RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14439
(245 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 66.7 bits (164), Expect = 5e-15
Identities = 23/56 (41%), Positives = 37/56 (66%), Gaps = 5/56 (8%)
Query: 79 RREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFL 134
RR+AH + E++RRD I ++ L++L+PT KLSKA +L+ +I+YI+ L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPNK-----KLSKAEILRLAIEYIKHL 51
>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 = 65.7 bits (161), Expect = 2e-14
Identities = 25/64 (39%), Positives = 41/64 (64%), Gaps = 4/64 (6%)
Query: 76 KERRREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLV 135
++ RREAH E++RR+ I +D L+ L+PT + KLSKA +L+K++DYI+ L
Sbjct: 1 RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSK----KLSKAEILRKAVDYIKSLQ 56
Query: 136 QQKK 139
+ +
Sbjct: 57 ELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 58.0 bits (141), Expect = 1e-11
Identities = 20/55 (36%), Positives = 35/55 (63%), Gaps = 4/55 (7%)
Query: 86 AEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQKKK 140
E++RR I + +D L+ L+PT + KLSKA +L+ +I+YI+ L ++ +K
Sbjct: 3 RERRRRRKINEAFDELRSLLPTLPKNK----KLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 30.1 bits (68), Expect = 1.2
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 134 LVQQKKKLEEERNGLRKEVVALRIMQANYDIMVKAQ 169
LV+ + EEE LRKE+ L + + + +
Sbjct: 179 LVKALDEAEEELANLRKELRQLEKEKQRLERLRRLL 214
>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 = 1.2
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 113 SSGYKLSKATVLQKSIDYIQFLVQQKKKLEEERNGLRKEVVALRIMQANYDIMVKAQQTP 172
S + + KA ++ ++ Q+ KKLEEE+ L K V L + + ++
Sbjct: 107 SVAFGMRKALQAEQGKSELE---QEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQ- 162
Query: 173 LGQTEARLSDEVKF 186
E R +DE+ F
Sbjct: 163 --IEEKRHADEIAF 174
>gnl|CDD|165563 PHA03308, PHA03308, transcriptional regulator ICP4; Provisional.
Length = 1463
Score = 29.8 bits (66), Expect = 1.9
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 28 AEPISPNSMVSYSRSNSNGSFQSASNNVGNNSSSS-GHEDEESGSPLNYKERRREAHTQA 86
A + P +S S S + S S+S++ ++SSSS EE G N KE R A
Sbjct: 1235 AGAMPPCPDLSESSSTMHSSSSSSSSSCSSSSSSSDSSSSEEDGDEKNEKEDRERAGGGK 1294
Query: 87 EQKR-----RDAIKKGYD 99
+ R RD + +G D
Sbjct: 1295 RRGRQRLPIRDRVYRGRD 1312
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 29.0 bits (66), Expect = 2.1
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 77 ERRREAHTQAEQKRRDAIKKG 97
E RRE +AE+K +A ++G
Sbjct: 45 EERREVREEAEEKYEEAKEEG 65
>gnl|CDD|215270 PLN02490, PLN02490, MPBQ/MSBQ methyltransferase.
Length = 340
Score = 29.1 bits (65), Expect = 2.4
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 4 GSLNSDLH-SHLPSINEVGSDRNMKAEPISPNSMVSYSRSNSNGSF 48
G SDLH P S R+ + ++ S SR S F
Sbjct: 24 GFSGSDLHGRSFPKKLLSSSRRSPRLRTLAARCSSSSSRPASQPRF 69
>gnl|CDD|219500 pfam07655, Secretin_N_2, Secretin N-terminal domain. This is a
short domain found in bacterial type II/III secretory
system proteins. The architecture of these proteins
suggest that this family may be functionally analogous
to pfam03958.
Length = 95
Score = 27.3 bits (61), Expect = 2.8
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 35 SMVSYSRSNSNGSFQSASNNVGNNSSSSG 63
VS S SNS+ S ++SN ++SSSSG
Sbjct: 24 GSVSSSGSNSSSSSSNSSNGGSSSSSSSG 52
Score = 25.8 bits (57), Expect = 9.2
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 25 NMKAEPISPNSMVS--YSRSNSNGSFQSASNNVGNNSSSSGHEDEESGS 71
NMK S S+ S S S SN S S++++ G +SSSS D SG+
Sbjct: 10 NMKRSGSSNTSVTSGSVSSSGSNSSSSSSNSSNGGSSSSSSSGDSSSGT 58
>gnl|CDD|198358 cd07781, FGGY_RBK, Ribulokinases; belongs to the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial ribulokinases (RBK) which catalyze
the MgATP-dependent phosphorylation of L(or D)-ribulose
to produce L(or D)-ribulose 5-phosphate and ADP. RBK
also phosphorylates a variety of other sugar substrates
including ribitol and arabitol. The reason why L-RBK can
phosphorylate so many different substrates is not yet
clear. The presence of Mg2+ is required for catalytic
activity. This group belongs to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 498
Score = 28.7 bits (65), Expect = 2.9
Identities = 16/75 (21%), Positives = 23/75 (30%), Gaps = 11/75 (14%)
Query: 109 HQTDSSGYKLSKATVLQKSIDYIQFLVQQKKKLEEERNGLRKEVVALRIMQANYD----- 163
L LQ DYI+ L ++ +E +VV + + D
Sbjct: 36 GVMGEYLPDLPPNQALQHPADYIEGLETAIPEVLKEAGVDPDDVVGIGV-----DTTGST 90
Query: 164 -IMVKAQQTPLGQTE 177
I V TPL
Sbjct: 91 PIPVDEDGTPLCLLP 105
>gnl|CDD|227578 COG5253, MSS4, Phosphatidylinositol-4-phosphate 5-kinase [Signal
transduction mechanisms].
Length = 612
Score = 28.8 bits (64), Expect = 3.2
Identities = 21/118 (17%), Positives = 39/118 (33%), Gaps = 9/118 (7%)
Query: 16 SINEVGSDRNMKAEPISPNSMVSYSRSNSNGSFQSASNNVGNNSSSSGHEDEESGSPLNY 75
+ +DR+M + + S +N N + + + S H+
Sbjct: 19 DKSTRPNDRSMSNDSSLCGLNQA-SDANGNEYSPNNKVSKKDTFSDQLHDALSK--EFTL 75
Query: 76 KERRREAHTQAEQKRR------DAIKKGYDSLQDLVPTCHQTDSSGYKLSKATVLQKS 127
+ R + + I + + + +D V + T SSG LS A V S
Sbjct: 76 ERERDRLQLNKRKYQAIRLQTSTPIVEIFKNNKDAVDPPNHTRSSGNNLSNANVKTLS 133
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 28.5 bits (64), Expect = 4.2
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 8/85 (9%)
Query: 117 KLSKATVLQKSIDYIQFLVQQKKKLEEERNGLRKEVVALRIMQANYD-----IMVKAQQT 171
K + + Q + + + L ++ KKLE + E+ L + Q
Sbjct: 274 KFERDKIKQLASELEKKLEKELKKLENKLEKQEDELEELEKAAEELRQKGELLYANLQLI 333
Query: 172 PLGQTEARLSDEVKFQVFQSIMDEL 196
G RL+D F + I EL
Sbjct: 334 EEGLKSVRLAD---FYGNEEIKIEL 355
>gnl|CDD|236965 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase
subunit C/D; Provisional.
Length = 575
Score = 28.3 bits (64), Expect = 4.4
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 1 MARGSLNSDLHSHLPSINEVGSD 23
+ RGSL SDL +L SI+ V SD
Sbjct: 550 VIRGSLVSDLIVYLGSIDFVMSD 572
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 28.0 bits (63), Expect = 5.1
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 77 ERRREAHTQAEQKRRDAIKKG 97
E RRE +AE+K +A++KG
Sbjct: 92 EERREIREEAEEKWEEALEKG 112
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 28.0 bits (63), Expect = 5.7
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 6/73 (8%)
Query: 115 GYKLSKATVLQKSIDYIQFLVQQKKKLEEERNGLRKEVVALRIMQANYD-----IMVKAQ 169
K + V QK D + + + +KLE++ L KE+ + NY +
Sbjct: 282 SKKAERDRVKQKRSDLEKRVENELEKLEKKLEKLEKELEEAENAE-NYRLYGELLTANLY 340
Query: 170 QTPLGQTEARLSD 182
G E L +
Sbjct: 341 AIKKGMKEVELPN 353
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and
archaea also match the model The seed members used to
make the model include Nitrate reductases from
Pseudomonas fluorescens (GP:11344601), E.coli and
B.subtilis. All seed members are experimentally
characterized. Some unpublished nitrate reductases, that
are shorter sequences, and probably fragments fall in
between the noise and trusted cutoffs. Pfam models
pfam00384 (Molybdopterin oxidoreductase) and
pfam01568(Molydopterin dinucleotide binding domain) will
also match the nitrate reductase, alpha subunit [Energy
metabolism, Anaerobic].
Length = 1235
Score = 28.0 bits (62), Expect = 6.0
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 12 SHLPSINEVGSDRNMKAEPISPNSMVSYS 40
S++ ++ G DR + PI SMVSY+
Sbjct: 172 SNVYTVKNYGPDRVVGFSPIPAMSMVSYA 200
>gnl|CDD|218712 pfam05710, Coiled, Coiled coil. This region is found in a group
of Dictyostelium discoideum proteins. It is likely to
form a coiled-coil. Some of the proteins are regulated
by cyclic AMP and are expressed late in development.
Length = 90
Score = 26.0 bits (57), Expect = 7.6
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 31 ISPNSMVSYSRSNSNGSFQSASNNVGNNSSSSG 63
IS S +S SF S+S ++G+NS + G
Sbjct: 7 ISSIGNSKSSSKSSISSFGSSSLSMGSNSIACG 39
>gnl|CDD|129272 TIGR00168, infC, translation initiation factor IF-3. infC uses
abnormal initiation codons such as AUA, AUC, and CUG
which render its expression particularly sensitive to
excess of its gene product IF-3 thereby regulating its
own expression [Protein synthesis, Translation factors].
Length = 165
Score = 27.0 bits (60), Expect = 8.1
Identities = 27/112 (24%), Positives = 46/112 (41%), Gaps = 33/112 (29%)
Query: 89 KRRDAIKKGYDSLQDLV--------PTCHQTDSSGYKLSKATVLQKSIDYIQFLVQQKKK 140
R +A++ ++ DLV P C K +DY ++ +Q+KK
Sbjct: 24 SREEALEIAEEAGLDLVLISPNAKPPVC-----------------KIMDYGKYKYEQEKK 66
Query: 141 LEEERNGLR----KEVVALRIMQANYDIMVKAQQTPLGQTEARLSDEVKFQV 188
+E + + KEV +R +D+ K +Q + E D+VKF V
Sbjct: 67 KKEAKKNQKIIQVKEVK-MRPTIDEHDLQFKLKQA-IRFLEK--GDKVKFTV 114
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 27.3 bits (60), Expect = 8.8
Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 1/104 (0%)
Query: 77 ERRREAHTQAEQKRRDAIKKGYDSLQDLVPTCHQTDSSGYKLSK-ATVLQKSIDYIQFLV 135
++ R+ Q+ A + + Q+L Q +L A ++ Q L
Sbjct: 112 QKARQEREAVRQELAAARQNLAKAQQELARLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQ 171
Query: 136 QQKKKLEEERNGLRKEVVALRIMQANYDIMVKAQQTPLGQTEAR 179
+K+L+ L+ +V+ L++ A + + T +AR
Sbjct: 172 ASQKQLQASATQLKSQVLDLKLRSAQIEQEAQNLATRANAAQAR 215
>gnl|CDD|221244 pfam11818, DUF3340, C-terminal domain of tail specific protease
(DUF3340). This presumed domain is found at the
C-terminus of tail specific proteases. Its function is
unknown. This family is found in bacteria and
eukaryotes. This presumed domain is typically between 88
to 187 amino acids in length.
Length = 139
Score = 26.4 bits (59), Expect = 9.2
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 72 PLNYKERRREAHTQAEQKRRDAIKKGYDSL 101
LN ER+ E + E+KR + +L
Sbjct: 74 SLNEAERKAE-REEDEKKRLKRENERRKAL 102
>gnl|CDD|185600 PTZ00410, PTZ00410, NAD-dependent SIR2; Provisional.
Length = 349
Score = 27.1 bits (60), Expect = 9.4
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 38 SYSRSNSNGSFQSASNNVGNNSSSS 62
S ++ + S S S++ + SSSS
Sbjct: 261 SVAKEGRSSSSSSRSSSDSSTSSSS 285
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 26.9 bits (60), Expect = 9.5
Identities = 10/44 (22%), Positives = 19/44 (43%)
Query: 139 KKLEEERNGLRKEVVALRIMQANYDIMVKAQQTPLGQTEARLSD 182
KK + E L K + AL I + + V ++ + + R+
Sbjct: 34 KKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKR 77
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 27.4 bits (61), Expect = 9.9
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 12 SHLPSINEVGSDRNMKAEPISPNSMVSYS 40
+++ +I G DR PI SMVSY+
Sbjct: 174 ANVYTIKTYGPDRVAGFSPIPAMSMVSYA 202
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
0.310 0.124 0.341
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,566,486
Number of extensions: 1031639
Number of successful extensions: 970
Number of sequences better than 10.0: 1
Number of HSP's gapped: 941
Number of HSP's successfully gapped: 56
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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 (21.8 bits)
S2: 58 (26.0 bits)