 455 EKKI--------PVSKVSSLGPSTLRPIQEKAEQ 480
>gnl|CDD|220651 pfam10248, Mlf1IP, Myelodysplasia-myeloid leukemia factor
1-interacting protein. This entry is the conserved
central region of a group of proteins that are putative
transcriptional repressors. The structure contains a
putative 14-3-3 binding motif involved in the
subcellular localisation of various regulatory
molecules, and it may be that interaction with the
transcription factor DREF could be regulated through
this motif. DREF regulates proliferation-related genes
in Drosophila. Mlf1IP is expressed in both the nuclei
and the cytoplasm and thus may have multi-functions.
Length = 177
Score = 28.3 bits (63), Expect = 1.4
Identities = 16/52 (30%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 98 QGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPM 149
GPP G + P MMGM M M MM M M+ G
Sbjct: 30 PGPPGGQQSLRVTP---FGMMGMGGMFMDMFNMMEDMHRNMERMSGGSNCQS 78
>gnl|CDD|235884 PRK06917, PRK06917, hypothetical protein; Provisional.
Length = 447
Score = 28.9 bits (65), Expect = 1.4
Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 1/68 (1%)
Query: 11 TYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPFGNK 70
L D P++ +C R V Q + + I+ A + A IA G
Sbjct: 154 VSLLEDYPTISAPYCY-RCPVQKVYPTCQLACATELETAIERIGAEHIAAFIAEPIIGAA 212
Query: 71 GGAAIPPP 78
G A +PP
Sbjct: 213 GAAVVPPK 220
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 28.3 bits (63), Expect = 1.6
Identities = 14/41 (34%), Positives = 14/41 (34%)
Query: 123 GMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQR 163
G G GG GGMG M MGP G G
Sbjct: 191 GGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGGMGAPGQGNA 231
Score = 26.8 bits (59), Expect = 5.7
Identities = 15/48 (31%), Positives = 15/48 (31%)
Query: 112 GMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQD 159
G M G G MG MG GG G MG G Q
Sbjct: 192 GGGGGMGGGGGGGMGEMGGMGPQGGGGGYGGMGAPGQGNAYNQGYRQG 239
>gnl|CDD|172745 PRK14257, PRK14257, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 329
Score = 27.8 bits (61), Expect = 2.6
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 20 VRKTHCQGRKHKDNVKFYYQKWMEEQAQNLI------DATTAAYKAGKIA 63
V + Q ++ D F+YQ W+EE + + T Y +GKI
Sbjct: 280 VTHSMAQAQRISDETVFFYQGWIEEAGETKTIFIHPKNKRTKDYISGKIG 329
>gnl|CDD|221827 pfam12881, NUT_N, NUT protein N terminus. This family includes the
NUT protein. The gene encoding for NUT protein (Nuclear
Testis protein) is found fused to BRD3 or BRD4 genes, in
some aggressive types of carcinoma, due to chromosomal
translocations. Proteins of the BRD family contain two
bromodomains that bind transcriptionally active
chromatin through associations with acetylated histones
H3 and H4. Such proteins are crucial for the regulation
of cell cycle progression. On the other hand, little is
known about NUT protein. NUT is known to have a Nuclear
Export Sequence (NES) as well as a Nuclear Localization
Signal (NLS), both located towards the C-terminal end of
the protein. A fused NUT-GFP protein showed either
cytoplasmic or nuclear localization, suggesting that it
is subject to nuclear/cytoplasmic shuttling. Consistent
with this possibility, treatment with leptomycin B an
inhibitor of CRM1-dependent nuclear export resulted in
re-distribution of NUT-GFP to the nucleus. Inspection of
NUT revealed a C-terminal sequence similar to known
nuclear export sequences (NES) which are often regulated
by phosphorylation.
Length = 328
Score = 27.6 bits (61), Expect = 2.9
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 70 KGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRP 129
GA++ P + L L P Q PP PPP ++ PG N +++ P M P
Sbjct: 10 NPGASLSPFAALPFLPPAPQ--PPDQPFWEPPPPLVTAGFSPG-NPLVLSALPSM----P 62
Query: 130 MMGGMGGMGPMMA 142
++ GG G A
Sbjct: 63 LVTEGGGPGLSGA 75
>gnl|CDD|219897 pfam08549, SWI-SNF_Ssr4, Fungal domain of unknown function
(DUF1750). This is a fungal domain of unknown function.
Length = 669
Score = 27.7 bits (61), Expect = 3.4
Identities = 13/46 (28%), Positives = 14/46 (30%), Gaps = 1/46 (2%)
Query: 77 PPSNLSSLMPPRQVGPP-PGMQQGPPPGMMPGMMPPGMNMMMMGMN 121
PP + M RQ P PG GPP P G
Sbjct: 216 PPGPYPNAMVGRQPFYPQPGAVAGPPKRRGGHKAPRGHRASQAAGQ 261
>gnl|CDD|219358 pfam07271, Cytadhesin_P30, Cytadhesin P30/P32. This family
consists of several Mycoplasma species specific
Cytadhesin P32 and P30 proteins. P30 has been found to
be membrane associated and localised on the tip
organelle. It is thought that it is important in
cytadherence and virulence.
Length = 279
Score = 27.3 bits (60), Expect = 3.5
Identities = 23/69 (33%), Positives = 23/69 (33%), Gaps = 4/69 (5%)
Query: 92 PPPGMQQGP----PPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMG 147
P PGM P P MMP M PG G N M P M G P M P
Sbjct: 209 PMPGMPPRPGFNQNPNMMPNMNRPGFRPQPGGFNHPGTPMGPNMQQRPGFNPNQGMNPPP 268
Query: 148 PMGPMRPPM 156
M R
Sbjct: 269 HMAGPRAGF 277
Score = 27.0 bits (59), Expect = 5.7
Identities = 29/80 (36%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 90 VGPPPGMQQGPP--PGMMPGMMPPGMNMMM-MGMNPGMMGMRPMMGGMGGMG----PMMA 142
+G PG Q PP PGM P M PG N M M PG MM M G P
Sbjct: 182 MGMRPGFNQMPPHMPGMPPNQMRPGFNPMPGMPPRPGFNQNPNMMPNMNRPGFRPQPGGF 241
Query: 143 MGPMGPMGPMRPPMMQDHPQ 162
P PMGP +P
Sbjct: 242 NHPGTPMGPNMQQRPGFNPN 261
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 27.4 bits (61), Expect = 3.5
Identities = 17/77 (22%), Positives = 19/77 (24%), Gaps = 10/77 (12%)
Query: 86 PPRQVGPPPGMQQGPPPGMMPGMMPPGMNMM------MMGMNPGMMGMRPMMGGMGGMGP 139
P V P PPP +P G NP P G G
Sbjct: 55 APPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALP--AGPAGPTI 112
Query: 140 MMAMGPMGPMGPMRPPM 156
G + P P M
Sbjct: 113 QTEPGQLYP--VQVPVM 127
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 27.6 bits (62), Expect = 3.5
Identities = 17/75 (22%), Positives = 20/75 (26%), Gaps = 8/75 (10%)
Query: 88 RQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMG 147
++ P PG G PPG P G GG +A P
Sbjct: 388 QEGPPSPGGGGGGPPGGGGAPGAPA--------AAAAPGAAAAAPAAGGPAAALAAVPDA 439
Query: 148 PMGPMRPPMMQDHPQ 162
PP PQ
Sbjct: 440 AAAAAAPPAPAAAPQ 454
>gnl|CDD|107252 cd01539, PBP1_GGBP, Periplasmic glucose/galactose-binding protein
(GGBP) involved in chemotaxis towards, and active
transport of, glucose and galactose in various bacterial
species. Periplasmic glucose/galactose-binding protein
(GGBP) involved in chemotaxis towards, and active
transport of, glucose and galactose in various bacterial
species. GGBP is a member of the pentose/hexose
sugar-binding protein family of the type I periplasmic
binding protein superfamily which consists of two
alpha/beta globular domains connected by a
three-stranded hinge. This Venus flytrap-like domain
undergoes transition from an open to a closed
conformational state upon ligand binding. Moreover, the
periplasmic GGBP is homologous to the ligand-binding
domain of eukaryotic receptors such as glutamate
receptor (GluR) and DNA-binding transcriptional
repressors such as LacI and GalR.
Length = 303
Score = 27.2 bits (61), Expect = 4.7
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 41 WMEEQAQNLIDATTAAYKAGKI----ANN 65
W QA++ +DA Y KI ANN
Sbjct: 182 WDRAQAKDKMDALLLKYG-DKIEAVIANN 209
>gnl|CDD|227507 COG5180, PBP1, Protein interacting with poly(A)-binding protein
[RNA processing and modification].
Length = 654
Score = 27.4 bits (60), Expect = 4.7
Identities = 24/54 (44%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 111 PGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMG---PMRPPMMQDHP 161
PGMN M GMN G M PM G PMM G MG P +P M HP
Sbjct: 510 PGMNPAM-GMNMGGMMGFPMGGPSASPNPMMNGFAAGSMGMYMPFQPQPMFYHP 562
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 27.0 bits (60), Expect = 4.8
Identities = 13/37 (35%), Positives = 15/37 (40%)
Query: 68 GNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGM 104
G + G PPS P V PP G + PP M
Sbjct: 48 GGRSGGTTAPPSVQEDGKPKIDVNPPKGTRDFPPEDM 84
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 26.9 bits (60), Expect = 5.1
Identities = 20/95 (21%), Positives = 29/95 (30%), Gaps = 10/95 (10%)
Query: 67 FGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMM-------MG 119
FG P + PP + G G G PG PG + G
Sbjct: 87 FGGGAPRPPPAAPAVQPPAPPARPGWGSGGPSQQGAGQQPGYAQPGPGSFLGGAAQTAAG 146
Query: 120 MNPGMM---GMRPMMGGMGGMGPMMAMGPMGPMGP 151
+ GM+ G+ + GG ++ G G
Sbjct: 147 VAGGMLLGNGLENLFGGHSQPAEIVDAIGEGGDGS 181
>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional.
Length = 991
Score = 27.1 bits (60), Expect = 5.1
Identities = 14/45 (31%), Positives = 16/45 (35%)
Query: 67 FGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPP 111
FG G P ++ PP GPP Q PPP P
Sbjct: 895 FGPGTGRVATAPGGDAASAPPPGAGPPAPPQAVPPPRTTQPPAAP 939
Score = 26.7 bits (59), Expect = 7.0
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 59 AGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQ-QGPPP 102
G++A P G+ AA PP PP+ V PP Q PP
Sbjct: 899 TGRVATAPGGD---AASAPPPGAGPPAPPQAVPPPRTTQPPAAPP 940
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 27.0 bits (59), Expect = 5.2
Identities = 20/96 (20%), Positives = 28/96 (29%), Gaps = 11/96 (11%)
Query: 44 EQAQNLIDATTAAYKAGKIANNPFGNKGGAAIPPPS---------NLSSLMPPRQVGPPP 94
E+A N + T+A K KI+ + I S P +V PP
Sbjct: 77 EKAPNTNEEKTSASKIEKISQPKQEEQKSLNISATPAPKQEQSQTTTESTTPKTKVTTPP 136
Query: 95 GMQQGPPPGMMPGMMP--PGMNMMMMGMNPGMMGMR 128
P P P + M P +R
Sbjct: 137 STNTPQPMQSTKSDTPQSPTIKQAQTDMTPKYEDLR 172
>gnl|CDD|184110 PRK13523, PRK13523, NADPH dehydrogenase NamA; Provisional.
Length = 337
Score = 27.0 bits (60), Expect = 5.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 38 YQKWMEEQAQNLIDATTAA 56
Y KWM+EQ +LID ++ A
Sbjct: 232 YAKWMKEQGVDLIDVSSGA 250
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 27.0 bits (60), Expect = 6.0
Identities = 10/32 (31%), Positives = 12/32 (37%)
Query: 71 GGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPP 102
GA PP + + P PPP PP
Sbjct: 379 RGAPAPPSAAWGAPTPAAPAAPPPAAAPPVPP 410
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 26.9 bits (59), Expect = 6.0
Identities = 12/27 (44%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 85 MPPRQVGPPPGMQQGPPPGMMPGMMPP 111
+PP PPP PPPG P PP
Sbjct: 4 LPPGNPPPPP-----PPPGFEPPSQPP 25
>gnl|CDD|234383 TIGR03895, protease_PatA, cyanobactin maturation protease,
PatA/PatG family. This model describes a protease
domain associated with the maturation of various members
of the cyanobactin family of ribosomally produced,
heavily modified bioactive metabolites. Members include
the PatA protein and C-terminal domain of the PatG
protein of Prochloron didemni, TenA and a region of TenG
from Nostoc spongiaeforme var. tenue, etc.
Length = 602
Score = 27.0 bits (60), Expect = 6.1
Identities = 11/54 (20%), Positives = 18/54 (33%)
Query: 60 GKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGM 113
G I ++ G A P + P + P Q G++P + P
Sbjct: 253 GTIESSTSVIPPGRAAEPAPVSIPVAAPGEGATPAAAQIELSAGVLPNAISPAT 306
>gnl|CDD|216807 pfam01956, DUF106, Integral membrane protein DUF106. This
archaebacterial protein family has no known function.
Members are predicted to be integral membrane proteins.
Length = 168
Score = 26.5 bits (59), Expect = 6.1
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 108 MMPPGMNMMMMGMNPGMMGMRPMMGGMGGM 137
+M MMM M P M P + G +
Sbjct: 78 LMEDQKEMMMDMMKPNFAIMIPQILIFGWI 107
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 26.8 bits (60), Expect = 6.2
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 10/36 (27%)
Query: 124 MMGMRPM----------MGGMGGMGPMMAMGPMGPM 149
+ G+RP+ GG+G +G M +G GP
Sbjct: 81 LEGLRPVRWWRVLPVKFFGGLGTLGSGMVLGREGPT 116
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 26.7 bits (59), Expect = 6.7
Identities = 11/50 (22%), Positives = 14/50 (28%), Gaps = 10/50 (20%)
Query: 69 NKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMM 118
+ GA P PS +S +Q P G M G
Sbjct: 67 HNTGANNPAPSVMSPAFQSQQKFSSPY----------GGSMADGTAPKPT 106
>gnl|CDD|234573 PRK00013, groEL, chaperonin GroEL; Reviewed.
Length = 542
Score = 26.6 bits (60), Expect = 6.8
Identities = 6/12 (50%), Positives = 6/12 (50%)
Query: 129 PMMGGMGGMGPM 140
G GGMG M
Sbjct: 531 APPMGGGGMGGM 542
Score = 26.6 bits (60), Expect = 7.1
Identities = 8/17 (47%), Positives = 8/17 (47%), Gaps = 4/17 (23%)
Query: 121 NPGMMGMRPMMGGMGGM 137
MG GGMGGM
Sbjct: 530 AAPPMGG----GGMGGM 542
>gnl|CDD|183992 PRK13353, PRK13353, aspartate ammonia-lyase; Provisional.
Length = 473
Score = 26.9 bits (60), Expect = 6.8
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 21/63 (33%)
Query: 45 QAQNLIDAT--------------TAAYKAGKIANN-------PFGNKGGAAIPPPSNLSS 83
A++L+DAT A KIAN+ P G +P SS
Sbjct: 260 GAEDLVDATQNTDAFVEVSGALKVCAVNLSKIANDLRLLSSGPRTGLGEINLPAVQPGSS 319
Query: 84 LMP 86
+MP
Sbjct: 320 IMP 322
>gnl|CDD|226830 COG4395, COG4395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 281
Score = 26.7 bits (59), Expect = 7.2
Identities = 12/66 (18%), Positives = 21/66 (31%), Gaps = 6/66 (9%)
Query: 79 SNLSSLMPPRQVGP-PPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGM 137
+ S+ P Q P P GM+ ++MG++ G G G+
Sbjct: 2 TRSSTATPSTQTAPAAAAAAPAARPSFFSGMLGGLAGGLLMGLSGMFFG-----GLFFGI 56
Query: 138 GPMMAM 143
+
Sbjct: 57 AAFLIF 62
>gnl|CDD|227538 COG5213, FIP1, Polyadenylation factor I complex, subunit FIP1 [RNA
processing and modification].
Length = 266
Score = 26.2 bits (57), Expect = 8.5
Identities = 14/58 (24%), Positives = 17/58 (29%), Gaps = 4/58 (6%)
Query: 68 GNKGGAAIPPP-SNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGM 124
GA N+ + M R GP + M G P M PGM
Sbjct: 199 DGPNGANGSNDNGNMGNGMGGRPNGPAGPKEPSFGGLGMFGDFEP---FPYEEMGPGM 253
>gnl|CDD|219837 pfam08430, Fork_head_N, Forkhead N-terminal region. The region
described in this family is found towards the N-terminus
of various eukaryotic fork head/HNF-3-related
transcription factors (which contain the pfam00250
domain). These proteins play key roles in embryogenesis,
maintenance of differentiated cell states, and
tumorigenesis.
Length = 137
Score = 25.7 bits (56), Expect = 8.5
Identities = 20/78 (25%), Positives = 29/78 (37%)
Query: 79 SNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMG 138
+++++ P PG M + M GM+PG G MG MG
Sbjct: 22 NSMNTYGPMNTSQGSANSSMNMSGYAGPGAMNGMSSSSMNGMSPGYGGAGSPMGMMGMSS 81
Query: 139 PMMAMGPMGPMGPMRPPM 156
++ P G MG M P
Sbjct: 82 MGTSLSPSGTMGAMGPMP 99
>gnl|CDD|216650 pfam01696, Adeno_E1B_55K, Adenovirus EB1 55K protein / large
t-antigen. This family consists of adenovirus E1B 55K
protein or large t-antigen. E1B 55K binds p53 the tumour
suppressor protein converting it from a transcriptional
activator which responds to damaged DNA in to an
unregulated repressor of genes with a p53 binding site.
This protects the virus against p53 induced host
antiviral responses and prevents apoptosis as induced by
the adenovirus E1A protein. The E1B region of adenovirus
encodes two proteins E1B 55K the large t-antigen as
found in this family and E1B 19K pfam01691 the small
t-antigen which is not found in this family; both of
these proteins inhibit E1A induced apoptosis. This
family shows distant similarities to the pectate lyase
superfamily.
Length = 387
Score = 26.5 bits (59), Expect = 8.5
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 110 PPGMNMMMMGMNPGMMGM 127
+ M M PG++GM
Sbjct: 104 GVAFRVYMQSMGPGVVGM 121
>gnl|CDD|238504 cd01031, EriC, ClC chloride channel EriC. This domain is found in
the EriC chloride transporters that mediate the extreme
acid resistance response in eubacteria and archaea. This
response allows bacteria to survive in the acidic
environments by decarboxylation-linked proton
utilization. As shown for Escherichia coli EriC, these
channels can counterbalance the electric current
produced by the outwardly directed virtual proton pump
linked to amino acid decarboxylation. The EriC proteins
belong to the ClC superfamily of chloride ion channels,
which share a unique double-barreled architecture and
voltage-dependent gating mechanism. The
voltage-dependent gating is conferred by the permeating
anion itself, acting as the gating charge. In
Escherichia coli EriC, a glutamate residue that
protrudes into the pore is thought to participate in
gating by binding to a Cl- ion site within the
selectivity filter.
Length = 402
Score = 26.4 bits (59), Expect = 8.9
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 13/40 (32%)
Query: 124 MMGMRPMM----------GGMGGMGPMMAMGPMGP---MG 150
+ G+ P GG+ +G +++G GP +G
Sbjct: 74 LAGLLPPNWWRVLPVKFVGGVLALGSGLSLGREGPSVQIG 113
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 0.136 0.450
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,667,298
Number of extensions: 788391
Number of successful extensions: 2180
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1683
Number of HSP's successfully gapped: 259
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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: 55 (25.1 bits)