RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10169
(390 letters)
>gnl|CDD|218841 pfam05986, ADAM_spacer1, ADAM-TS Spacer 1. This family
represents the Spacer-1 region from the ADAM-TS family
of metalloproteinases.
Length = 114
Score = 78.0 bits (193), Expect = 9e-18
Identities = 29/55 (52%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 17 AIRNMSGHYYLNGNWRIDYPKPLWFAGTVFYYERNTFYAPESISALGPTTEPLYV 71
A++N G YYLNGNW I + AGTVF Y R + APE ++A GPT EPL V
Sbjct: 42 ALKNSDGEYYLNGNWTISWSGTFELAGTVFEYSR-SDDAPERLTATGPTNEPLTV 95
>gnl|CDD|214559 smart00209, TSP1, Thrombospondin type 1 repeats. Type 1 repeats in
thrombospondin-1 bind and activate TGF-beta.
Length = 53
Score = 38.7 bits (90), Expect = 2e-04
Identities = 17/58 (29%), Positives = 21/58 (36%), Gaps = 6/58 (10%)
Query: 126 WLTSEWTGCDHLCGDGKQKRSVKCYREDKDGHREVVPDSACNEEKPESEKPCNLRPCE 183
SEW+ C CG G Q R+ C C E E+ CN +PC
Sbjct: 2 SEWSEWSPCSVTCGGGVQTRTRSCCS-----PPPQNGGGPCTGEDVETR-ACNEQPCP 53
Score = 30.6 bits (69), Expect = 0.13
Identities = 14/50 (28%), Positives = 17/50 (34%), Gaps = 6/50 (12%)
Query: 73 CDHLCGDGKQKRSVKCYREDKDGHREVVPDSACNEEKPESEKPCNLRPCE 122
C CG G Q R+ C C E E+ CN +PC
Sbjct: 10 CSVTCGGGVQTRTRSCCS-----PPPQNGGGPCTGEDVETR-ACNEQPCP 53
Score = 30.6 bits (69), Expect = 0.14
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 250 WSKCSAKCGTGIQTRKVFC 268
WS CS CG G+QTR C
Sbjct: 7 WSPCSVTCGGGVQTRTRSC 25
Score = 27.2 bits (60), Expect = 2.3
Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 309 GPWSKCSKTYGGGTMV-SRTARDEVIPVEPTGKVAEADEEEECEEEE 354
WS CS T GGG +R+ E E C E+
Sbjct: 5 SEWSPCSVTCGGGVQTRTRSCCSPPPQNGGGPCTGEDVETRACNEQP 51
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 31.5 bits (72), Expect = 0.23
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
A +++EE EEEEE+ E
Sbjct: 68 AAAAAAAAAAEEKKEEEEEEEEKEES 93
Score = 30.7 bits (70), Expect = 0.36
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
AE +EEE EEEE+E E
Sbjct: 69 AAAAAAAAAEEKKEEEEEEEEKEESE 94
Score = 29.9 bits (68), Expect = 0.66
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
A A EE++ EEEEEE +E
Sbjct: 66 AAAAAAAAAAAAEEKKEEEEEEEEKE 91
Score = 29.5 bits (67), Expect = 0.87
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 336 EPTGKVAEADEEEECEEEEEEGEE 359
E EEEE EEE+EE EE
Sbjct: 72 AAAAAAEEKKEEEEEEEEKEESEE 95
Score = 28.8 bits (65), Expect = 1.7
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 342 AEADEEEECEEEEEEGEET 360
A A+E++E EEEEEE EE+
Sbjct: 75 AAAEEKKEEEEEEEEKEES 93
Score = 27.6 bits (62), Expect = 4.7
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
+ +EEEE EE+EE EE
Sbjct: 71 AAAAAAAEEKKEEEEEEEEKEESEEE 96
Score = 27.6 bits (62), Expect = 4.8
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 340 KVAEADEEEECEEEEEEGEE 359
K E +EEEE EE EEE
Sbjct: 80 KKEEEEEEEEKEESEEEAAA 99
Score = 27.2 bits (61), Expect = 6.4
Identities = 13/44 (29%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 330 DEVI------PVEPTGKVAEADEEEECEEEEEEGEETVNNDTDE 367
+E I PV A A EE++EE EE + E
Sbjct: 51 EEAIKKAAAAPVAAAAAAAAAAAAAAAEEKKEEEEEEEEKEESE 94
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 32.9 bits (76), Expect = 0.25
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 331 EVIPVEPTGKVAEADEEEECEEEEEEGEE 359
EV+ + AE +EEEE EEEEEE E
Sbjct: 290 EVLSAQAQAAAAEEEEEEEEEEEEEEPSE 318
Score = 31.0 bits (71), Expect = 0.94
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
E +EEEE EEEEE EE
Sbjct: 294 AQAQAAAAEEEEEEEEEEEEEEPSEE 319
Score = 30.6 bits (70), Expect = 1.2
Identities = 16/30 (53%), Positives = 18/30 (60%)
Query: 330 DEVIPVEPTGKVAEADEEEECEEEEEEGEE 359
+E+ V A A EEEE EEEEEE EE
Sbjct: 286 EELKEVLSAQAQAAAAEEEEEEEEEEEEEE 315
Score = 30.2 bits (69), Expect = 1.9
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 328 ARDEVIPVEPTGKVAEADEEEECEEEEEEGEETV 361
A DE + + + A EEE EEEEEE EE
Sbjct: 283 ALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEP 316
Score = 29.1 bits (66), Expect = 4.3
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGE 358
+ E +EEEE EEE E E
Sbjct: 296 AQAAAAEEEEEEEEEEEEEEPSEEE 320
Score = 27.9 bits (63), Expect = 8.4
Identities = 8/28 (28%), Positives = 10/28 (35%)
Query: 331 EVIPVEPTGKVAEADEEEECEEEEEEGE 358
+ E +EEEE EEE
Sbjct: 296 AQAAAAEEEEEEEEEEEEEEPSEEEAAA 323
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 31.2 bits (71), Expect = 0.26
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 330 DEVI------PVEPTGKVAEADEEEECEEEEEEGEETVNNDTDE 367
+E I PV A A E EEEEEE EE +++E
Sbjct: 51 EEAIKKAAAAPVAAAAAAAAAAAAAEEEEEEEEEEEEEEEESEE 94
Score = 27.7 bits (62), Expect = 4.7
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 336 EPTGKVAEADEEEECEEEEEEGEE 359
+ E +EEEE EEEEE EE
Sbjct: 72 AAAAEEEEEEEEEEEEEEEESEEE 95
>gnl|CDD|215709 pfam00090, TSP_1, Thrombospondin type 1 domain.
Length = 48
Score = 29.7 bits (67), Expect = 0.26
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 248 TQWSKCSAKCGTGIQTRKVFC 268
++WS CS CG GI+TR+ C
Sbjct: 4 SEWSPCSVTCGKGIRTRQRTC 24
Score = 28.5 bits (64), Expect = 0.77
Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 9/55 (16%)
Query: 128 TSEWTGCDHLCGDGKQKRSVKCYREDKDGHREVVPDSACNEEKPESEKPCNLRPC 182
SEW+ C CG G + R C C + E+E C + C
Sbjct: 3 WSEWSPCSVTCGKGIRTRQRTCNSPFGGPP--------CTGDVQETEA-CMMDKC 48
Score = 26.2 bits (58), Expect = 4.7
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 309 GPWSKCSKTYGGGTMVSRTARDEVIPVEPTGKVAEADEEEECEEEE 354
WS CS T G G + + P + E E C ++
Sbjct: 4 SEWSPCSVTCGKGIRTRQRTCNS--PFGGPPCTGDVQETEACMMDK 47
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 30.3 bits (69), Expect = 0.38
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 337 PTGKVAEADEEEECEEEEEEGEE 359
A A+EE++ EEEEEE ++
Sbjct: 59 AAAAAAAAEEEKKEEEEEEEEDD 81
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 30.2 bits (68), Expect = 0.51
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
K E +EE++ EEE+EE EE
Sbjct: 71 AAAAEEKAEEKEEEKKKEEEKEEEEE 96
Score = 30.2 bits (68), Expect = 0.67
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
+ AE EEE+ +EEE+E EE
Sbjct: 70 AAAAAEEKAEEKEEEKKKEEEKEEEE 95
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 32.0 bits (73), Expect = 0.61
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 340 KVAEADEEEECEEEEEEGEETVNNDTDEW 368
E DEEEE EE+E+EG ++D +E+
Sbjct: 390 DEEEEDEEEEEEEDEDEGPSKEHSDDEEF 418
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 29.2 bits (66), Expect = 1.0
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 337 PTGKVAEADEEEECEEEEEEGEE 359
AEA +EE+ EEEEEE ++
Sbjct: 74 AAAAAAEAKKEEKKEEEEEESDD 96
>gnl|CDD|225521 COG2974, RdgC, DNA recombination-dependent growth factor C [DNA
replication, recombination, and repair].
Length = 303
Score = 30.8 bits (70), Expect = 1.1
Identities = 16/66 (24%), Positives = 23/66 (34%), Gaps = 7/66 (10%)
Query: 176 PCNLRPCEGVDWLTSEWT----GCEEKCGSSLETRTAVCATKNGKIYPESFC---LKAKT 228
PC D WT + + +CA K KI P S L+AK
Sbjct: 28 EAAFTPCGSQDMTKFGWTSPLGSHSDALVHVANDQILLCARKEEKILPASVVKDALEAKI 87
Query: 229 PELQRE 234
E++ +
Sbjct: 88 EEIEAK 93
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.1 bits (70), Expect = 1.1
Identities = 15/26 (57%), Positives = 17/26 (65%)
Query: 343 EADEEEECEEEEEEGEETVNNDTDEW 368
E +EEEE EEEEEE EE + EW
Sbjct: 873 EEEEEEEEEEEEEEEEENEEPLSLEW 898
Score = 30.7 bits (69), Expect = 1.8
Identities = 13/17 (76%), Positives = 14/17 (82%)
Query: 343 EADEEEECEEEEEEGEE 359
E +EEEE EEEEEE EE
Sbjct: 866 EEEEEEEEEEEEEEEEE 882
Score = 30.3 bits (68), Expect = 2.1
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 343 EADEEEECEEEEEEGEETVNNDTDE 367
E +EEEE EEEEEE EE + +E
Sbjct: 868 EEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 29.6 bits (66), Expect = 3.6
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 339 GKVAEADEEEECEEEEEEGEETVNNDTDE 367
G +E +EEEE EEEEEE EE + +E
Sbjct: 860 GGDSEEEEEEEEEEEEEEEEEEEEEEEEE 888
Score = 29.6 bits (66), Expect = 4.0
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 343 EADEEEECEEEEEEGEETVNNDTDEWTVDYVWTQ 376
E +EEEE EEEEEE EE + +E + W +
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPE 900
Score = 28.8 bits (64), Expect = 5.7
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 339 GKVAEADEEEECEEEEEEGEETVNNDTDE 367
G E +EEEE EEEEEE EE + +E
Sbjct: 861 GDSEEEEEEEEEEEEEEEEEEEEEEEEEE 889
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 29.3 bits (66), Expect = 1.4
Identities = 13/18 (72%), Positives = 14/18 (77%)
Query: 342 AEADEEEECEEEEEEGEE 359
AEADE EE E+EEE EE
Sbjct: 81 AEADEAEEEEKEEEAEEE 98
Score = 27.4 bits (61), Expect = 5.8
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 336 EPTGKVAEADEEEECEEEEEEGEE 359
A+ EEEE EEE EE +
Sbjct: 77 AEAAAEADEAEEEEKEEEAEEESD 100
Score = 27.0 bits (60), Expect = 6.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGEE 359
G A A+ +E EEE+EE E
Sbjct: 71 AAAAAGAEAAAEADEAEEEEKEEEAE 96
>gnl|CDD|100108 cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P1, P2, and L12p.
Ribosomal proteins P1 and P2 are the eukaryotic proteins
that are functionally equivalent to bacterial L7/L12.
L12p is the archaeal homolog. Unlike other ribosomal
proteins, the archaeal L12p and eukaryotic P1 and P2 do
not share sequence similarity with their bacterial
counterparts. They are part of the ribosomal stalk
(called the L7/L12 stalk in bacteria), along with 28S
rRNA and the proteins L11 and P0 in eukaryotes (23S
rRNA, L11, and L10e in archaea). In bacterial ribosomes,
L7/L12 homodimers bind the extended C-terminal helix of
L10 to anchor the L7/L12 molecules to the ribosome.
Eukaryotic P1/P2 heterodimers and archaeal L12p
homodimers are believed to bind the L10 equivalent
proteins, eukaryotic P0 and archaeal L10e, in a similar
fashion. P1 and P2 (L12p, L7/L12) are the only proteins
in the ribosome to occur as multimers, always appearing
as sets of dimers. Recent data indicate that most
archaeal species contain six copies of L12p (three
homodimers), while eukaryotes have two copies each of P1
and P2 (two heterodimers). Bacteria may have four or six
copies (two or three homodimers), depending on the
species. As in bacteria, the stalk is crucial for
binding of initiation, elongation, and release factors
in eukaryotes and archaea.
Length = 105
Score = 28.8 bits (64), Expect = 1.7
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEG 357
EP K EA EEEE EE+E+ G
Sbjct: 78 TAEPAEKAEEAKEEEEEEEDEDFG 101
Score = 26.8 bits (59), Expect = 8.5
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 336 EPTGKVAEADEEEECEEEEEEGEE 359
T + AE EE + EEEEEE E+
Sbjct: 76 AATAEPAEKAEEAKEEEEEEEDED 99
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
subunit. The alpha-subunit of the TRAP complex (TRAP
alpha) is a single-spanning membrane protein of the
endoplasmic reticulum (ER) which is found in proximity
of nascent polypeptide chains translocating across the
membrane.
Length = 281
Score = 30.1 bits (68), Expect = 1.9
Identities = 18/54 (33%), Positives = 26/54 (48%)
Query: 317 TYGGGTMVSRTARDEVIPVEPTGKVAEADEEEECEEEEEEGEETVNNDTDEWTV 370
T+G G +A+D E V + DEE+E EE+E E T + +E V
Sbjct: 20 TFGNGKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEV 73
>gnl|CDD|219009 pfam06404, PSK, Phytosulfokine precursor protein (PSK). This
family consists of several plant specific phytosulfokine
precursor proteins. Phytosulfokines, are active as
either a pentapeptide or a C-terminally truncated
tetrapeptide. These compounds were first isolated
because of their ability to stimulate cell division in
somatic embryo cultures of Asparagus officinalis.
Length = 74
Score = 27.7 bits (62), Expect = 2.1
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 333 IPVEPTGKVAEADEEEECEEEEEE 356
I + KV E + ECE E EE
Sbjct: 29 IEAAESSKVDEDEVVSECEGEGEE 52
>gnl|CDD|205506 pfam13326, PSII_Pbs27, Photosystem II Pbs27. This family of
proteins contains Pbs27, a highly conserved component
of photosystem II. Pbs27 is comprised of four helices
arranged in a right handed up-down-up-down fold, with a
less ordered region located at the N-terminus.
Length = 110
Score = 28.4 bits (64), Expect = 2.4
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 13 DMQVAIRNMSGHYYLNGN 30
M A+ +++GHY GN
Sbjct: 71 TMYTALNSLAGHYSSYGN 88
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 30.0 bits (68), Expect = 2.8
Identities = 16/39 (41%), Positives = 19/39 (48%)
Query: 326 RTARDEVIPVEPTGKVAEADEEEECEEEEEEGEETVNND 364
R R P EP + E +E E EEEEEE EE +
Sbjct: 294 RRRRPPPSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEE 332
Score = 28.5 bits (64), Expect = 7.5
Identities = 16/35 (45%), Positives = 17/35 (48%)
Query: 326 RTARDEVIPVEPTGKVAEADEEEECEEEEEEGEET 360
R R P P E +EEEE EEEEE EE
Sbjct: 291 RRRRRRRPPPSPPEPEEEEEEEEEVPEEEEEEEEE 325
>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic
N-terminal. This is the very acidic N-terminal region
of the early transcription elongation factor Spt5. The
Spt5-Spt4 complex regulates early transcription
elongation by RNA polymerase II and has an imputed role
in pre-mRNA processing via its physical association with
mRNA capping enzymes. The actual function of this
N-terminal domain is not known although it is
dispensable for binding to Spt4.
Length = 92
Score = 27.8 bits (62), Expect = 3.3
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 342 AEADEEEECEEEEEEGEETVNNDTDE 367
AE D+EEE EEEEE+ E ++++ +
Sbjct: 6 AEVDDEEEEEEEEEDDLEDLSDEDEF 31
>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 = 28.6 bits (64), Expect = 4.5
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 343 EADEEEECEEEEEEGEETVNNDTDE 367
+ DEE+E +EEEEE EE + D D+
Sbjct: 167 DVDEEDEKDEEEEEEEEEEDEDFDD 191
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 28.8 bits (65), Expect = 4.7
Identities = 8/25 (32%), Positives = 9/25 (36%)
Query: 334 PVEPTGKVAEADEEEECEEEEEEGE 358
A A EEEEEE +
Sbjct: 279 AAAAAAAAAAAAAAPAEEEEEEEDD 303
Score = 28.4 bits (64), Expect = 6.9
Identities = 8/23 (34%), Positives = 8/23 (34%)
Query: 337 PTGKVAEADEEEECEEEEEEGEE 359
A A EEEE EE
Sbjct: 279 AAAAAAAAAAAAAAPAEEEEEEE 301
>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family. This
family includes the HABP4 family of hyaluronan-binding
proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1.
HABP4 has been observed to bind hyaluronan (a
glucosaminoglycan), but it is not known whether this is
its primary role in vivo. It has also been observed to
bind RNA, but with a lower affinity than that for
hyaluronan. PAI-1 mRNA-binding protein specifically
binds the mRNA of type-1 plasminogen activator inhibitor
(PAI-1), and is thought to be involved in regulation of
mRNA stability. However, in both cases, the sequence
motifs predicted to be important for ligand binding are
not conserved throughout the family, so it is not known
whether members of this family share a common function.
Length = 106
Score = 27.4 bits (61), Expect = 4.8
Identities = 15/61 (24%), Positives = 21/61 (34%)
Query: 308 SGPWSKCSKTYGGGTMVSRTARDEVIPVEPTGKVAEADEEEECEEEEEEGEETVNNDTDE 367
G W T ++ E EA++E EEEE E EE +E
Sbjct: 24 RGNWGSVKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKEMTLEE 83
Query: 368 W 368
+
Sbjct: 84 Y 84
>gnl|CDD|205161 pfam12956, DUF3845, Domain of Unknown Function with PDB structure.
Member PDB:3GF6 has statistically significant similarity
to TNF-like jelly roll fold may indicate an
immunomodulatory function or a bioadhesion role.
Length = 244
Score = 28.8 bits (64), Expect = 4.9
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 356 EGEETVNNDTDEWTVDYVWTQLNG 379
+GE T+ D EW +DYV+ QL G
Sbjct: 138 KGELTLTGD--EWMIDYVYAQLAG 159
>gnl|CDD|218815 pfam05935, Arylsulfotrans, Arylsulfotransferase (ASST). This
family consists of several bacterial
Arylsulfotransferase proteins. Arylsulfotransferase
(ASST) transfers a sulfate group from phenolic sulfate
esters to a phenolic acceptor substrate.
Length = 459
Score = 28.5 bits (64), Expect = 6.3
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 315 SKTYGGGTMVSRTARDEVIPVEPTGKV 341
Y G T D +I ++ TG+V
Sbjct: 207 ESNYRGDGDGVDTVEDTIIEIDKTGEV 233
>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex
subunit beta; Reviewed.
Length = 463
Score = 28.5 bits (64), Expect = 6.7
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 337 PTGKVAEADEEEECEEEEEEGEETV 361
P + A+EEEE EEEEEE EE V
Sbjct: 397 PVVERWAAEEEEEEEEEEEEEEEPV 421
>gnl|CDD|240331 PTZ00254, PTZ00254, 40S ribosomal protein SA; Provisional.
Length = 249
Score = 28.1 bits (63), Expect = 7.6
Identities = 15/42 (35%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 334 PVEPTGKVAEADEEEECE------EEEEEGEETVNNDTDEWT 369
P E K A E E E EEGEE V +EW
Sbjct: 207 PEEAEEKEEAAAETAGVEDAAAAAAEAEEGEEWVAAANNEWE 248
>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family.
This family contains a number of defence peptides
secreted from the skin of amphibians, including the
opiate-like dermorphins and deltorphins, and the
antimicrobial dermoseptins and temporins. The alignment
for this family includes the signal peptide.
Length = 46
Score = 25.4 bits (56), Expect = 9.3
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 347 EEECEEEEEEGEETVNNDTDE 367
EEE E+EEE E+ +
Sbjct: 22 EEEKREDEEENEDEEEGEEQS 42
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 0.133 0.439
Gapped
Lambda K H
0.267 0.0602 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,142,005
Number of extensions: 1707988
Number of successful extensions: 2348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2122
Number of HSP's successfully gapped: 99
Length of query: 390
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 291
Effective length of database: 6,546,556
Effective search space: 1905047796
Effective search space used: 1905047796
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: 60 (27.2 bits)