RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14769
(90 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 59.4 bits (145), Expect = 9e-14
Identities = 22/53 (41%), Positives = 37/53 (69%), Gaps = 1/53 (1%)
Query: 15 KRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFMR 67
+R HN ER+RRD I D+F LR+ +P+ +K+ S+A+IL+ A +YI+ ++
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPNKKL-SKAEILRLAIEYIKHLQ 52
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four
helix bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide
sequences such as N-box (5-CACGc/aG-3), those which
have a COE domain (Collier/Olf-1/EBF) which is involved
in both in dimerization and in DNA binding, and those
which bind pentanucleotides ACGTG or GCGTG and have a
PAS domain which allows the dimerization between PAS
proteins, the binding of small molecules (e.g.,
dioxin), and interactions with non-PAS proteins.
Length = 60
Score = 55.7 bits (135), Expect = 3e-12
Identities = 24/60 (40%), Positives = 36/60 (60%)
Query: 12 SAEKRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFMRRKNA 71
+R HN ER+RR+ I D+F LR +P+L K S+A+IL+KA DYI+ ++
Sbjct: 1 RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 49.5 bits (119), Expect = 6e-10
Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 20 NALERKRRDHIKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFMRRKNAS 72
NA ER+RR I ++F LR +P+L K S+A+IL+ A +YI+ ++ +
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|237017 PRK11904, PRK11904, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1038
Score = 28.6 bits (65), Expect = 0.37
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 28 DHIKDSFSSLRDSVPSLQGEKVASRAQILKKAAD 61
+ ++ + ++ R + P+ V RA IL++AAD
Sbjct: 585 EQVEQALAAARAAFPAWSRTPVEERAAILERAAD 618
>gnl|CDD|128486 smart00189, IL2, Interleukin-2 family. Interleukin-2 is a cytokine
produced by T-helper cells in response to antigenic or
mitogenic stimulation. This protein is required for
T-cell proliferation and other activities crucial to the
regulation of the immune response.
Length = 154
Score = 27.5 bits (61), Expect = 0.78
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 29 HIKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFMRR 68
HIKD S++ +V L+G + Q ++ ++F+ R
Sbjct: 102 HIKDFISNINVTVLKLKGSETRFTCQYDDESVTIVEFLNR 141
>gnl|CDD|219907 pfam08566, Pam17, Mitochondrial import protein Pam17. The
presequence translocase-associated motor (PAM) drives
the completion of preprotein translocation into the
mitochondrial matrix. The Pam17 subunit is required for
formation of a stable complex between cochaperones Pam16
and Pam18 and promotes the association of Pam16-Pam18
with the presequence translocase. Mitochondria lacking
Pam17 are selectively impaired in the import of matrix
proteins.
Length = 174
Score = 27.3 bits (61), Expect = 0.84
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 22 LERKRRDHIKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFMRRKNA 71
LER +++ + S S + VP GEK+ S A Y Q++R + A
Sbjct: 123 LERIKKNRVDPSSQSFSNPVPDYYGEKIGS-------LAGYRQWLRDQRA 165
>gnl|CDD|143443 cd07125, ALDH_PutA-P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, PutA. The proline catabolic enzymes of
the aldehyde dehydrogenase (ALDH) protein superfamily,
proline dehydrogenase and
Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH,
(EC=1.5.1.12 )), catalyze the two-step oxidation of
proline to glutamate; P5CDH catalyzes the oxidation of
glutamate semialdehyde, utilizing NAD+ as the electron
acceptor. In some bacteria, the two enzymes are fused
into the bifunctional flavoenzyme, proline utilization A
(PutA) These enzymes play important roles in cellular
redox control, superoxide generation, and apoptosis. In
certain prokaryotes such as Escherichia coli, PutA is
also a transcriptional repressor of the proline
utilization genes.
Length = 518
Score = 27.2 bits (61), Expect = 1.2
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 28 DHIKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFMR 67
+ + + + + V RA+IL+KAAD ++ R
Sbjct: 69 EDVDAALAIAAAAFAGWSATPVEERAEILEKAADLLEANR 108
>gnl|CDD|171796 PRK12883, ubiA, prenyltransferase UbiA-like protein; Reviewed.
Length = 277
Score = 27.0 bits (60), Expect = 1.3
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 5/37 (13%)
Query: 30 IKDSFSSLRDSVPSLQGEKVASRAQILKKAADYIQFM 66
+ ++ LR+ + A + Q L K A ++ +
Sbjct: 237 LYAAYLVLRN-----PDRETAHKGQKLLKIAIFLAVI 268
>gnl|CDD|143441 cd07123, ALDH_F4-17_P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, ALDH families 4 and 17.
Delta(1)-pyrroline-5-carboxylate dehydrogenase
(EC=1.5.1.12 ), families 4 and 17: a proline catabolic
enzyme of the aldehyde dehydrogenase (ALDH) protein
superfamily. Delta(1)-pyrroline-5-carboxylate
dehydrogenase (P5CDH), also known as ALDH4A1 in humans,
is a mitochondrial homodimer involved in proline
degradation and catalyzes the NAD + -dependent
conversion of P5C to glutamate. This is a necessary step
in the pathway interconnecting the urea and
tricarboxylic acid cycles. The preferred substrate is
glutamic gamma-semialdehyde, other substrates include
succinic, glutaric and adipic semialdehydes. Also
included in this CD is the Aldh17 Drosophila
melanogaster (Q9VUC0) P5CDH and similar sequences.
Length = 522
Score = 26.8 bits (60), Expect = 1.7
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 11/40 (27%)
Query: 50 ASRAQILKKAADYIQ--FMRRKNAS---------HQQDID 78
RA I KAAD + + NA+ Q +ID
Sbjct: 91 EDRAAIFLKAADLLSGKYRYELNAATMLGQGKNVWQAEID 130
>gnl|CDD|236393 PRK09147, PRK09147, succinyldiaminopimelate transaminase;
Provisional.
Length = 396
Score = 25.6 bits (57), Expect = 4.2
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 34 FSSL--RDSVPSLQGEKVASRAQILKK 58
F SL R +VP L+ VA A +LKK
Sbjct: 240 FHSLSKRSNVPGLRSGFVAGDAALLKK 266
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 25.6 bits (56), Expect = 4.7
Identities = 9/56 (16%), Positives = 21/56 (37%)
Query: 35 SSLRDSVPSLQGEKVASRAQILKKAADYIQFMRRKNASHQQDIDDLKRQNAILEAQ 90
+R + A + ++ + + ++ Q+ I+ L + NA L Q
Sbjct: 64 DKVRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119
>gnl|CDD|226683 COG4230, COG4230, Delta 1-pyrroline-5-carboxylate dehydrogenase
[Energy production and conversion].
Length = 769
Score = 25.1 bits (55), Expect = 6.8
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 34 FSSLRDSVPSLQGEKVASRAQILKKAADYIQ 64
+ + P A RA IL++AAD ++
Sbjct: 156 LEAAVAAAPIWSATPPAERAAILERAADLME 186
>gnl|CDD|219897 pfam08549, SWI-SNF_Ssr4, Fungal domain of unknown function
(DUF1750). This is a fungal domain of unknown function.
Length = 669
Score = 25.0 bits (54), Expect = 6.9
Identities = 8/39 (20%), Positives = 19/39 (48%)
Query: 52 RAQILKKAADYIQFMRRKNASHQQDIDDLKRQNAILEAQ 90
++ KK AD + + H + ++ R +A+ +A+
Sbjct: 366 ADRVAKKVADMTAEIEKLKKRHARRMEKFNRTSALKDAE 404
>gnl|CDD|117915 pfam09373, PMBR, Pseudomurein-binding repeat.
Methanothermobacter thermautotrophicus is a
methanogenic Gram-positive microorganism with a cell
wall consisting of pseudomurein. This repeat
specifically binds to pseudomurein. This repeat is
found at the N terminus of PeiW and PeiP which are
pseudomurein binding phage proteins.
Length = 33
Score = 23.2 bits (51), Expect = 8.1
Identities = 4/18 (22%), Positives = 8/18 (44%)
Query: 51 SRAQILKKAADYIQFMRR 68
S + L A+ + F+
Sbjct: 6 SYEEYLDMASRVLNFIES 23
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 24.9 bits (54), Expect = 8.6
Identities = 20/80 (25%), Positives = 36/80 (45%)
Query: 3 DDERDYDIESAEKRAHHNALERKRRDHIKDSFSSLRDSVPSLQGEKVASRAQILKKAADY 62
RD S E+ ++ R RR + S SLR S ++ R++ ++ +
Sbjct: 32 SRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQH 91
Query: 63 IQFMRRKNASHQQDIDDLKR 82
+ +R ++ S+Q DD KR
Sbjct: 92 RRRLRDRSPSNQWRKDDKKR 111
>gnl|CDD|222785 PHA00368, PHA00368, internal virion protein D.
Length = 1315
Score = 24.7 bits (54), Expect = 8.7
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 10 IESAEKRAHHNALERKRRDHIKDSFSSLRDSV--PSLQG 46
IE E +A+ ERK D +K+ F R+ + P++ G
Sbjct: 605 IERPELQANLTKAERKVMDILKEHFDLKREMMENPAIFG 643
>gnl|CDD|221798 pfam12831, FAD_oxidored, FAD dependent oxidoreductase. This family
of proteins contains FAD dependent oxidoreductases and
related proteins.
Length = 415
Score = 24.4 bits (54), Expect = 8.9
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 49 VASRAQILKKAADYIQFMRR 68
+ R QI + Y+ +R
Sbjct: 247 IEGREQIRDEHKRYLLGLRY 266
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 0.127 0.336
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,533,442
Number of extensions: 363719
Number of successful extensions: 520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 62
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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: 41 (21.5 bits)
S2: 53 (24.1 bits)