RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2227
(175 letters)
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab)
or POZ (for Pox virus and Zinc finger) domain is
present near the N-terminus of a fraction of zinc
finger (pfam00096) proteins and in proteins that
contain the pfam01344 motif such as Kelch and a family
of pox virus proteins. The BTB/POZ domain mediates
homomeric dimerisation and in some instances
heteromeric dimerisation. The structure of the
dimerised PLZF BTB/POZ domain has been solved and
consists of a tightly intertwined homodimer. The
central scaffolding of the protein is made up of a
cluster of alpha-helices flanked by short beta-sheets
at both the top and bottom of the molecule. POZ domains
from several zinc finger proteins have been shown to
mediate transcriptional repression and to interact with
components of histone deacetylase co-repressor
complexes including N-CoR and SMRT. The POZ or BTB
domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 97.7 bits (244), Expect = 4e-27
Identities = 34/94 (36%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
Query: 5 LGYLLENQILVDVTLMCNTHTLKVHKVVLASCSPYFEGVLQKQLGTHPLIVLKDMKFSVL 64
L L EN L DVTL+ HK VLA+CSPYF+ + I L+D+
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFKALFTGNKEVE--ITLEDVSPEDF 58
Query: 65 RSLIEFMYCGETSIAEDNLPALLDAAKFFEVKGL 98
+L+EF+Y G+ I E+N+ LL A ++ L
Sbjct: 59 EALLEFIYTGKLEITEENVDDLLALADKLQIPAL 92
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 81.6 bits (202), Expect = 8e-21
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 16 DVTLMCNTHTLKVHKVVLASCSPYFEGVLQKQLG--THPLIVLKDMKFSVLRSLIEFMYC 73
DVTL+ HK VLA+ SPYF+ + I L D+ R+L+ F+Y
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPEDFRALLNFLYT 60
Query: 74 GETSIAEDNLPALLDAAKFFEVKGLASM 101
G+ + E+N+ LL+ A + ++ GL +
Sbjct: 61 GKLDLPEENVEELLELADYLQIPGLVEL 88
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 45.1 bits (107), Expect = 5e-06
Identities = 21/92 (22%), Positives = 45/92 (48%), Gaps = 4/92 (4%)
Query: 7 YLLENQILVDVTLMCNTH--TLKVHKVVLASCSPYFEGVLQKQLGTHPLIVLKDMKFSVL 64
Y E Q D +++ +KVHK++L+S S YF+ + + + + + D
Sbjct: 2 YSFELQKFCDESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNIDYD--SF 59
Query: 65 RSLIEFMYCGETSIAEDNLPALLDAAKFFEVK 96
+I+++Y G+ +I +N+ +L A + +
Sbjct: 60 NEVIKYIYTGKINITSNNVKDILSIANYLIID 91
>gnl|CDD|240410 PTZ00418, PTZ00418, Poly(A) polymerase; Provisional.
Length = 593
Score = 38.6 bits (90), Expect = 0.001
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 83 LPALLDAAKFFEVKGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEH 142
LPA + + E ++ TS+ TT +S + + N++ S+ T+SS E
Sbjct: 527 LPAFVLSQTPEEPV----KTKANTKTNTSSATTSGQSGSSGSTSNSNSNESSPTMSSTEL 582
Query: 143 TASSNTSITGS 153
S+TS TGS
Sbjct: 583 LNVSSTSTTGS 593
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 37.1 bits (85), Expect = 0.004
Identities = 21/72 (29%), Positives = 37/72 (51%)
Query: 95 VKGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSL 154
++ A+ S A S S +T+ +T +++ T TT +T+++ ST SSN T + I +
Sbjct: 273 LEAFANGSASANSTSNSNSTSNSTTNSNSTTTTNSTTSTNSTSSSNSSTIAGCIDIAANF 332
Query: 155 AIASSKCLLFLM 166
IA L+
Sbjct: 333 TIALQNLQALLL 344
Score = 36.7 bits (84), Expect = 0.005
Identities = 16/62 (25%), Positives = 40/62 (64%)
Query: 98 LASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIA 157
LA++ A ++ +T+ + +++ T + +T+T+ ST S+N ++S++++I G + IA
Sbjct: 270 LAALEAFANGSASANSTSNSNSTSNSTTNSNSTTTTNSTTSTNSTSSSNSSTIAGCIDIA 329
Query: 158 SS 159
++
Sbjct: 330 AN 331
Score = 32.1 bits (72), Expect = 0.13
Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 82 NLPALLDAAKFFEVKGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNE 141
NL A++ A G S S ++ S ST+ + +T S + T ++ +T+T++++ SS+
Sbjct: 86 NLIAMISANIQAIQSGSGSASGNSSSSANSTSNSNSTTSNNSTTSSNSTTTTSNSTSSSN 145
Query: 142 HTASSNTS 149
T+S TS
Sbjct: 146 STSSGLTS 153
>gnl|CDD|221093 pfam11359, gpUL132, Glycoprotein UL132. Glycoprotein UL132 is a
low-abundance structural component of Human
cytomegalovirus (HCMV). The function of this protein is
not fully understood.
Length = 235
Score = 34.6 bits (79), Expect = 0.016
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 107 SQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAI----ASSKCL 162
S T TT T T+ T + ST+ +T + TA + +T L I S +
Sbjct: 4 STTTPANTTATVTVTVATSNTTSVSTNVTTALTASTTAEPGSVLTELLGIIIYCVSGVSI 63
Query: 163 LFLMSILLALI 173
L + +L+A++
Sbjct: 64 LSFLLVLVAVL 74
Score = 28.1 bits (62), Expect = 2.5
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 114 TTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSN--TSITGSLAIASSKCLLFLMSILL 170
T +T + + T T T T A+ SN + S+N T++T S L L+ I++
Sbjct: 1 MTSSTTTPANTTAT-VTVTVAT---SNTTSVSTNVTTALTASTTAEPGSVLTELLGIII 55
>gnl|CDD|226406 COG3889, COG3889, Predicted solute binding protein [General
function prediction only].
Length = 872
Score = 34.1 bits (78), Expect = 0.032
Identities = 14/66 (21%), Positives = 28/66 (42%)
Query: 107 SQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIASSKCLLFLM 166
+ T T T +T+ + + T++ T +S T S + + TG ++ L
Sbjct: 802 TSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTTSPSQTTTGGGICGPIVIIVGLA 861
Query: 167 SILLAL 172
++ L L
Sbjct: 862 ALALLL 867
Score = 27.9 bits (62), Expect = 3.0
Identities = 12/52 (23%), Positives = 20/52 (38%)
Query: 100 SMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSIT 151
+ A TS TT+G + + T +T + + SN TS+
Sbjct: 754 RIMDPASGTGTSITTSGTFTAEVPQSPTKTETTLSYSAYSNTSILIETTSVV 805
Score = 27.9 bits (62), Expect = 3.8
Identities = 14/77 (18%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 99 ASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIAS 158
++ S ++ T++ TV+ ++T TT + S + +T + T+++ T+
Sbjct: 790 SAYSNTSILIETTSVVITKTVTQTQT-TTSSPSPTQTTSPTQTSTSTTTTTSPSQTTTGG 848
Query: 159 SKCLLFLMSILLALIPV 175
C ++ + LA + +
Sbjct: 849 GICGPIVIIVGLAALAL 865
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 33.0 bits (75), Expect = 0.072
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 100 SMSRDAMSQPTSTTTTGNTVSTSKTNTTPNT--STSASTLSSNEHTASSNTSITGSL 154
S S A S + ++ + + +K+N++P + S + S SS+ S
Sbjct: 317 SSSAAAGSIGSKSSKSAKHSNRNKSNSSPKSHSSANGSVPSSSVSDNESKQKRASKS 373
Score = 26.8 bits (59), Expect = 6.6
Identities = 12/56 (21%), Positives = 22/56 (39%)
Query: 98 LASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGS 153
+ S++ S +S +SK+ N + S S+ S+ S S + S
Sbjct: 306 STNGSKETTSNSSSAAAGSIGSKSSKSAKHSNRNKSNSSPKSHSSANGSVPSSSVS 361
>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 814
Score = 32.5 bits (74), Expect = 0.11
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 109 PTSTTTTGNT--VSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIA 157
P ++T T V + T NT T + ++ E +SS T+ T
Sbjct: 36 PATSTEAEQTTPVESDATEEADNTETPVAATTAAEAPSSSETAETSDPTSE 86
Score = 27.9 bits (62), Expect = 3.3
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 107 SQPTSTTTTGNTVS----TSKTNTTPNTSTSASTLSSNEHTASSNTSITGSL 154
+ T T S + TP +T+A+ S+ TA ++ + +
Sbjct: 37 ATSTEAEQTTPVESDATEEADNTETPVAATTAAEAPSSSETAETSDPTSEAT 88
Score = 27.5 bits (61), Expect = 4.8
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 105 AMSQPTSTTTTGNTVSTSKTNTTPN---TSTSASTLSSNEHTASSNTSIT 151
A S TT + +T + + T +T+A SS+E +S+ +
Sbjct: 37 ATSTEAEQTTPVESDATEEADNTETPVAATTAAEAPSSSETAETSDPTSE 86
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 32.1 bits (72), Expect = 0.16
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 3/69 (4%)
Query: 94 EVKGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTL---SSNEHTASSNTSI 150
G S + + PTS TT+ +TS T + ++ T S + S +
Sbjct: 473 TPTGTTSSTLPEDTSPTSRTTSATPNATSPTPAVTTPNATSPTTQKTSDTPNATSPTPIV 532
Query: 151 TGSLAIASS 159
G A+S
Sbjct: 533 IGVTTTATS 541
Score = 29.0 bits (64), Expect = 1.5
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 109 PTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNT 148
PTS T TG T ST +T+P + T+++T ++ T + T
Sbjct: 469 PTSGTPTGTTSSTLPEDTSPTSRTTSATPNATSPTPAVTT 508
>gnl|CDD|219426 pfam07489, Tir_receptor_C, Translocated intimin receptor (Tir)
C-terminus. Intimin and its translocated intimin
receptor (Tir) are bacterial proteins that mediate
adhesion between mammalian cells and attaching and
effacing (A/E) pathogens. A unique and essential feature
of A/E bacterial pathogens is the formation of
actin-rich pedestals beneath the intimately adherent
bacteria and localised destruction of the intestinal
brush border. The bacterial outer membrane adhesin,
intimin, is necessary for the production of the A/E
lesion and diarrhoea. The A/E bacteria translocate their
own receptor for intimin, Tir, into the membrane of
mammalian cells using the type III secretion system. The
translocated Tir triggers additional host signalling
events and actin nucleation, which are essential for
lesion formation. This family represents the Tir
C-terminal domain which has been reported to bind
uninfected host cells and beta-1 integrins although the
role of intimin binding to integrins is unclear. This
intimin C-terminal domain has also been shown to be
sufficient for Tir recognition.
Length = 222
Score = 31.1 bits (70), Expect = 0.20
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 110 TSTTTTGNTVSTSKTNTTPNTSTSASTLSSN-EHTASSNTSITGSLAIASS 159
T+TTTT T +T + NT +T +S E TASS S S A +
Sbjct: 62 TTTTTTTTTHTTVENKPANNTPAQGNTDTSGAEETASSRRSSQASTASTTW 112
Score = 27.6 bits (61), Expect = 3.0
Identities = 23/53 (43%), Positives = 26/53 (49%), Gaps = 9/53 (16%)
Query: 110 TSTTTTGNTVSTSKTNTTP---NTSTS------ASTLSSNEHTASSNTSITGS 153
T+TTTT TV N TP NT TS +S SS TAS+ S T S
Sbjct: 65 TTTTTTHTTVENKPANNTPAQGNTDTSGAEETASSRRSSQASTASTTWSDTSS 117
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 31.1 bits (70), Expect = 0.31
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 6/49 (12%)
Query: 8 LLENQILVDVTL-MCNTHTLKVHKVVLASCSPYFEGVLQKQLGTHPLIV 55
LL++ IL DV + + + +K HK +LA+ S YF + L T P+I+
Sbjct: 19 LLDDDILCDVIITIGDGEEIKAHKTILAAGSKYF-----RTLFTTPMII 62
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 30.2 bits (67), Expect = 0.51
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 111 STTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTS 149
ST T N +T+ T NT+TS + ++N +T S+ +
Sbjct: 309 STNTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNT 347
Score = 30.2 bits (67), Expect = 0.56
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 100 SMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTS-ASTLSSNEHTASSNTSITGS 153
+ + + + T+T T ST NT NT+++ + ++N + SSN + S
Sbjct: 311 NTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNSS 365
Score = 29.0 bits (64), Expect = 1.3
Identities = 17/60 (28%), Positives = 33/60 (55%)
Query: 100 SMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIASS 159
S + +A T+T T N +TS + NT+T+++T +++ A+ +S S + AS+
Sbjct: 309 STNTNANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNSSASA 368
>gnl|CDD|240314 PTZ00208, PTZ00208, 65 kDa invariant surface glycoprotein;
Provisional.
Length = 436
Score = 29.9 bits (67), Expect = 0.58
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 79 AEDNLPALLDAAKFFEVKGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTST 132
E L ++ AAK KG A + A + T+T +T S + +T
Sbjct: 301 QEKPLSEVIVAAKEAGKKG-AKIIIPAAAPATATESTKGEDSAISEHVDRGIAT 353
>gnl|CDD|223031 PHA03273, PHA03273, envelope glycoprotein C; Provisional.
Length = 486
Score = 28.8 bits (64), Expect = 1.8
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 99 ASMSRDAMSQPTSTTTTGNTVSTSKTNTTP-NTSTSASTLSSNEHTASSNTSIT 151
AS + + S S +T ST T T + TS ++ T ++ T T
Sbjct: 25 ASGASTSSSIENSDNSTAEMQSTPATPTHTTSNLTSPFGTGTDNSTNANGTEST 78
>gnl|CDD|113196 pfam04415, DUF515, Protein of unknown function (DUF515). Family of
hypothetical Archaeal proteins.
Length = 416
Score = 28.7 bits (64), Expect = 1.8
Identities = 18/53 (33%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 107 SQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIASS 159
SQ TST+++ +T S+S++++T + AS +S S+TS + S + +SS
Sbjct: 284 SQSTSTSSSSST-SSSESSSTSYSPGDASIQNSQRSQLQSSTSQSESESASSS 335
>gnl|CDD|218190 pfam04651, Pox_A12, Poxvirus A12 protein.
Length = 188
Score = 28.2 bits (63), Expect = 1.9
Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 5/75 (6%)
Query: 74 GETSIAEDNLPALLDAAKFFEVKGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTS 133
GE + NL + EVK ++ + S+ +T STSKT +S S
Sbjct: 34 GEQANRGGNLAGPENNPSDNEVKAGKRVTSASSSKSKRCST-----STSKTKPCSRSSRS 88
Query: 134 ASTLSSNEHTASSNT 148
S TA +
Sbjct: 89 RSGAPRRRGTAFGSM 103
>gnl|CDD|147982 pfam06112, Herpes_capsid, Gammaherpesvirus capsid protein. This
family consists of several Gammaherpesvirus capsid
proteins. The exact function of this family is unknown.
Length = 148
Score = 27.5 bits (61), Expect = 2.6
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 102 SRDAMSQPTSTTTTGNTVSTSKTNTTPN-----TSTSASTLSSNEHTASSNTSITGSLAI 156
R A Q +S+ + + S+S + P + +S S LSS + SS++S++GS A
Sbjct: 77 LRGAGPQTSSSIGSALSASSSSASGVPGGANQLSGSSGSALSSGPGSLSSSSSLSGSGAG 136
Query: 157 ASS 159
A
Sbjct: 137 AGD 139
>gnl|CDD|227416 COG5084, YTH1, Cleavage and polyadenylation specificity factor
(CPSF) Clipper subunit and related makorin family
Zn-finger proteins [General function prediction only].
Length = 285
Score = 27.9 bits (62), Expect = 2.9
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 3/72 (4%)
Query: 97 GLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAI 156
G +S ++S PT +T+ NT S ++ + +T +
Sbjct: 42 GAKQIS-PSLSSPTFKNKANLMQNTNDNFVPGNTVACISRNFNSIRGSRLSTPNNHVNPV 100
Query: 157 ASSK--CLLFLM 166
SS C FL
Sbjct: 101 LSSSVVCKFFLR 112
>gnl|CDD|221315 pfam11921, DUF3439, Domain of unknown function (DUF3439). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 46 to 94 amino acids in length. This domain is
found associated with pfam01462, pfam00560.
Length = 122
Score = 27.2 bits (60), Expect = 2.9
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 109 PTSTTTTGNTVSTSKTNTTPNTSTSAS 135
PT+TTTT T +T T TT T+T S
Sbjct: 46 PTTTTTTTTTTTTMPTTTTLPTTTKMS 72
>gnl|CDD|191251 pfam05283, MGC-24, Multi-glycosylated core protein 24 (MGC-24).
This family consists of several MGC-24 (or Cd164
antigen) proteins from eukaryotic organisms.
MGC-24/CD164 is a sialomucin expressed in many normal
and cancerous tissues. In humans, soluble and
transmembrane forms of MGC-24 are produced by
alternative splicing.
Length = 187
Score = 27.7 bits (61), Expect = 2.9
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 107 SQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIASSK 160
S +TTT T ST+K TP+ +TS + T+ T+ T + +
Sbjct: 107 SCSVATTTPVPTNSTAKPTITPSPTTSHHHV-----TSEPKTNTTVTPTSQPDR 155
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
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 = 378
Score = 27.9 bits (62), Expect = 3.2
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 106 MSQP-TSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNT 148
+S+P T T +T + TP S AS S +S
Sbjct: 74 VSKPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAV 117
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 27.8 bits (62), Expect = 3.3
Identities = 9/69 (13%), Positives = 20/69 (28%), Gaps = 16/69 (23%)
Query: 107 SQPTSTTTTG----------------NTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSI 150
Q ST T ++ T K + ++ + + +S++ S
Sbjct: 30 PQKDSTAKTTSHDSKKSNDDETSKDTSSKDTDKADNNNTSNQDNNDKKFSTIDSSTSDSN 89
Query: 151 TGSLAIASS 159
I +
Sbjct: 90 NIIDFIYKN 98
Score = 27.1 bits (60), Expect = 5.3
Identities = 9/50 (18%), Positives = 21/50 (42%)
Query: 100 SMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTS 149
S + S + +++N+ P + +A+ SS++ S + S
Sbjct: 178 SSNNTKPSTSNKQPNSPKPTQPNQSNSQPASDDTANQKSSSKDNQSMSDS 227
>gnl|CDD|215814 pfam00242, DNA_pol_viral_N, DNA polymerase (viral) N-terminal
domain.
Length = 379
Score = 27.5 bits (61), Expect = 3.9
Identities = 8/55 (14%), Positives = 22/55 (40%)
Query: 97 GLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSIT 151
AS S Q T +++STS+ +++ + ++ ++ + +
Sbjct: 294 NRASSSSSCFHQSAVRETAYSSLSTSERHSSSGHAVELRSIPGGSVSSQNAGPLL 348
>gnl|CDD|221173 pfam11702, DUF3295, Protein of unknown function (DUF3295). This
family is conserved in fungi but the function is not
known.
Length = 509
Score = 27.2 bits (60), Expect = 5.5
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 100 SMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSIT 151
++ A+ ST+TT + S+ ++TPN ++S ++ SS+ A +TS+
Sbjct: 112 DPNQQALESTESTSTTSADCNDSEQSSTPNLNSSDTSTSSSG--ALPSTSVV 161
>gnl|CDD|219500 pfam07655, Secretin_N_2, Secretin N-terminal domain. This is a
short domain found in bacterial type II/III secretory
system proteins. The architecture of these proteins
suggest that this family may be functionally analogous
to pfam03958.
Length = 95
Score = 25.8 bits (57), Expect = 5.8
Identities = 14/51 (27%), Positives = 29/51 (56%)
Query: 101 MSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSIT 151
M R S + T+ + ++ ++ ++++ N+S S+ SS+ +SS T IT
Sbjct: 11 MKRSGSSNTSVTSGSVSSSGSNSSSSSSNSSNGGSSSSSSSGDSSSGTRIT 61
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 27.0 bits (60), Expect = 6.4
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 101 MSRDAMSQPTSTTTTGNTVSTSKTNT----TPNTSTSASTLSSNEHTASSNTSITGS 153
M+R+A +Q S ++ S N N +S S + T S+ S+ S
Sbjct: 532 MAREASNQAESALHGFSSSIASAWNQLSQFGSNRGSSDSVTGGADSTMSAQDSMMAS 588
>gnl|CDD|182170 PRK09961, PRK09961, exoaminopeptidase; Provisional.
Length = 344
Score = 27.0 bits (60), Expect = 6.4
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 45 QKQLGTHPLIVLKDMKFSVLRSLIEFMYCGETSIAEDNLPALLD 88
+Q+G P++VL D L ++ ET AE +P D
Sbjct: 236 HRQIGNGPMLVLSDKSLIAPPKLTAWI---ETVAAEIGIPLQAD 276
>gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 1062
Score = 27.0 bits (59), Expect = 7.3
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 96 KGLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTAS 145
+G +SRDA GN +S NTTP T T+ + S+E S
Sbjct: 145 EGAKLLSRDA---------NGNIGISSNPNTTPGTKTNTGEIFSSEQKHS 185
>gnl|CDD|132198 TIGR03154, sulfolob_CbsA, cytochrome b558/566, subunit A. Members
of this protein family are CbsA, one subunit of a highly
glycosylated, heterodimeric, mono-heme cytochrome
b558/566, found in Sulfolobus acidocaldarius and several
other members of the Sulfolobales, a branch of the
Crenarchaeota.
Length = 465
Score = 26.5 bits (58), Expect = 8.7
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 112 TTTTGNTVSTSKTNTTPNTSTSAS 135
TT +++ T+T+P+T+TS++
Sbjct: 413 VTTPPTPPTSTTTSTSPSTTTSSA 436
>gnl|CDD|165513 PHA03255, PHA03255, BDLF3; Provisional.
Length = 234
Score = 26.0 bits (56), Expect = 9.9
Identities = 15/63 (23%), Positives = 24/63 (38%)
Query: 97 GLASMSRDAMSQPTSTTTTGNTVSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAI 156
G S ++ T + + T T T TS S+ +SS TS T +
Sbjct: 85 GTTVTPVPTTSNASTINVTTKVTAQNITATEAGTGTSTGVTSNVTTRSSSTTSATTRITN 144
Query: 157 ASS 159
A++
Sbjct: 145 ATT 147
>gnl|CDD|234527 TIGR04263, SasC_Mrp_aggreg, SasC/Mrp/FmtB intercellular aggregation
domain. This domain, about 375 amino acids long on
average, occurs only in Staphylococcus and
Streptococcus. It occurs as a non-repetitive N-terminal
domain of LPXTG-anchored surface proteins, including
SasC, Mrp, and FmtB. This region in SasC was shown to be
involved in cell aggregation and biofilm formation,
which may explain the methicillin resistance seen for
Mrp and FmtB.
Length = 366
Score = 26.1 bits (58), Expect = 10.0
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 119 VSTSKTNTTPNTSTSASTLSSNEHTASSNTSITGSLAIASSK 160
VS S + + +T+ T SSN T ++ IT ++ + +S
Sbjct: 273 VSNSGATSNYDRNTNTLTFSSNGLTPGTSKDITYTVRLPNST 314
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
0.316 0.126 0.345
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,862,386
Number of extensions: 657900
Number of successful extensions: 1153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 985
Number of HSP's successfully gapped: 104
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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: 56 (25.3 bits)