RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13379
(828 letters)
>gnl|CDD|237989 cd00022, BIR, Baculoviral inhibition of apoptosis protein repeat
domain; Found in inhibitors of apoptosis proteins (IAPs)
and other proteins. In higher eukaryotes, BIR domains
inhibit apoptosis by acting as direct inhibitors of the
caspase family of protease enzymes. In yeast, BIR
domains are involved in regulating cytokinesis. This
novel fold is stabilized by zinc tetrahedrally
coordinated by one histidine and three cysteine residues
and resembles a classical zinc finger.
Length = 69
Score = 85.4 bits (212), Expect = 2e-20
Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 347 RFLSSAQWYRDDDRAIWALPDQMAQAGFYHQPSGTGDDRAMCFTCIVCLVCWEPTDEPWA 406
R + W ++ P+++A+AGFY+ G D CF C + L WEP D+PW
Sbjct: 3 RLKTFKNW----PISLKVTPEKLAEAGFYYTGRG---DEVKCFFCGLELKNWEPGDDPWE 55
Query: 407 EHERHSPCCPFVKG 420
EH+R SP CPFV
Sbjct: 56 EHKRWSPNCPFVLL 69
Score = 51.1 bits (123), Expect = 2e-08
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 245 AARRETFAKWPHMDYKWALPDQMAQAGFYHQPSGTGYDRAMCF 287
AR +TF WP P+++A+AGFY+ G D CF
Sbjct: 1 EARLKTFKNWPISL--KVTPEKLAEAGFYYTGRG---DEVKCF 38
>gnl|CDD|216045 pfam00653, BIR, Inhibitor of Apoptosis domain. BIR stands for
'Baculovirus Inhibitor of apoptosis protein Repeat'. It
is found repeated in inhibitor of apoptosis proteins
(IAPs), and in fact it is also known as IAP repeat.
These domains characteristically have a number of
invariant residues, including 3 conserved cysteines and
one conserved histidine that coordinate a zinc ion. They
are usually made up of 4-5 alpha helices and a
three-stranded beta-sheet. BIR is also found in other
proteins known as BIR-domain-containing proteins
(BIRPs), such as Survivin.
Length = 69
Score = 78.5 bits (194), Expect = 5e-18
Identities = 28/54 (51%), Positives = 37/54 (68%), Gaps = 3/54 (5%)
Query: 366 PDQMAQAGFYHQPSGTGDDRAMCFTCIVCLVCWEPTDEPWAEHERHSPCCPFVK 419
P+++A+AGFY+ +G DR CF C + L WEP D+PW EH+R SP CPFV
Sbjct: 19 PEKLAEAGFYYTGTG---DRVRCFYCGLELDNWEPDDDPWEEHKRWSPNCPFVL 69
Score = 47.7 bits (114), Expect = 3e-07
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 247 RRETFAKWPHMDYKWAL-PDQMAQAGFYHQPSGTGYDRAMCF 287
R TF WP + P+++A+AGFY+ +G DR CF
Sbjct: 1 RLATFKNWPIALKQAKPSPEKLAEAGFYYTGTG---DRVRCF 39
>gnl|CDD|197595 smart00238, BIR, Baculoviral inhibition of apoptosis protein
repeat. Domain found in inhibitor of apoptosis proteins
(IAPs) and other proteins. Acts as a direct inhibitor of
caspase enzymes.
Length = 71
Score = 78.1 bits (193), Expect = 7e-18
Identities = 27/61 (44%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 360 RAIWALPDQMAQAGFYHQPSGTGDDRAMCFTCIVCLVCWEPTDEPWAEHERHSPCCPFVK 419
P+Q+A+AGFY+ G D CF C L WEP D+PW EH++ SP CPFV+
Sbjct: 14 YNSKCTPEQLAEAGFYYTGVG---DEVKCFFCGGELDNWEPGDDPWEEHKKWSPNCPFVR 70
Query: 420 G 420
Sbjct: 71 N 71
Score = 48.9 bits (117), Expect = 2e-07
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 243 SEAARRETFAKWPHMDYKWALPDQMAQAGFYHQPSGTGYDRAMCF 287
SE AR +TF WP+ P+Q+A+AGFY+ G D CF
Sbjct: 1 SEEARLKTFQNWPY--NSKCTPEQLAEAGFYYTGVG---DEVKCF 40
>gnl|CDD|216992 pfam02358, Trehalose_PPase, Trehalose-phosphatase. This family
consist of trehalose-phosphatases EC:3.1.3.12 these
enzyme catalyze the de-phosphorylation of
trehalose-6-phosphate to trehalose and orthophosphate.
The aligned region is present in trehalose-phosphatases
and comprises the entire length of the protein it is
also found in the C-terminus of trehalose-6-phosphate
synthase EC:2.4.1.15 adjacent to the
trehalose-6-phosphate synthase domain - pfam00982. It
would appear that the two equivalent genes in the E.
coli otsBA operon otsA the trehalose-6-phosphate
synthase and otsB trehalose-phosphatase (this family)
have undergone gene fusion in most eukaryotes.
Trehalose is a common disaccharide of bacteria, fungi
and invertebrates that appears to play a major role in
desiccation tolerance.
Length = 235
Score = 33.5 bits (77), Expect = 0.33
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 24 PIVRDPDSVIYHPNL-NILIVLSRNAECIVVDINSGCVLRKCAFAEEGQPIKGAYL 78
PIV DPD+ + L ++L L+ + V I SG R AF + + L
Sbjct: 10 PIVEDPDAAVPSDRLLSLLNRLASDPPNTVA-IISG---RSRAFEDLFFGVPNLGL 61
>gnl|CDD|239480 cd03385, PAP2_BcrC_like, PAP2_like proteins, BcrC_like subfamily.
Several members of this family have been annotated as
bacitracin transport permeases, as it was suspected that
they form the permease component of an ABC transporter
system. It was shown, however, that BcrC from Bacillus
subtilis posesses undecaprenyl pyrophosphate (UPP)
phospatase activity, and it is hypothesized that it
competes with bacitracin for UPP, increasing the cell's
resistance to bacitracin.
Length = 144
Score = 30.7 bits (70), Expect = 1.5
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 18/63 (28%)
Query: 201 KRQNRHVPALAIASAINERLNCL------HPTPF------------PIDSQPSDHRNLMF 242
++Q + V IA A+ +N + HP PF S PSDH L F
Sbjct: 29 EKQRKVVLFATIAVAVALLINYIIGLLYFHPRPFVVGLGHNLLPHAADSSFPSDHTTLFF 88
Query: 243 SEA 245
S A
Sbjct: 89 SIA 91
>gnl|CDD|218652 pfam05602, CLPTM1, Cleft lip and palate transmembrane protein 1
(CLPTM1). This family consists of several eukaryotic
cleft lip and palate transmembrane protein 1 sequences.
Cleft lip with or without cleft palate is a common birth
defect that is genetically complex. The nonsyndromic
forms have been studied genetically using linkage and
candidate-gene association studies with only partial
success in defining the loci responsible for orofacial
clefting. CLPTM1 encodes a transmembrane protein and has
strong homology to two Caenorhabditis elegans genes,
suggesting that CLPTM1 may belong to a new gene family.
This family also contains the human cisplatin resistance
related protein CRR9p which is associated with
CDDP-induced apoptosis.
Length = 437
Score = 30.7 bits (70), Expect = 3.2
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 12 GKEEEEKEEEEGPIVRDPDSVIYHPNLNILIV 43
GK E+E+ EEE D +HPNL + +V
Sbjct: 161 GKSEKEEPEEEKTPAPDKIVSHWHPNLTLSVV 192
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 30.3 bits (69), Expect = 4.6
Identities = 24/115 (20%), Positives = 41/115 (35%), Gaps = 21/115 (18%)
Query: 473 NYIRQLKTLPRCLAISRSYHETVPCWYSTMY------DLVWRIARLPSPWSRVQFPPEGG 526
++R P ++R+ + + WY ++ +L+WR+ L W R+ EG
Sbjct: 137 FWLRSGLRRPTPRRLARALGQLLRSWYIYLFHLPVLPELLWRLG-LGRAWPRLLRRVEG- 194
Query: 527 FYPEQIMLDLGTADILLSCPPHAAWLYPAHITRQYRAG--------TQLYTTTQD 573
+ I +D H LY A++ R QL T D
Sbjct: 195 TPVDPIPTQTTLSDGA-----HGVKLYRANMIRSLSRPRERYTDVPVQLIVPTGD 244
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 30.2 bits (68), Expect = 5.8
Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 11/86 (12%)
Query: 561 YRAGTQLYTTTQDITTLSGYILLISRDST-------VLVLNYVRQLKVENEFSVSKLCYD 613
Y +G +L T T YI + +L + Q+ V E+ + L D
Sbjct: 866 YDSGRKLLTGTN----KGLYISNRKDNVNRFNKPIDLLQEPNISQIIVIEEYKLMLLLSD 921
Query: 614 YGLSHSELKVSAAAIAANVKHSSKAS 639
L L V A+ NVK S +
Sbjct: 922 KKLYSCPLDVIDASTEENVKKSRIVN 947
>gnl|CDD|238579 cd01174, ribokinase, Ribokinase catalyses the phosphorylation of
ribose to ribose-5-phosphate using ATP. This reaction is
the first step in the ribose metabolism. It traps ribose
within the cell after uptake and also prepares the sugar
for use in the synthesis of nucleotides and histidine,
and for entry into the pentose phosphate pathway.
Ribokinase is dimeric in solution.
Length = 292
Score = 29.8 bits (68), Expect = 6.2
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 500 STMYDLVWRIARLPSPW 516
S DLV R+ RLP P
Sbjct: 7 SINVDLVTRVDRLPKPG 23
>gnl|CDD|177486 PHA02752, PHA02752, hypothetical protein; Provisional.
Length = 242
Score = 29.3 bits (65), Expect = 7.4
Identities = 18/81 (22%), Positives = 22/81 (27%), Gaps = 9/81 (11%)
Query: 683 GGNPLAMDTELTSSPPPPSPHLCLLVLDFHYRPNKSPATAGTQTSAPGNKKAVSGTGTST 742
GG P T +S PP L PN + A G S
Sbjct: 25 GGGPNQQPTITGTSAPPAVTDL---------YPNAALANGFDGILIDDGHFNCDGGQCSI 75
Query: 743 ATVGGGKLIQVVKLSASPVKS 763
G +V A P+ S
Sbjct: 76 TASAVGSFRSIVAYGARPLSS 96
>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 = 29.2 bits (65), Expect = 8.5
Identities = 21/117 (17%), Positives = 38/117 (32%), Gaps = 24/117 (20%)
Query: 662 VGARMKTTGEDLYQLKQRLESG---GNPLAMDTELTSSPPPPSPHLCLLVLDFHYRPNKS 718
V +T E +Q+ + L + GN A + +S + +
Sbjct: 98 VDEYSETYKEKKFQVLETLGTYNQLGNAGASASITKTSNGSDA--------------ATT 143
Query: 719 PATAGTQTSAPGNKKAVSGTGTSTATVGGGKLIQVVKLSASPVKSLTPATPGEGIRK 775
+TA T +A K + +T VG + + + T TP +K
Sbjct: 144 SSTANTPAAAKVLKANAASAPNTTTGVGSAAT-------TAAISATTATTPTTTQKK 193
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 29.4 bits (66), Expect = 8.7
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 10/60 (16%)
Query: 714 RPNKSPATAGTQTSAPGNKKAVSGTGTSTATVGGGKLIQVVKLSASPVKSLTPATPGEGI 773
R +SPA + + N+ + V + VK ++ P EG+
Sbjct: 370 RGVESPARSPGGSPRTTNR-------SGPRNVASVSPMTSVK---KIDPNMKPGAASEGV 419
>gnl|CDD|233715 TIGR02086, IPMI_arch, 3-isopropylmalate dehydratase, large subunit.
This subfamily is a subset of the larger HacA family
(Homoaconitate hydratase family, TIGR01343) and is most
closely related to the 3-isopropylmalate dehydratase,
large subunits which form TIGR00170. This subfamily
includes the members of TIGR01343 which are gene
clustered with other genes of leucine biosynthesis. The
rest of the subfamily includes mainly archaeal species
which exhibit two hits to this model. In these cases it
is possible that one or the other of the hits does not
have a 3-isopropylmalate dehydratase activity but rather
one of the other related aconitase-like activities.
Length = 412
Score = 29.3 bits (66), Expect = 9.3
Identities = 10/41 (24%), Positives = 18/41 (43%)
Query: 516 WSRVQFPPEGGFYPEQIMLDLGTADILLSCPPHAAWLYPAH 556
R+ P G Y ++I +DL + L++ P + P
Sbjct: 239 EFRILRPDPGAKYDDEIEIDLSDLEPLVAVPHSVDNVRPVS 279
>gnl|CDD|221783 pfam12807, eIF3_p135, Translation initiation factor eIF3 subunit
135. Translation initiation factor eIF3 is a
multi-subunit protein complex required for initiation of
protein biosynthesis in eukaryotic cells. The complex
promotes ribosome dissociation, the binding of the
initiator methionyl-tRNA to the 40 S ribosomal subunit,
and mRNA recruitment to the ribosome. The protein
product from TIF31 genes in yeast is p135 which
associates with the eIF3 but does not seem to be
necessary for protein translation initiation.
Length = 169
Score = 28.5 bits (64), Expect = 9.4
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 10/67 (14%)
Query: 177 WNIICLELKHASFKTACYSLVCELKRQNRHVPALAIASAINERLNCL---HPTPFPIDSQ 233
+ E+ + K L+ R VPA +++AI+ LNCL P P
Sbjct: 42 KRLCVSEMIARAAK-------HILRTYLRGVPAPDLSAAISHFLNCLLGSESNPDPEAEI 94
Query: 234 PSDHRNL 240
Sbjct: 95 DESRSAS 101
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
0.318 0.133 0.404
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 41,447,380
Number of extensions: 4015644
Number of successful extensions: 3418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3411
Number of HSP's successfully gapped: 24
Length of query: 828
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 723
Effective length of database: 6,280,432
Effective search space: 4540752336
Effective search space used: 4540752336
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: 63 (28.1 bits)