RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4604
(302 letters)
>gnl|CDD|219683 pfam07986, TBCC, Tubulin binding cofactor C. Members of this
family are involved in the folding pathway of tubulins
and form a beta helix structure.
Length = 119
Score = 131 bits (332), Expect = 2e-38
Identities = 41/87 (47%), Positives = 56/87 (64%)
Query: 198 PVSLSNIDSCVVKVNGNASTIHLNNIKNSQIFLGPVSNSVFIDNCTDSTLYLACHQLRMH 257
V+LSN+ +C + + S++ ++N K+ I LGPVS SVFI +C + T+ +AC QLR+H
Sbjct: 3 DVTLSNLSNCTIYLLDPLSSLTIDNCKDCTIILGPVSGSVFIRDCENCTIVVACRQLRIH 62
Query: 258 TSHKCSVYLHVTSRPIIEHCKNIGFAP 284
C YLH TSRPIIE I FAP
Sbjct: 63 DCTNCDFYLHTTSRPIIEDSSGIRFAP 89
>gnl|CDD|197827 smart00673, CARP, Domain in CAPs (cyclase-associated proteins) and
X-linked retinitis pigmentosa 2 gene product.
Length = 38
Score = 35.6 bits (83), Expect = 0.001
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 204 IDSCVVKVNGNASTIHLNNIKNSQIFLGPVSNSVFIDN 241
+SC ++V+G +TI ++ K I+LGPVS S I N
Sbjct: 1 CESCTIQVSGKVNTISIDKCKKCSIYLGPVSGSPEIVN 38
Score = 26.3 bits (59), Expect = 2.5
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 223 IKNSQIFLGPVSNSVFIDNCTDSTLYL 249
++ I + N++ ID C ++YL
Sbjct: 1 CESCTIQVSGKVNTISIDKCKKCSIYL 27
>gnl|CDD|206339 pfam14171, SpoIISA_toxin, Toxin SpoIISA, type II toxin-antitoxin
system. SpoIISA is a toxin which causes lysis of
vegetatively growing cells. It forms part of a type II
toxin-antitoxin system, where the SpoIISB protein,
pfam14185, acts as an antitoxin. It is a transmembrane
protein, with a cytoplasmic domain accounting for
approximately two-thirds of the protein. The structure
of the cytoplasmic domain resembles that of the GAF
domains, Pfam: PF01590. SpoIISB binds to the cytoplasmic
domain of SpoIISA with high affinity.
Length = 240
Score = 31.6 bits (72), Expect = 0.41
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 87 ILLLNHVIVDAKIFLTSYDMKIYNNKLQELTEQCNILETKLL 128
I+ + +DA IFLT Y K+ +N+L+ TE+ + L
Sbjct: 68 IVAVFFAFIDAFIFLTPYIKKLGSNELETDTEKTLEANNETL 109
>gnl|CDD|197369 cd09909, HIV-1-like_HR1-HR2, heptad repeat 1-heptad repeat 2 region
(ectodomain) of the gp41 subunit of human
immunodeficiency virus (HIV-1), and related domains.
This domain family spans both heptad repeats of the
glycoprotein (gp)/transmembrane subunit of various
endogenous retroviruses (ERVs) and infectious
retroviruses, including human, simian, and feline
immunodeficiency viruses (HIV, SIV, and FIV), bovine
immunodeficiency-like virus (BIV), equine infectious
anaemia virus (EIAV), and Jaagsiekte sheep retrovirus
(JSRV), mouse mammary tumour virus (MMTV) and various
ERVs including sheep enJSRV-26, and human ERVs (HERVs):
HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs
to a larger superfamily containing the HR1-HR2 domain of
ERVs and infectious retroviruses, including Ebola virus,
and Rous sarcoma virus. Proteins in this family lack the
canonical CSK17-like immunosuppressive sequence, and the
intrasubunit disulfide bond-forming CX6C motif found in
linker region between HR1 and HR2 in the
Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2
region is a fusion peptide (FP), and C-terminal is a
membrane-spanning region (MSR). Viral infection involves
the formation of a trimer-of-hairpins structure (three
HR1 helices, buttressed by three HR2 helices lying in
antiparallel orientation). In this structure, the FP
(inserted in the host cell membrane) and MSR (inserted
in the viral membrane) are in close proximity. ERVs are
likely to originate from ancient germ-line infections by
active retroviruses. Some modern ERVs, those that
integrated into the host genome post-speciation, have a
currently active exogenous counterpart, such as JSRV.
Some ERVs play specific roles in the host, including
placental development, protection of the host from
infection by related pathogenic and exogenous
retroviruses, and genome plasticity. Included in this
subgroup are ERVs from domestic sheep that are related
to JSRV, the agent of transmissible lung cancer in
sheep, for example enJSRV-26 that retains an intact
genome. These endogenous JSRVs protect the sheep against
JSRV infection and are required for sheep placental
development. HERV-K_c12q14.1 is potentially a complete
envelope protein; however, it does not appear to be
fusogenic.
Length = 128
Score = 29.7 bits (67), Expect = 0.80
Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 14/88 (15%)
Query: 13 NIPERLLKREQERISAIEKRQEKKGDKEHDGFS--------NMFNENYDKIKGMINEIDV 64
N+ ++K+ R+ A+E R + + H + +++ + D
Sbjct: 29 NLLYWVVKQLGARVQALEFRLK---IQCHLNLWGCVTKQPYCHTDVPWNRSWNHLQGND- 84
Query: 65 DPNSGSVNKEELKEKFADINKQILLLNH 92
N S+ +E + K D+ ++IL L
Sbjct: 85 --NWISLTWQEWENKIDDLEEKILNLLE 110
>gnl|CDD|226691 COG4240, COG4240, Predicted kinase [General function prediction
only].
Length = 300
Score = 30.6 bits (69), Expect = 0.91
Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 7/74 (9%)
Query: 121 NILETKLLPRKKFGFKKVDKVKLGGQGDKTDEAEKKILPKDDVDFVKPRQHEEETYIGFY 180
N+L + DK G GD+ + + D V E ++GF
Sbjct: 124 NVLNAIARGGPTVPLPRFDKSAFAGAGDRAPQTQWIKFEVDIVIL-------EGWFVGFR 176
Query: 181 NRSNETLELPSEDV 194
E L P +
Sbjct: 177 PIDPELLAAPVNAL 190
>gnl|CDD|225962 COG3428, COG3428, Predicted membrane protein [Function unknown].
Length = 494
Score = 30.5 bits (69), Expect = 1.3
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 10/58 (17%)
Query: 102 TSYDMKIYNNKLQELTEQCNILETKLLPRKKFGFKKVDKVKLGGQGDKTDEAEKKILP 159
+ ++ +LQ +T + ++L R+ FG+ VD V G GD +LP
Sbjct: 281 VTIPLR----RLQAVTLRESLL------RRLFGYAAVDVVTAGVHGDSQSSGSTPLLP 328
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 26.6 bits (60), Expect = 1.8
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 54 KIKGMINEIDVDPNSGSVNKEELKEKFADI 83
++K D D G ++ EE K+ +
Sbjct: 1 ELKEAFRLFDKD-GDGKIDFEEFKDLLKAL 29
>gnl|CDD|219330 pfam07201, HrpJ, HrpJ-like domain. This family represents a
conserved region approximately 200 residues long within
a number of bacterial hypersensitivity response
secretion protein HrpJ and similar proteins. HrpJ forms
part of a type III secretion system through which, in
phytopathogenic bacterial species, virulence factors
are thought to be delivered to plant cells. This family
also includes the InvE invasion protein from
Salmonella. This protein is involved in host parasite
interactions and mutations in the InvE gene render
Salmonella typhimurium non-invasive. InvE S.
typhimurium mutants fail to elicit a rapid Ca2+
increase in cultured cells, an important event in the
infection procedure and internalisation of S.
typhimurium into epithelial cells. This family includes
bacterial SepL and SsaL proteins. SepL plays an
essential role in the infection process of
enterohemorrhagic Escherichia coli and is thought to be
responsible for the secretion of EspA, EspD, and EspB.
SsaL of Salmonella typhimurium is thought to be a
component of the type III secretion system.
Length = 161
Score = 28.5 bits (64), Expect = 2.5
Identities = 12/82 (14%), Positives = 31/82 (37%), Gaps = 7/82 (8%)
Query: 17 RLLKREQERISAIEKRQEKKGDKEHDGFSNMFNENYDKIKGMINEIDVDPNSGSVNKEEL 76
+ R + +E+ + ++ D + +K++ + + +S L
Sbjct: 13 KRSDRRKSESEKLEELSDLL-ERVLDLEAE------EKLRELRQLLKSGRSSLPQLLAYL 65
Query: 77 KEKFADINKQILLLNHVIVDAK 98
+ F D + Q L L ++ A+
Sbjct: 66 ESLFPDPSDQDLALRALLQQAR 87
>gnl|CDD|193456 pfam12983, DUF3867, Protein of unknown function (DUF3867). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 190 amino acids in length.
Length = 186
Score = 28.1 bits (63), Expect = 4.1
Identities = 34/125 (27%), Positives = 50/125 (40%), Gaps = 13/125 (10%)
Query: 1 MENENISLGQEVNIPERLLKREQERISAIEKRQEKKG-DKEHDGFSNMFNENYDKIKGMI 59
ME NIS + +NI ++ ++R S IEK+ + G D G S+ EN K
Sbjct: 50 MEENNISQEKFMNIQKKFMERYGFDPSEIEKQLKNLGIDPSGLGSSSNDYENIRKTLSFQ 109
Query: 60 NEIDVDPNSGSVNKEELKEKFADINKQILLLNHVIV--DAKI---------FLTSYDMKI 108
+ +V +K D+ K I+ VI+ KI FL SY
Sbjct: 110 EKYKSKIKVKTVITYFIKNDKNDL-KVIIEEEKVILISSKKIDLQDSELNEFLCSYKKVF 168
Query: 109 YNNKL 113
+ KL
Sbjct: 169 EDKKL 173
>gnl|CDD|216421 pfam01299, Lamp, Lysosome-associated membrane glycoprotein (Lamp).
Length = 305
Score = 28.5 bits (64), Expect = 4.5
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 10/58 (17%)
Query: 196 KKPVSLSNIDSCVVKVNGN----ASTIHLNNIKNSQIFLGPVSNSVFIDNCTDSTLYL 249
K L NI+ +G+ +T+ L+ + + F N + S YL
Sbjct: 138 KTATRLFNINPNKTTASGSCGSQTATLELSFENGTVL------TFTFTMNNSSSKFYL 189
>gnl|CDD|224176 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
secretion].
Length = 552
Score = 28.5 bits (64), Expect = 5.3
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 42 DGFSNMFNENYDKIKGMINEID--VDPNSGSVNKEELKEKFADINKQI 87
N N Y+++ + +I+ + VN L ++ AD+NKQI
Sbjct: 141 QTLVNQINNTYEQLTDLRKDINAEIAATVDEVN--SLLKQIADLNKQI 186
>gnl|CDD|216897 pfam02140, Gal_Lectin, Galactose binding lectin domain.
Length = 79
Score = 26.5 bits (59), Expect = 6.0
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 232 PVSNSVFIDNCTDSTLYLA 250
P SNSVF D C + YL
Sbjct: 56 PASNSVFGDPCPGTYKYLE 74
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 28.5 bits (64), Expect = 6.2
Identities = 25/132 (18%), Positives = 54/132 (40%), Gaps = 19/132 (14%)
Query: 1 MENENISLGQEVNIPERL-------LKREQERISAIEKRQEKKGDKEHDGFSNMFNENYD 53
++ E SL E+ E L +I IEK E+ +E +
Sbjct: 686 LKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEE------------E 733
Query: 54 KIKGMINEIDVDPNSGSVNKEELKEKFADINKQILLLNHVIVDAKIFLTSYDMKIYNNKL 113
K+K + E++ D +S E +K + ++ +I L + + L + ++ ++++
Sbjct: 734 KLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRI 793
Query: 114 QELTEQCNILET 125
E+ + + LE
Sbjct: 794 PEIQAELSKLEE 805
>gnl|CDD|217011 pfam02388, FemAB, FemAB family. The femAB operon codes for two
nearly identical approximately 50-kDa proteins involved
in the formation of the Staphylococcal pentaglycine
interpeptide bridge in peptidoglycan. These proteins are
also considered as a factor influencing the level of
methicillin resistance.
Length = 408
Score = 28.0 bits (63), Expect = 6.5
Identities = 25/114 (21%), Positives = 47/114 (41%), Gaps = 14/114 (12%)
Query: 34 EKKG--DKEHDGFSNMFNENYDKIKGMINEIDVDPNSGSVNKEELKEKFADINKQILLLN 91
E+KG D+ D + + + DK + M+ ++ KE ++ +++ L
Sbjct: 208 ERKGFHDRSLDYYEKLLDTYGDKAEFMLAYLN------------FKEYLDELQEKLEKLE 255
Query: 92 HVIVDAKIFLTSYDMKIYNNKLQELTEQCNILETKLLPRKKFGFKKVDKVKLGG 145
+ + L NKL EL +Q LE ++ K+ K ++V L G
Sbjct: 256 KDLAKLEEKLEKNPNSKKKNKLAELEQQLASLEKRIDEAKELIAKYGNEVPLAG 309
>gnl|CDD|235574 PRK05711, PRK05711, DNA polymerase III subunit epsilon;
Provisional.
Length = 240
Score = 27.9 bits (63), Expect = 6.7
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 12/66 (18%)
Query: 77 KEKFADINKQILLLNHVIVDAK--IFLTSYDMKIYNNKLQEL-------TEQCNILETKL 127
K FA++ + L I A+ I +D+ + + L C + +T
Sbjct: 70 KPTFAEVADEFL---DFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLA 126
Query: 128 LPRKKF 133
+ R+ F
Sbjct: 127 MARRMF 132
>gnl|CDD|218266 pfam04790, Sarcoglycan_1, Sarcoglycan complex subunit protein. The
dystrophin glycoprotein complex (DGC) is a
membrane-spanning complex that links the interior
cytoskeleton to the extracellular matrix in muscle. The
sarcoglycan complex is a subcomplex within the DGC and
is composed of several muscle-specific, transmembrane
proteins (alpha-, beta-, gamma-, delta- and
zeta-sarcoglycan). The sarcoglycans are
asparagine-linked glycosylated proteins with single
transmembrane domains. This family contains beta, gamma
and delta members.
Length = 264
Score = 27.7 bits (62), Expect = 7.0
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 214 NASTIHLNNIKNSQIFLGPVSNSVFIDNCTDSTLYLA 250
+AS++ LN + S G + C D L+L
Sbjct: 219 DASSVMLNRLPISSGESGSRQGQYKLCVCPDGKLFLV 255
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 27.4 bits (61), Expect = 7.3
Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 12/84 (14%)
Query: 16 ERLLKREQERISAIEKRQEKKGDKEHDGFSNMFNENYDKIKGM--INEIDVDPNSGSVNK 73
E +RE+++ K +E++ KE E Y+K+K + E D S
Sbjct: 47 ELEEEREKKKEEEERKEREEQARKEQ--------EEYEKLKSSFVVEEEGTDKLSADEES 98
Query: 74 EELKEKFAD--INKQILLLNHVIV 95
EL E F + K+++ L +
Sbjct: 99 NELLEDFINYIKLKKVVNLEELSA 122
>gnl|CDD|181958 PRK09564, PRK09564, coenzyme A disulfide reductase; Reviewed.
Length = 444
Score = 28.1 bits (63), Expect = 7.5
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 178 GFYNRSNETLELPSEDVHKKPVSLSNIDSCVVKVNGNASTIHLNNIKNSQIF 229
GF++ N + E+ K + + + VVKV+ TI + N+K IF
Sbjct: 50 GFFDDPNTMIARTPEEFIKSGIDV-KTEHEVVKVDAKNKTITVKNLKTGSIF 100
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 28.1 bits (63), Expect = 7.8
Identities = 20/114 (17%), Positives = 52/114 (45%), Gaps = 7/114 (6%)
Query: 16 ERLLKREQERISAIEKRQEKKGDKEHDGFSNMFNENYDKIKGMINEIDVDPNSGSVNKEE 75
ER L + + ++E+R+E+ + + E ++++ ++E++ + EE
Sbjct: 806 ERRLDALERELESLEQRRERLEQEIEE-----LEEEIEELEEKLDELEEELEELEKELEE 860
Query: 76 LKEKFADINKQILLLNHVIVDAKIFLTSYD--MKIYNNKLQELTEQCNILETKL 127
LKE+ ++ + L + + + + ++ ++L EL E+ L +L
Sbjct: 861 LKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERL 914
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 27.7 bits (61), Expect = 9.4
Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 2/130 (1%)
Query: 29 IEKRQEKKGDKEHDGFSNMFNENYDKIKGMINEIDVDPNSGSVNKEELKEKFADINKQIL 88
I K ++ +HD N E+ DK KG +E D + + NKE ++ D+ + +
Sbjct: 1469 ILKIKKDNATNDHDFNINELKEHIDKSKGCKDEADKNAKAIEKNKELFEQYKKDVTELLN 1528
Query: 89 LLNHVIVDAKIFLTSYDMKIYNNKLQELTEQCNILETKLLPRKKFGFKKVDKVKLGGQGD 148
+ + + K T D +I ++++ ++ ILE + +K KK +K ++
Sbjct: 1529 KYSALAIKNKFAKTKKDSEIIIKEIKDAHKKF-ILEAEKSEQKIKEIKK-EKFRIEDDAA 1586
Query: 149 KTDEAEKKIL 158
K D++ K +
Sbjct: 1587 KNDKSNKAAI 1596
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
0.315 0.133 0.377
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,050,022
Number of extensions: 1443912
Number of successful extensions: 1255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1239
Number of HSP's successfully gapped: 75
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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: 42 (22.0 bits)
S2: 59 (26.6 bits)