RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12687
(143 letters)
>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
Dyneins are described as motor proteins of eukaryotic
cells, as they can convert energy derived from the
hydrolysis of ATP to force and movement along
cytoskeletal polymers, such as microtubules. This region
is found C-terminal to the dynein heavy chain N-terminal
region 1 (pfam08385) in many members of this family. No
functions seem to have been attributed specifically to
this region.
Length = 408
Score = 84.9 bits (211), Expect = 3e-20
Identities = 33/61 (54%), Positives = 48/61 (78%), Gaps = 4/61 (6%)
Query: 81 WFKNFKD----WEEKLMLLQEIIDEWVKVQQTWMYLEPIFSSPDIQAQMPEEGRRFSAMD 136
+ K F++ WE+KL L+QE+++ W+KVQ+ W+YLEPIFSS DI+ Q+PEE +RFS +D
Sbjct: 198 YVKPFEEEADEWEKKLNLIQEVLELWLKVQRKWVYLEPIFSSSDIKKQLPEESKRFSNVD 257
Query: 137 K 137
K
Sbjct: 258 K 258
>gnl|CDD|225705 COG3164, COG3164, Predicted membrane protein [Function unknown].
Length = 1271
Score = 28.2 bits (63), Expect = 1.8
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 105 VQQTWMYLEPIFSSPDIQAQMPEEGRRFSAMDKL 138
+Q +W P + DI+A P+ GR +A L
Sbjct: 57 LQGSWRNFGPTLEAQDIRAGDPDGGRLSAARVTL 90
>gnl|CDD|212687 cd11737, HSPA4_NBD, Nucleotide-binding domain of HSPA4. Human
HSPA4 (also known as 70-kDa heat shock protein 4, APG-2,
HS24/P52, hsp70 RY, and HSPH2; the human HSPA4 gene maps
to 5q31.1) responds to acidic pH stress, is involved in
the radioadaptive response, is required for normal
spermatogenesis and is overexpressed in hepatocellular
carcinoma. It participates in a pathway along with NBS1
(Nijmegen breakage syndrome 1, also known as p85 or
nibrin), heat shock transcription factor 4b (HDF4b), and
HSPA14 (belonging to a different HSP70 subfamily) that
induces tumor migration, invasion, and transformation.
HSPA4 expression in sperm was increased in men with
oligozoospermia, especially in those with varicocele.
HSPA4 belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as nucleotide
exchange factors (NEFs), to remove ADP from their HSP70
chaperone partners during the ATP hydrolysis cycle.
HSP70 chaperones assist in protein folding and assembly,
and can direct incompetent "client" proteins towards
degradation. Like HSP70 chaperones, HSP105/110s have an
N-terminal nucleotide-binding domain (NBD) and a
C-terminal substrate-binding domain (SBD). For HSP70
chaperones, the nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. Hsp70 chaperone
activity is also regulated by J-domain proteins.
Length = 383
Score = 27.7 bits (61), Expect = 2.5
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 1 MLLNEVKDEYMSSIKKAVVDFAIHDP----REPQLSIMEKEQVPSLN 43
MLL ++K+ S++KK VVD + P + S+M+ Q+ LN
Sbjct: 119 MLLTKLKETAESALKKPVVDCVVSVPCFYTDAERRSVMDATQIAGLN 165
>gnl|CDD|232890 TIGR00235, udk, uridine kinase. Model contains a number of longer
eukaryotic proteins and starts bringing in
phosphoribulokinase hits at scores of 160 and below
[Purines, pyrimidines, nucleosides, and nucleotides,
Salvage of nucleosides and nucleotides].
Length = 207
Score = 26.6 bits (59), Expect = 4.1
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 86 KDWEEKLMLLQEIIDEWVKVQQTWMYLEPIFSSPDIQ---AQMPEEGRRFSAMDKL 138
+D E+ L +ID++ K + MY F P Q +PE GR A++ L
Sbjct: 146 RDINERGRSLDSVIDQYRKTVR-PMYE--QFVEPTKQYADLIIPEGGRNEVAINVL 198
>gnl|CDD|234199 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
protein UrtE. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 230
Score = 26.7 bits (60), Expect = 4.1
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 14/55 (25%)
Query: 27 RE--PQLSIMEKEQVPSLNPMLEMGSEFKDTFDQNKKKLDNSLFTIHPVLSEMSN 79
RE P+L++ E N L G + +K+ + ++ + PVL EM
Sbjct: 84 REIFPRLTVEE-------N--LLTGLA---ALPRRSRKIPDEIYELFPVLKEMLG 126
>gnl|CDD|221815 pfam12864, DUF3822, Protein of unknown function (DUF3822). This
is a family of uncharacterized bacterial proteins.
However, structural-similarity searches indicate the
family takes on an actin-like ATPase fold.
Length = 248
Score = 26.5 bits (59), Expect = 4.6
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 21 FAIHDPREPQLSIMEKEQVPSLNPMLEMGSEFKDTFDQN 59
F I+DP ++ +E Q + P + + K FD++
Sbjct: 30 FCIYDPAGKEILALEDYQFDPVTP-ESLLANLKQIFDEH 67
>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
Length = 679
Score = 26.4 bits (58), Expect = 6.1
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 29 PQLSIMEKEQVPSLNPMLEMGSEFKD 54
P+L++M KEQ S+NP LE+ + F
Sbjct: 97 PKLAVM-KEQALSINPFLEI-TPFPA 120
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 26.3 bits (58), Expect = 6.4
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 32 SIMEKEQVPSLNPMLE 47
S +Q+PSL PMLE
Sbjct: 30 SATTAQQMPSLAPMLE 45
>gnl|CDD|234812 PRK00694, PRK00694, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Validated.
Length = 606
Score = 26.3 bits (58), Expect = 7.2
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 14 IKKAVVDFAIHDPREPQLSIMEKEQVPSLNPMLE 47
+ KA+ I E L + VP L M E
Sbjct: 371 VPKAMRSSPIVSELEKHLLVFHHHDVPCLYEMNE 404
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 26.2 bits (58), Expect = 7.7
Identities = 19/69 (27%), Positives = 37/69 (53%)
Query: 36 KEQVPSLNPMLEMGSEFKDTFDQNKKKLDNSLFTIHPVLSEMSNIWFKNFKDWEEKLMLL 95
K ++ SL LE E K + +KKLD + +L E+ + F++ ++ EE+L L
Sbjct: 538 KGEIKSLKKELEKLEELKKKLAELEKKLDELEEELAELLKELEELGFESVEELEERLKEL 597
Query: 96 QEIIDEWVK 104
+ +E+++
Sbjct: 598 EPFYNEYLE 606
>gnl|CDD|212688 cd11738, HSPA4L_NBD, Nucleotide-binding domain of HSPA4L. Human
HSPA4L (also known as 70-kDa heat shock protein 4-like,
APG-1, HSPH3, and OSP94; the human HSPA4L gene maps to
4q28) is expressed ubiquitously and predominantly in the
testis. It is required for normal spermatogenesis and
plays a role in osmotolerance. HSPA4L belongs to the
105/110 kDa heat shock protein (HSP105/110) subfamily of
the HSP70-like family. HSP105/110s are believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 383
Score = 26.1 bits (57), Expect = 8.7
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 1 MLLNEVKDEYMSSIKKAVVDFAIHDPR----EPQLSIMEKEQVPSLN 43
MLL ++K+ +++KK V D I P + S+M QV LN
Sbjct: 119 MLLAKLKETSENALKKPVADCVISIPSFFTDAERRSVMAAAQVAGLN 165
>gnl|CDD|215530 PLN02980, PLN02980, 2-oxoglutarate decarboxylase/ hydro-lyase/
magnesium ion binding / thiamin pyrophosphate binding.
Length = 1655
Score = 26.0 bits (57), Expect = 8.7
Identities = 26/128 (20%), Positives = 47/128 (36%), Gaps = 12/128 (9%)
Query: 8 DEYMSSIKKAVVDFAIHDPREPQLSIMEKEQVPSLNPMLEMGSEFKDTFDQNKKKLDNSL 67
++ SS+ F PQ+ + E E+V L+ L TF+Q ++S+
Sbjct: 148 NKESSSVNSKAGSFYFF---VPQIELDEHEEVSILSATLAWDDSLSYTFEQAISSYESSI 204
Query: 68 FTI--HPVLSEMSNIWFKNFKDWEEKLMLLQEIIDEWVKVQQTWMYLEPIFSSPDIQAQM 125
+ + H + + WFK K K + +E + +M S D A
Sbjct: 205 YQVSSHFWPTA-EDHWFKLLKSSLAKASV-----EEIHPAELVYMGFF-TLSGRDQAAVK 257
Query: 126 PEEGRRFS 133
+ + S
Sbjct: 258 ELKSIQSS 265
>gnl|CDD|152383 pfam11948, DUF3465, Protein of unknown function (DUF3465). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 131 to 151 amino acids in
length. This protein has a conserved HWTH sequence
motif.
Length = 131
Score = 25.3 bits (56), Expect = 8.8
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 5 EVKDEYMSSIKKAVVDFAIHDPREP 29
E EY + K V+ + HDPR
Sbjct: 93 EFYGEYEWNPKGGVIHWTHHDPRGR 117
>gnl|CDD|233605 TIGR01865, cas_Csn1, CRISPR-associated protein Cas9/Csn1, subtype
II/NMEMI. CRISPR loci appear to be mobile elements with
a wide host range. This model represents a protein found
only in CRISPR-containing species, near other
CRISPR-associated proteins (cas), as part of the NMENI
subtype of CRISPR/Cas locus. The species range so far
for this protein is animal pathogens and commensals only
[Mobile and extrachromosomal element functions, Other].
Length = 805
Score = 25.8 bits (57), Expect = 9.5
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 53 KDTFDQNKKKLDNS--LFTIHPVLSEMSNIWFKNFKDWEEKLM---LLQEIIDEWVK 104
K T+ +K+ L VL+E++N+ + E K++ QE++D K
Sbjct: 269 KCTYLPEEKRAPKHSLLAEKFTVLNELNNVRIIILEQGETKILSKEEKQELLDLLFK 325
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 0.132 0.394
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,419,696
Number of extensions: 661349
Number of successful extensions: 636
Number of sequences better than 10.0: 1
Number of HSP's gapped: 635
Number of HSP's successfully gapped: 35
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 54 (24.5 bits)