RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4036
(93 letters)
>gnl|CDD|218688 pfam05680, ATP-synt_E, ATP synthase E chain. This family
consists of several ATP synthase E chain sequences
which are components of the CF(0) subunit.
Length = 83
Score = 71.4 bits (175), Expect = 4e-18
Identities = 36/79 (45%), Positives = 48/79 (60%)
Query: 4 PPPVSVSPLIKFARWTMLSAGILYGVSRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKR 63
PPV+VSPLI R++ L AG++YG Q SL+KKEEK+R AQ+K I+ AK A KK+
Sbjct: 1 MPPVAVSPLINVLRYSALVAGVVYGAKHQRSLKKKEEKIREYEAQEKLIEKAKAAYAKKK 60
Query: 64 ANEVSRISLKKNHVAIFII 82
+ SL + A F
Sbjct: 61 QAKQEAKSLAEGSSAPFDE 79
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 29.5 bits (67), Expect = 0.14
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 34 SLEKKEEKLRVIRAQ-KKAIKDAKLAEEKKRANEVSRISLKKN 75
LEK+ +L +K ++ + EEK+ A+E++ LKK
Sbjct: 138 ELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIAF--LKKQ 178
>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the heterodimeric topo I from
Leishmania donvanni. Topo I enzymes are divided into:
topo type IA (bacterial) and type IB (eukaryotic). Topo
I relaxes superhelical tension in duplex DNA by creating
a single-strand nick, the broken strand can then rotate
around the unbroken strand to remove DNA supercoils and,
the nick is religated, liberating topo I. These enzymes
regulate the topological changes that accompany DNA
replication, transcription and other nuclear processes.
Human topo I is the target of a diverse set of
anticancer drugs including camptothecins (CPTs). CPTs
bind to the topo I-DNA complex and inhibit re-ligation
of the single-strand nick, resulting in the accumulation
of topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topo I play putative roles in
organizing the kinetoplast DNA network unique to these
parasites. This family may represent more than one
structural domain.
Length = 212
Score = 29.1 bits (65), Expect = 0.23
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 35 LEKKEEKLRVIRAQKKAIKDAKLAEEKK 62
L +KE+K + +KKA+K+ K E +
Sbjct: 92 LREKEKKKSRTKEEKKALKEEKDKEAEP 119
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 29.1 bits (66), Expect = 0.24
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 35 LEKKEEKLRVIRAQKKAIKDAKLAEE 60
L +KEE LRV + A D KLA+E
Sbjct: 242 LLEKEEALRV-EELQNAEFDRKLAQE 266
>gnl|CDD|217286 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 28.7 bits (65), Expect = 0.34
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKK 62
+KE+K + + +KKAIK+ K E+
Sbjct: 97 AEKEKKKAMSKEEKKAIKEEKDKLEEP 123
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 28.4 bits (64), Expect = 0.39
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 35 LEKKEEKLRVIRAQKKAIKDAKLAEEKK 62
E+KE+K + + +KKAIK+ K E+
Sbjct: 95 EEEKEKKKAMSKEEKKAIKEEKEKLEEP 122
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 28.2 bits (62), Expect = 0.66
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKK 74
+KK ++ + KK +AK AEE K+A+E + K
Sbjct: 1496 KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAK 1534
Score = 26.6 bits (58), Expect = 2.0
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 29 VSRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR 69
+ +K EEK + A+KKA + K E KK+A E +
Sbjct: 1289 KKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKK 1329
Score = 26.6 bits (58), Expect = 2.4
Identities = 14/39 (35%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 31 RQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR 69
+++ KK ++ + KKA +AK AEEKK+A+E+ +
Sbjct: 1516 KKAEEAKKADEAKKAEEAKKA-DEAKKAEEKKKADELKK 1553
Score = 26.3 bits (57), Expect = 2.5
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 30 SRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRI 70
++++ K EE + A+KKA +DA+ AEE ++A + +
Sbjct: 1103 AKKTETGKAEEARKAEEAKKKA-EDARKAEEARKAEDARKA 1142
Score = 26.3 bits (57), Expect = 3.0
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 31 RQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR 69
+ + + + + A+KKA K AEEKK+A+E +
Sbjct: 1360 EAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKK 1398
Score = 25.9 bits (56), Expect = 4.1
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKK 74
+KK ++ + KKA +AK AEE K+A+E + KK
Sbjct: 1509 KKKADEAKKAEEAKKA-DEAKKAEEAKKADEAKKAEEKK 1546
Score = 25.9 bits (56), Expect = 4.6
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 31 RQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR 69
+++ +KK ++ + +KKA + K AEE K+A+E +
Sbjct: 1284 KKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKK 1322
Score = 25.5 bits (55), Expect = 5.2
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKKRANE 66
+K EEK + A+KKA +D K A+E K+A
Sbjct: 1385 KKAEEKKKADEAKKKAEEDKKKADELKKAAA 1415
Score = 25.5 bits (55), Expect = 6.2
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 39 EEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKK 74
E K + A+KKA K AEE K+A E ++ +
Sbjct: 1319 EAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEA 1354
Score = 25.1 bits (54), Expect = 6.4
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 30 SRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSR 69
+++ + +K E R +KA +DAK AE ++A EV +
Sbjct: 1151 AKRVEIARKAEDARKAEEARKA-EDAKKAEAARKAEEVRK 1189
Score = 25.1 bits (54), Expect = 8.5
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 29 VSRQSSLEKKEEKLRVIRAQ--KKAIKDAKLAEEKKRANEVSR 69
+ L+K EE+ ++ A+ KKA +D K AEE K+A E +
Sbjct: 1646 KKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEK 1688
Score = 24.7 bits (53), Expect = 9.5
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKK 74
++ EE + +KK ++ K AEE K+A E ++I ++
Sbjct: 1696 KEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 27.6 bits (62), Expect = 0.96
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 33 SSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKKN 75
+L E K ++ + Q+KA K A+ E +K A + + K
Sbjct: 404 GNLSPAERK-KLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKK 445
Score = 25.7 bits (57), Expect = 3.6
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 33 SSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKKN 75
+ +K +K R +A+KKA K+ K+ E + K
Sbjct: 409 AERKKLRKKQR--KAEKKAEKEEAEKAAAKKKAEAAAKKAKGP 449
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 27.3 bits (60), Expect = 1.3
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLK 73
+ + ++ K+A K A+LAEEK RA E + + K
Sbjct: 7 DAGAPAVEKKQSDKEARKAARLAEEKARAAEKAALVEK 44
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 27.1 bits (61), Expect = 1.3
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 49 KKAIKDAKLAEEKKRANEVSRISLKK 74
+KAI AK E ++A E++R
Sbjct: 374 EKAIAAAKAREAARKARELTRRKSAL 399
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 26.1 bits (58), Expect = 2.5
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 36 EKKEEKLRVIRAQKKAIKDAKLAEEKK 62
+KEEK + + +KKAIK K E++
Sbjct: 96 AQKEEKKAMSKEEKKAIKAEKEKLEEE 122
>gnl|CDD|215128 PLN02211, PLN02211, methyl indole-3-acetate methyltransferase.
Length = 273
Score = 26.4 bits (58), Expect = 2.6
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 51 AIKDAKLAEEKKRANEVSRISLKKNHVAIFIIHQ 84
A++ A+ EE ++V R+ +K H + Q
Sbjct: 196 ALRSARFEEETGDIDKVPRVYIKTLHDHVVKPEQ 229
>gnl|CDD|237205 PRK12792, flhA, flagellar biosynthesis protein FlhA; Reviewed.
Length = 694
Score = 25.8 bits (57), Expect = 3.5
Identities = 12/46 (26%), Positives = 22/46 (47%)
Query: 11 PLIKFARWTMLSAGILYGVSRQSSLEKKEEKLRVIRAQKKAIKDAK 56
P + FA + A + Y + R+ + E +V R ++ A +AK
Sbjct: 305 PFLPFALLGGVMAFVAYTIPRRRAARAAAEAAKVKREEESAQAEAK 350
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 25.8 bits (56), Expect = 3.7
Identities = 15/39 (38%), Positives = 26/39 (66%), Gaps = 4/39 (10%)
Query: 27 YGVSRQSSLEKKEEKL----RVIRAQKKAIKDAKLAEEK 61
+ VS ++ L++KE KL ++I AQ+KAI++ + EK
Sbjct: 93 WKVSIEAELKQKENKLQENRKIIEAQRKAIQELQFENEK 131
>gnl|CDD|223193 COG0115, IlvE, Branched-chain amino acid
aminotransferase/4-amino-4-deoxychorismate lyase [Amino
acid transport and metabolism / Coenzyme metabolism].
Length = 284
Score = 25.8 bits (57), Expect = 3.7
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 21 LSAGILYGVSRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKK---RANEVSRISLKKNHV 77
LS GIL G++R S LE +E + + ++D K A+E A V+ + L V
Sbjct: 203 LSGGILPGITRDSLLELAKELGLTVEERPITLEDLKQADEVFLTNTAAGVTPVGLIDGRV 262
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 25.4 bits (56), Expect = 5.5
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 32 QSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKR 63
Q E+KE R +K ++ K +E ++
Sbjct: 554 QREKEEKEALKEQKRLRKLKKQEEKKKKELEK 585
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 25.4 bits (56), Expect = 5.8
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 30 SRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLK 73
S Q ++E+ EK+ ++K A K A AE+ +R +
Sbjct: 1 SSQEAVEESGEKI----SKKAAKKAAAKAEKLRREATAKAAAAS 40
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 25.0 bits (54), Expect = 7.1
Identities = 14/57 (24%), Positives = 25/57 (43%)
Query: 19 TMLSAGILYGVSRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVSRISLKKN 75
++LS+ I V RQ L++K +R A +K I+ + N+ + L
Sbjct: 317 SLLSSDIDQVVKRQLVLQQKGSDVRSFLASRKRIRQGAETLAAEEENDDNSSKLDDT 373
>gnl|CDD|216296 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 343
Score = 24.7 bits (54), Expect = 7.9
Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 3/83 (3%)
Query: 12 LIKFARWT---MLSAGILYGVSRQSSLEKKEEKLRVIRAQKKAIKDAKLAEEKKRANEVS 68
++K W ++ YG +LE + + + A + E+
Sbjct: 113 ILKHFGWKRVAVIYDDDDYGEGGLEALEDALREAGLNVVAVASEVIASDDDFTALLKELK 172
Query: 69 RISLKKNHVAIFIIHQDLQVFMK 91
I K + + DL+ ++
Sbjct: 173 DIKSKARVIVVCGSSDDLRQILR 195
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 0.131 0.351
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,597,435
Number of extensions: 370963
Number of successful extensions: 798
Number of sequences better than 10.0: 1
Number of HSP's gapped: 784
Number of HSP's successfully gapped: 120
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (21.8 bits)
S2: 53 (24.1 bits)