RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16661
(190 letters)
>gnl|CDD|216184 pfam00907, T-box, T-box. The T-box encodes a 180 amino acid domain
that binds to DNA. Genes encoding T-box proteins are
found in a wide range of animals, but not in other
kingdoms such as plants. Family members are all thought
to bind to the DNA consensus sequence TCACACCT. they are
found exclusively in the nucleus, and perform
DNA-binding and transcriptional activation/repression
roles. They are generally required for development of
the specific tissues they are expressed in, and
mutations in T-box genes are implicated in human
conditions such as DiGeorge syndrome and X-linked cleft
palate, which feature malformations.
Length = 182
Score = 175 bits (445), Expect = 4e-56
Identities = 58/107 (54%), Positives = 70/107 (65%), Gaps = 11/107 (10%)
Query: 71 KFHN-----------RRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAG 119
KFH RRMFP KV V GLD A Y +L+D V DD RYKFHN W+VAG
Sbjct: 12 KFHELGTEMIITKSGRRMFPTLKVSVSGLDPNALYSVLLDFVPVDDHRYKFHNGEWVVAG 71
Query: 120 KADPEMPKRMYIHPDSPSTGDQWMQKVVSFHKLKLTNNISDKHGFVM 166
KA+P P R+YIHPDSP+TG WM++ VSF K+KLTNN D +G ++
Sbjct: 72 KAEPHPPPRVYIHPDSPATGAHWMKQPVSFDKVKLTNNKLDGNGHII 118
Score = 65.4 bits (160), Expect = 1e-13
Identities = 23/36 (63%), Positives = 25/36 (69%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDDFRYKFHN 36
MFP +K VSGLD A Y +LLD V DD RYKFHN
Sbjct: 29 MFPTLKVSVSGLDPNALYSVLLDFVPVDDHRYKFHN 64
>gnl|CDD|238106 cd00182, TBOX, T-box DNA binding domain of the T-box family of
transcriptional regulators. The T-box family is an
ancient group that appears to play a critical role in
development in all animal species. These genes were
uncovered on the basis of similarity to the DNA binding
domain of murine Brachyury (T) gene product, the
defining feature of the family. Common features shared
by T-box family members are DNA-binding and
transcriptional regulatory activity, a role in
development and conserved expression patterns, most of
the known genes in all species being expressed in
mesoderm or mesoderm precursors.
Length = 188
Score = 169 bits (431), Expect = 6e-54
Identities = 57/107 (53%), Positives = 72/107 (67%), Gaps = 11/107 (10%)
Query: 71 KFHN-----------RRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAG 119
KFH RRMFP KV+V GLD A Y +LMD+V DD RYKF +W+VAG
Sbjct: 14 KFHELGTEMIITKSGRRMFPTLKVKVSGLDPNALYSVLMDLVPVDDHRYKFSGGKWVVAG 73
Query: 120 KADPEMPKRMYIHPDSPSTGDQWMQKVVSFHKLKLTNNISDKHGFVM 166
KA+P +P R+Y+HPDSP+TG WM++ VSF KLKLTNN D +G ++
Sbjct: 74 KAEPHLPPRVYVHPDSPATGAHWMKQPVSFDKLKLTNNTLDNNGHII 120
Score = 61.1 bits (149), Expect = 6e-12
Identities = 20/38 (52%), Positives = 26/38 (68%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDDFRYKFHNRQ 38
MFP +K +VSGLD A Y +L+D+V DD RYKF +
Sbjct: 31 MFPTLKVKVSGLDPNALYSVLMDLVPVDDHRYKFSGGK 68
>gnl|CDD|214656 smart00425, TBOX, Domain first found in the mice T locus
(Brachyury) protein.
Length = 190
Score = 156 bits (397), Expect = 8e-49
Identities = 56/91 (61%), Positives = 71/91 (78%)
Query: 75 RRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKRMYIHPD 134
RRMFP K +V GLD A Y +LMD+V DD RYKF+N +W+VAGKA+P MP R+Y+HPD
Sbjct: 28 RRMFPTLKYKVSGLDPNALYSVLMDLVPVDDKRYKFNNGKWVVAGKAEPHMPSRVYVHPD 87
Query: 135 SPSTGDQWMQKVVSFHKLKLTNNISDKHGFV 165
SP+TG WM++ VSF K+KLTNN SDK+G +
Sbjct: 88 SPATGAHWMKQPVSFDKVKLTNNQSDKNGHL 118
Score = 60.0 bits (146), Expect = 2e-11
Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDDFRYKFHNRQ 38
MFP +K++VSGLD A Y +L+D+V DD RYKF+N +
Sbjct: 30 MFPTLKYKVSGLDPNALYSVLMDLVPVDDKRYKFNNGK 67
>gnl|CDD|219316 pfam07162, B9-C2, Ciliary basal body-associated, B9 protein. The
B9-C2 domain is found in proteins associated with the
ciliary basal body. B9 domains were identified as a
specific family of C2 domains. There are three
sub-families represented by this family, notably,
Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins.
Mutations in human Mks1 result in the developmental
disorder Mechler-Gruber syndrome; mutations in mouse
Stumpy lead to perinatal hydrocephalus and severe
polycystic kidney disease. All the three distinct types
of B9-C2 proteins cooperatively localise to the basal
body or centrosome of cilia.
Length = 165
Score = 28.7 bits (65), Expect = 1.1
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 29 DFRYKFHNRQMFPQMKFRVSGLDA 52
D K N +PQ+ V LD+
Sbjct: 61 DLHLKTTNPFGWPQLVVTVWSLDS 84
>gnl|CDD|219773 pfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain.
Length = 128
Score = 28.0 bits (63), Expect = 1.5
Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 22/78 (28%)
Query: 29 DFRYKFHNRQMFPQMKFRVSGLDAKAKYILLLDIVASDDFRY--KFHNRRMFP------- 79
D ++ F +GL +V +D Y +F NR MFP
Sbjct: 41 DNLLNHLEKKGFDLELLLEAGL-----------LVKREDGGYYDRFRNRIMFPIRDESGR 89
Query: 80 --AYKVRVMGLDKKAKYI 95
+ R + ++ KY+
Sbjct: 90 VVGFGGRALDDEEPPKYL 107
>gnl|CDD|235551 PRK05667, dnaG, DNA primase; Validated.
Length = 580
Score = 28.3 bits (64), Expect = 3.1
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 10/33 (30%)
Query: 72 FHNRRMFPAY----KV-----RVMGLDKKAKYI 95
F NR MFP +V RV+G D K KY+
Sbjct: 195 FRNRIMFPIRDLRGRVIGFGGRVLG-DDKPKYL 226
>gnl|CDD|211330 cd02556, PseudoU_synth_RluB, Pseudouridine synthase, Escherichia
coli RluB like. This group is comprised of bacterial
and eukaryotic proteins similar to E. coli RluB.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required.
E.coli RluB makes psi2605 in 23S RNA. psi2605 has been
detected in eubacteria but, not in eukarya and archea
despite the presence of a precursor U at that site.
Length = 167
Score = 27.3 bits (61), Expect = 3.4
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 74 NRRMFPA------YKVRVMGLDKKAKYILLMDIVAADDCRYKFHN 112
NR M P+ Y VRV G + L V +D F +
Sbjct: 60 NRLMHPSNEIEREYAVRVFGQVTDEQLKSLKKGVELEDGFAGFKS 104
>gnl|CDD|219283 pfam07063, DUF1338, Domain of unknown function (DUF1338). This
domain is found in a variety of bacterial and fungal
hypothetical proteins of unknown function. The structure
of this domain has been solved by structural genomics.
The structure implies a zinc-binding function, so it is
a putative metal hydrolase (information derived from
TOPSAN for PDB:3iuz).
Length = 288
Score = 27.6 bits (62), Expect = 4.0
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 147 VSFHKLKLTNNISD------KHGFVMSASVDRIAGSNDLLLDKTSTQ 187
V ++L +I + GF +++S I GS D LL +TST+
Sbjct: 179 VRVNRLSGFLDIDAVNAALKELGFPLNSSGGEIKGSPDGLLRQTSTK 225
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 27.7 bits (62), Expect = 4.7
Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 142 WMQKVVSFHKLKLTNNISDK---HGF-VMSASVDRIAGSNDLLLDKTSTQN 188
W++++++ + L + + +K GF V +I G +D++LD +ST N
Sbjct: 7 WLKELINLENIDL-DTLINKLTLAGFEVEDILSVKIGGESDIILDISSTAN 56
>gnl|CDD|221746 pfam12739, TRAPPC-Trs85, ER-Golgi trafficking TRAPP I complex 85
kDa subunit. This family is one of the subunits of the
TRAPP Golgi trafficking complex. TRAPP subunits are
found in two different sized complexes, TRAPP I and
TRAPP II, and this Trs85 is in the smaller complex.
TRAPP I, but Not TRAPP II, functions in ER-Golgi
transport. Trs85p was reported to function in the
cytosol-to-vacuole targeting pathway, suggesting a role
for this subunit in autophagy as well as in secretion.
The overall architecture of TRAPP I shows the other
components to be Bet3p (TRAPPC3), Bet5p (TRAPPC1),
Trs20p (TRAPPC2), Trs23p (TRAPPC4), Trs31p (TRAPPC5),
Trs33p (TRAPPC6a and b) and Trs85p.
Length = 390
Score = 27.3 bits (61), Expect = 5.4
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 17 KYILLLDIVASDDFRYKFHNRQMFPQMKFRVSGLD 51
Y+ + D+ A F +F + + P M+ +V L+
Sbjct: 108 VYLSVSDVEAIRAFVREFVTQSLIPFMERKVRFLN 142
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
0.325 0.138 0.412
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,687,271
Number of extensions: 897035
Number of successful extensions: 795
Number of sequences better than 10.0: 1
Number of HSP's gapped: 794
Number of HSP's successfully gapped: 18
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.3 bits)