RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11948
(167 letters)
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 78.7 bits (195), Expect = 1e-18
Identities = 26/62 (41%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ ++R +Y GF+ PT IQ+ +P LL+ +D++G A+TGSGKT AF IPIL +
Sbjct: 4 LGLSPELLRGIYALGFEKPTPIQARAIP-PLLSGRDVIGQAQTGSGKTAAFLIPILEKLD 62
Query: 67 NK 68
Sbjct: 63 PS 64
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription
/ Translation, ribosomal structure and biogenesis].
Length = 513
Score = 76.0 bits (187), Expect = 1e-16
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
E+ + +++AL GF+ PT IQ +P +LA +D++G A+TG+GKT AF +P
Sbjct: 28 PPEFASLGLSPELLQALKDLGFEEPTPIQLAAIP-LILAGRDVLGQAQTGTGKTAAFLLP 86
Query: 61 ILTGIVNKLENPT 73
+L I+ +E
Sbjct: 87 LLQKILKSVERKY 99
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 62.5 bits (152), Expect = 5e-12
Identities = 30/64 (46%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 5 VKFN---IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
V F P+ I+++L GF PT IQ P AL R D++G AETGSGKTLAF +P
Sbjct: 130 VSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGR-DMIGIAETGSGKTLAFLLPA 188
Query: 62 LTGI 65
+ I
Sbjct: 189 IVHI 192
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 57.3 bits (139), Expect = 3e-10
Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ E+++ AL KG+ PT IQ+ +P AL R D++G+A TG+GKT AF +P L
Sbjct: 6 LELDESLLEALQDKGYTRPTAIQAEAIPPALDGR-DVLGSAPTGTGKTAAFLLPAL 60
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 54.4 bits (131), Expect = 1e-09
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 17 LYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+ + GF+ Q + + L +D++ AA TGSGKTLA +P L
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPAL 46
Score = 43.2 bits (102), Expect = 1e-05
Identities = 24/88 (27%), Positives = 29/88 (32%), Gaps = 40/88 (45%)
Query: 80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEES 139
S +D++ AA TGSGKTLA +P L
Sbjct: 22 SGLRDVILAAPTGSGKTLAALLPALE---------------------------------- 47
Query: 140 ANTTEFVKKTRNKLYALILAPTRELAIQ 167
K L+L PTRELA Q
Sbjct: 48 ------ALKRGKGGRVLVLVPTRELAEQ 69
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 53.0 bits (128), Expect = 2e-09
Identities = 21/37 (56%), Positives = 28/37 (75%), Gaps = 1/37 (2%)
Query: 26 TKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
T IQ+ +P A+L+ KD++ A TGSGKTLAF +PIL
Sbjct: 1 TPIQAQAIP-AILSGKDVLVQAPTGSGKTLAFLLPIL 36
Score = 50.0 bits (120), Expect = 3e-08
Identities = 26/85 (30%), Positives = 33/85 (38%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
KD++ A TGSGKTLAF +PIL
Sbjct: 15 KDVLVQAPTGSGKTLAFLLPIL-------------------------------------- 36
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
+ + + AL+LAPTRELA Q
Sbjct: 37 -QALLPKKGGPQALVLAPTRELAEQ 60
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 52.7 bits (127), Expect = 1e-08
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 6/71 (8%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F + ++ AL +KGF T IQ++ +P LA +D+ G A+TG+GKT+AF LT
Sbjct: 13 FALHPQVVEALEKKGFHNCTPIQALALP-LTLAGRDVAGQAQTGTGKTMAF----LTATF 67
Query: 67 NKL-ENPTEED 76
+ L +P ED
Sbjct: 68 HYLLSHPAPED 78
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 52.9 bits (127), Expect = 1e-08
Identities = 25/60 (41%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENP 72
I+ AL G++ P+ IQ+ +P LL +D++G A+TGSGKT AF +P+L + +L+ P
Sbjct: 17 ILEALNDLGYEKPSPIQAECIPH-LLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAP 75
Score = 42.1 bits (99), Expect = 6e-05
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
+D++G A+TGSGKT AF +P+L + +L+ P
Sbjct: 44 RDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQ--------------------------- 76
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
L+LAPTRELA+Q
Sbjct: 77 ------------ILVLAPTRELAVQ 89
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 51.0 bits (122), Expect = 4e-08
Identities = 21/50 (42%), Positives = 37/50 (74%), Gaps = 1/50 (2%)
Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
I+RA+ ++G++ PT IQ +P A+L +D++ +A+TG+GKT F +P+L
Sbjct: 12 ILRAVAEQGYREPTPIQQQAIP-AVLEGRDLMASAQTGTGKTAGFTLPLL 60
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 50.9 bits (122), Expect = 4e-08
Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
+P ++ L G++ PT IQ +P+AL + + ++ +A+TGSGKT +F +PI+
Sbjct: 127 GLPPKLLLNLETAGYEFPTPIQMQAIPAAL-SGRSLLVSADTGSGKTASFLVPII 180
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 50.2 bits (121), Expect = 9e-08
Identities = 21/42 (50%), Positives = 30/42 (71%), Gaps = 1/42 (2%)
Query: 21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
G+ T IQ+ +P A+LA KD++ A+TGSGKT AFG+ +L
Sbjct: 23 GYTEMTPIQAQSLP-AILAGKDVIAQAKTGSGKTAAFGLGLL 63
Score = 45.2 bits (108), Expect = 5e-06
Identities = 26/85 (30%), Positives = 35/85 (41%), Gaps = 39/85 (45%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
KD++ A+TGSGKT AFG+ +L KL +
Sbjct: 42 KDVIAQAKTGSGKTAAFGLGLL----QKL-----------------------------DV 68
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
F ++ AL+L PTRELA Q
Sbjct: 69 KRF------RVQALVLCPTRELADQ 87
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 45.0 bits (107), Expect = 2e-06
Identities = 24/85 (28%), Positives = 31/85 (36%), Gaps = 40/85 (47%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
+D++ AA TGSGKTLA +PIL
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILE------------------------------------- 23
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
+ + L+LAPTRELA Q
Sbjct: 24 ---LLDSLKGGQVLVLAPTRELANQ 45
Score = 40.0 bits (94), Expect = 1e-04
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 41 KDIVGAAETGSGKTLAFGIPILT 63
+D++ AA TGSGKTLA +PIL
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILE 23
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 45.7 bits (108), Expect = 3e-06
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
F++ ++ L GF T IQ++ +P AL D+ G A+TG+GKTLAF L ++
Sbjct: 14 FDLHPALLAGLESAGFTRCTPIQALTLPVALPGG-DVAGQAQTGTGKTLAF----LVAVM 68
Query: 67 NKL 69
N+L
Sbjct: 69 NRL 71
Score = 40.3 bits (94), Expect = 2e-04
Identities = 30/86 (34%), Positives = 38/86 (44%), Gaps = 34/86 (39%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLEN-PTEEDENDSGLEEEAEEVLEELEEESAN 141
D+ G A+TG+GKTLAF L ++N+L + P D E+
Sbjct: 47 GDVAGQAQTGTGKTLAF----LVAVMNRLLSRPALADRK----PEDPR------------ 86
Query: 142 TTEFVKKTRNKLYALILAPTRELAIQ 167
ALILAPTRELAIQ
Sbjct: 87 -------------ALILAPTRELAIQ 99
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 43.4 bits (102), Expect = 2e-05
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
FN+ ++ A++ GF T IQ+ V+ LA D +G A+TG+GKT AF I I+ +
Sbjct: 92 FNLAPELMHAIHDLGFPYCTPIQAQVL-GYTLAGHDAIGRAQTGTGKTAAFLISIINQL- 149
Query: 67 NKLENPTEED 76
L+ P ++
Sbjct: 150 --LQTPPPKE 157
Score = 39.9 bits (93), Expect = 3e-04
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 32/85 (37%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
D +G A+TG+GKT AF I I+ + L+ P ++
Sbjct: 125 HDAIGRAQTGTGKTAAFLISIINQL---LQTPPPKE------------------------ 157
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
+ + ALI+APTREL +Q
Sbjct: 158 -----RYMGEPRALIIAPTRELVVQ 177
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 43.3 bits (102), Expect = 2e-05
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 10/76 (13%)
Query: 8 NIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
+ E ++R +Y GF+ P+ IQ + P +L D +G A++G+GKT F I L I
Sbjct: 34 KLNEDLLRGIYSYGFEKPSAIQQRGIKP--ILDGYDTIGQAQSGTGKTATFVIAALQLID 91
Query: 67 NKLEN-------PTEE 75
L PT E
Sbjct: 92 YDLNACQALILAPTRE 107
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 40.3 bits (95), Expect = 2e-04
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
FNI + +R +++ F + T Q +P + + ++++ A TGSGKT A +P++ ++
Sbjct: 5 FNILDPRVREWFKRKFTSLTPPQRYAIP-EIHSGENVLIIAPTGSGKTEAAFLPVINELL 63
Query: 67 NKLENPTE 74
+ + E
Sbjct: 64 SLGKGKLE 71
Score = 30.3 bits (69), Expect = 0.44
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 88 AAETGSGKTLAFGIPILTGIVNKLENPTE 116
A TGSGKT A +P++ +++ + E
Sbjct: 43 IAPTGSGKTEAAFLPVINELLSLGKGKLE 71
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 34.7 bits (80), Expect = 0.017
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 36 ALLARKDIVGAAETGSGKTLAFGIPIL 62
+ +++V TGSGKT +F +PIL
Sbjct: 81 LIREGRNVVVTTGTGSGKTESFLLPIL 107
Score = 34.3 bits (79), Expect = 0.024
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 83 KDIVGAAETGSGKTLAFGIPIL 104
+++V TGSGKT +F +PIL
Sbjct: 86 RNVVVTTGTGSGKTESFLLPIL 107
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 34.4 bits (79), Expect = 0.019
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 3/65 (4%)
Query: 6 KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ +IPE R L ++G + +Q + + + LL ++++ + T SGKTL I L GI
Sbjct: 198 ELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTL---IGELAGI 254
Query: 66 VNKLE 70
L
Sbjct: 255 PRLLS 259
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood
widely spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 32.8 bits (75), Expect = 0.080
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAFGI 59
A W + ++ AL G P + Q+ A LA + +V A T SGK+LA+ +
Sbjct: 15 APWPAW-AHPDVVAALEAAGIHRPWQHQARA---AELAHAGRHVVVATGTASGKSLAYQL 70
Query: 60 PILTGIV 66
P+L+ +
Sbjct: 71 PVLSALA 77
Score = 27.8 bits (62), Expect = 3.6
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 85 IVGAAETGSGKTLAFGIPILTGIV 108
+V A T SGK+LA+ +P+L+ +
Sbjct: 54 VVVATGTASGKSLAYQLPVLSALA 77
>gnl|CDD|214484 smart00043, CY, Cystatin-like domain. Cystatins are a family of
cysteine protease inhibitors that occur mainly as single
domain proteins. However some extracellular proteins
such as kininogen, His-rich glycoprotein and fetuin also
contain these domains.
Length = 107
Score = 28.2 bits (63), Expect = 1.1
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 111 LENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNK 152
L P++ ND ++E A+ + E ++S + E
Sbjct: 3 LGGPSDVPPNDPEVQEAADFAVAEYNKKSNDKYELRVIKVVS 44
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 28.6 bits (64), Expect = 1.6
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 26 TKIQSMVMPSALLARKDIVGAAETGSGKT 54
T Q V+ A+LARK+I+ TGSGKT
Sbjct: 118 TAAQRDVLREAVLARKNILVVGGTGSGKT 146
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 28.7 bits (65), Expect = 1.6
Identities = 15/59 (25%), Positives = 27/59 (45%)
Query: 107 IVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELA 165
I +L +E+ LE+E +++ EL E + + KK +L + A + LA
Sbjct: 330 IKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSAIRKKAAKELEKEVTAELKALA 388
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 28.6 bits (64), Expect = 1.7
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 6 KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
+ + E I R L ++G + Q+ + S +L K++V A T SGKTL I +
Sbjct: 5 ELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEI----VM 60
Query: 66 VNKL 69
VNKL
Sbjct: 61 VNKL 64
>gnl|CDD|187773 cd09642, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-C subtype; also known as Csd1 family.
Length = 574
Score = 28.1 bits (63), Expect = 2.4
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 10/60 (16%)
Query: 112 ENPTEEDENDSGLEEEAEEVLEE----LEEESANTTEFVKK------TRNKLYALILAPT 161
++ TEEDE LEE ++ L + +KK + Y L L+
Sbjct: 271 DDSTEEDELFLSLEEPPDDDLLPDSRAATALDDRAGKRIKKGQPLRLDDTRFYVLGLSAN 330
>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890). This
family is conserved in dsDNA adenoviruses of
vertebrates. The function is not known.
Length = 172
Score = 27.6 bits (61), Expect = 2.9
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 115 TEEDENDSGLEEEAEEVLEELEEESANT 142
ED DS L+EE EE EE+EEE+A +
Sbjct: 37 EMEDWEDS-LDEEDEE-AEEVEEETAAS 62
>gnl|CDD|215481 PLN02889, PLN02889, oxo-acid-lyase/anthranilate synthase.
Length = 918
Score = 27.9 bits (62), Expect = 3.0
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
L E S TT+++ T KL L + TR+L +Q
Sbjct: 591 LHEGSTATTQWLDDTEQKLLGLKASATRKLEVQ 623
>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. The Xeroderma pigmentosum complementation
group G (XPG) nuclease plays a central role in
nucleotide excision repair (NER) in cleaving DNA bubble
structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. Members of this subgroup include the
H3TH (helix-3-turn-helix) domains of XPG and other
similar eukaryotic 5' nucleases. These nucleases contain
a PIN (PilT N terminus) domain with a helical arch/clamp
region/I domain (not included here) and inserted within
the PIN domain is an atypical helix-hairpin-helix-2
(HhH2)-like region. This atypical HhH2 region, the H3TH
domain, has an extended loop with at least three turns
between the first two helices, and only three of the
four helices appear to be conserved. Both the H3TH
domain and the helical arch/clamp region are involved in
DNA binding. Studies suggest that a glycine-rich loop
in the H3TH domain contacts the phosphate backbone of
the template strand in the downstream DNA duplex. These
nucleases have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+ or Mn2+) required for nuclease activity.
The first metal binding site is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site is composed generally of two
Asp residues from the PIN domain and one Asp residue
from the H3TH domain. Together with the helical arch and
network of amino acids interacting with metal binding
ions, the H3TH region defines a positively charged
active-site DNA-binding groove in structure-specific 5'
nucleases.
Length = 97
Score = 26.4 bits (59), Expect = 3.1
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 106 GIVNKLENPTEEDENDSGLEEEAEEVLEE----LEEESANTTEFVKKTRNKLYALILAPT 161
G VN +E +E + LE+ + E+ + EF +K +N L LIL P
Sbjct: 22 GPVNAMEILSEFP-GEEDLEKFKDWWENAQPEKSEDSDNDKQEFKRKHKNYLKNLILPPG 80
>gnl|CDD|220785 pfam10498, IFT57, Intra-flagellar transport protein 57. Eukaryotic
cilia and flagella are specialised organelles found at
the periphery of cells of diverse organisms.
Intra-flagellar transport (IFT) is required for the
assembly and maintenance of eukaryotic cilia and
flagella, and consists of the bidirectional movement of
large protein particles between the base and the distal
tip of the organelle. IFT particles contain multiple
copies of two distinct protein complexes, A and B, which
contain at least 6 and 11 protein subunits. IFT57 is
part of complex B but is not, however, required for the
core subunits to stay associated. This protein is known
as Huntington-interacting protein-1 in humans.
Length = 355
Score = 27.7 bits (62), Expect = 3.1
Identities = 14/30 (46%), Positives = 22/30 (73%)
Query: 109 NKLENPTEEDENDSGLEEEAEEVLEELEEE 138
+ + P EEDE ++ E++AE +LEE+EEE
Sbjct: 122 KRPKYPNEEDEEENVDEDDAEIILEEVEEE 151
>gnl|CDD|223520 COG0443, DnaK, Molecular chaperone [Posttranslational modification,
protein turnover, chaperones].
Length = 579
Score = 27.7 bits (62), Expect = 3.5
Identities = 25/111 (22%), Positives = 42/111 (37%), Gaps = 1/111 (0%)
Query: 44 VGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPI 103
V A + G+GK + I +G+ ++ ED +A D + I
Sbjct: 462 VTAKDLGTGKEQSITIKASSGLSDEEIERMVEDAEANAALDKKFRELVEARNEAESLIYS 521
Query: 104 LTGIVNKLEN-PTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKL 153
L + ++ EE E + EE LE +EE E +++ KL
Sbjct: 522 LEKALKEIVKVSEEEKEKIEEAITDLEEALEGEKEEIKAKIEELQEVTQKL 572
>gnl|CDD|172360 PRK13833, PRK13833, conjugal transfer protein TrbB; Provisional.
Length = 323
Score = 27.5 bits (61), Expect = 4.0
Identities = 14/29 (48%), Positives = 21/29 (72%)
Query: 26 TKIQSMVMPSALLARKDIVGAAETGSGKT 54
T+ Q+ V+ SA+ +R +IV + TGSGKT
Sbjct: 130 TEAQASVIRSAIDSRLNIVISGGTGSGKT 158
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 27.0 bits (60), Expect = 4.7
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKT-----LAFGIPILTGIV 66
+ T + Q+ + A+ ARK I+ T SGKT L IP IV
Sbjct: 124 EYGTISPEQAAYLWLAIEARKSIIICGGTASGKTTLLNALLDFIPPEERIV 174
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 27.3 bits (60), Expect = 5.0
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 112 ENPTEEDENDSGLEEEAEEVLEELEEE 138
++ EE+E + EEE EE EE EEE
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEE 888
Score = 27.3 bits (60), Expect = 5.5
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 112 ENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP 160
E EE+E + EEE EE EE E E + E+ + + + L L P
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQAIYLFLLP 913
>gnl|CDD|225152 COG2243, CobF, Precorrin-2 methylase [Coenzyme metabolism].
Length = 234
Score = 26.9 bits (60), Expect = 5.6
Identities = 17/61 (27%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 84 DIVGAAETGSGKTLAFGI--PILTGIVNKLE-----NPTEEDENDSGLEEEAEEVLEELE 136
D+V +LA I LT +E +E + EE A EV ELE
Sbjct: 29 DVVYVPSKKGKGSLAREIVEDYLTPGSRIVELHFPMTTDMREELEDAWEEAAAEVAAELE 88
Query: 137 E 137
Sbjct: 89 A 89
>gnl|CDD|150797 pfam10171, DUF2366, Uncharacterized conserved protein (DUF2366).
This is a family of proteins conserved from nematodes to
humans. The function is not known.
Length = 173
Score = 26.6 bits (59), Expect = 5.6
Identities = 11/66 (16%), Positives = 22/66 (33%)
Query: 83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
+D V A K + + L NP E+ D L+ +L + +
Sbjct: 33 RDTVKGARERPLKASVYLSLLGGLYYCCLTNPDEDSFMDQLLDASNRLLLVPPTIRNPTS 92
Query: 143 TEFVKK 148
+ ++
Sbjct: 93 DKHLQT 98
>gnl|CDD|153128 cd02437, CCC1_like_1, CCC1-related protein family. CCC1_like_1:
This is a protein family closely related to CCC1, a
family of proteins involved in iron and manganese
transport. Yeast CCC1 is a vacuole transmembrane protein
responsible for the iron and manganese accumulation in
vacuole. .
Length = 175
Score = 26.6 bits (59), Expect = 5.6
Identities = 15/50 (30%), Positives = 22/50 (44%)
Query: 95 KTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTE 144
G GI N L E+ + G+ EE E++L LE+ +T E
Sbjct: 36 IAAGLGGAFALGISNGLGAAVAEEGSLRGMLEEKEKILLRLEQMLTSTRE 85
>gnl|CDD|223252 COG0174, GlnA, Glutamine synthetase [Amino acid transport and
metabolism].
Length = 443
Score = 26.8 bits (60), Expect = 5.7
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 10/47 (21%)
Query: 103 ILTGIVNKLENPTEEDENDSGLEEEA----------EEVLEELEEES 139
L GI NKLE D N L E E L+ LE+
Sbjct: 357 GLDGIENKLEPGEPVDGNLYELSPEERKEPTLPASLREALDALEDSE 403
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 26.9 bits (60), Expect = 5.8
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 35 SALLARKDIVGAAETGSGKTLAFGIP--ILTGIV 66
ALL+ KD + TG GK+L + IP +L G+
Sbjct: 27 DALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLT 60
>gnl|CDD|182965 PRK11103, PRK11103, PTS system mannose-specific transporter subunit
IID; Provisional.
Length = 282
Score = 26.6 bits (59), Expect = 6.0
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 3 EWVKFNIPETIIRALYQKGFKTPTKIQSM---VMP 34
+W NIP + Q G T +Q++ +MP
Sbjct: 206 KWTHVNIPLVVSTITDQDGKTHVTTVQTILDQLMP 240
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 26.5 bits (59), Expect = 6.3
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 36 ALLARKDIVGAAETGSGKT 54
A+ ARK+I+ + TGSGKT
Sbjct: 21 AVEARKNILISGGTGSGKT 39
>gnl|CDD|107203 cd01560, Thr-synth_2, Threonine synthase catalyzes the final step
of threonine biosynthesis. The conversion of
O-phosphohomoserine into threonine and inorganic
phosphate is pyridoxal 5'-phosphate dependent. The
Thr-synth_1 CD includes members from higher plants,
cyanobacteria, archaebacteria and eubacterial groups.
This CD, Thr-synth_2, includes enzymes from fungi and
eubacterial groups, as well as, metazoan threonine
synthase-like proteins.
Length = 460
Score = 26.8 bits (60), Expect = 6.4
Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 2 AEWVKFNIPETIIRALYQKGFKTPTKIQS 30
A KF PE + AL ++ + P +++
Sbjct: 413 AHPAKF--PEAVKEALGEEPVELPEELEG 439
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 26.5 bits (59), Expect = 6.5
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 36 ALLARKDIVGAAETGSGKT 54
A+ +RK+I+ + TGSGKT
Sbjct: 140 AIASRKNIIISGGTGSGKT 158
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 26.8 bits (60), Expect = 6.6
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 111 LENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKL----YALILAPTRELAI 166
LE E E + + EEA+E EE E + E V + +++L AL + TR AI
Sbjct: 357 LEELEERLEEQNEVVEEADEQQEENEARAEAAEEEVDELKSQLADYQQALDVQQTR--AI 414
Query: 167 Q 167
Q
Sbjct: 415 Q 415
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 26.7 bits (60), Expect = 6.6
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 125 EEEAEEVLEELEEESANTTEFVKKTRNK 152
EE+ +E+L EL+++ ++ KK R +
Sbjct: 221 EEDVKEILAELKKKDFKVSKVKKKERKR 248
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 26.7 bits (59), Expect = 7.8
Identities = 15/51 (29%), Positives = 19/51 (37%)
Query: 104 LTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLY 154
L + K E EE + EE EE EE + E V NK +
Sbjct: 276 LKELKEKKEEKDEEKSEEVKTEEVDEEFEEEEKGFYYELYEKVNIEANKKF 326
>gnl|CDD|239656 cd03684, ClC_3_like, ClC-3-like chloride channel proteins. This CD
includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was
initially cloned from rat kidney. Expression of ClC-3
produces outwardly-rectifying Cl currents that are
inhibited by protein kinase C activation. It has been
suggested that ClC-3 may be a ubiquitous
swelling-activated Cl channel that has very similar
characteristics to those of native volume-regulated Cl
currents. The function of ClC-4 is unclear. Studies of
human ClC-4 have revealed that it gives rise to Cl
currents that rapidly activate at positive voltages, and
are sensitive to extracellular pH, with currents
decreasing when pH falls below 6.5. ClC-4 is broadly
distributed, especially in brain and heart. ClC-5 is
predominantly expressed in the kidney, but can be found
in the brain and liver. Mutations in the ClC-5 gene
cause certain hereditary diseases, including Dent's
disease, an X-chromosome linked syndrome characterised
by proteinuria, hypercalciuria, and kidney stones
(nephrolithiasis), leading to progressive renal failure.
These proteins belong to the ClC superfamily of
chloride ion channels, which share the unique
double-barreled architecture and voltage-dependent
gating mechanism. The gating is conferred by the
permeating anion itself, acting as the gating charge.
This domain is found in the eukaryotic halogen ion (Cl-
and I-) channel proteins, that perform a variety of
functions including cell volume regulation, the membrane
potential stabilization, transepithelial chloride
transport and charge compensation necessary for the
acidification of intracellular organelles.
Length = 445
Score = 26.4 bits (59), Expect = 7.9
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 77 ENDSARKDIVGAAETGSGKTLAFGIPI 103
N++ R++I+ AA +G +AFG PI
Sbjct: 122 RNEAKRREILSAA-AAAGVAVAFGAPI 147
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 26.7 bits (60), Expect = 8.1
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 47 AETGSGKTLAFGIPILTGIVNKLENPTE 74
A TGSGKTLA +P L + E P +
Sbjct: 35 APTGSGKTLAGFLPSLIDLAGP-EKPKK 61
Score = 26.7 bits (60), Expect = 8.1
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 89 AETGSGKTLAFGIPILTGIVNKLENPTE 116
A TGSGKTLA +P L + E P +
Sbjct: 35 APTGSGKTLAGFLPSLIDLAGP-EKPKK 61
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 26.3 bits (58), Expect = 8.6
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 112 ENPTEEDENDSGLEEEAEEVLEELEEE 138
E+ EEDE D EEE EE E+ +++
Sbjct: 166 EDVDEEDEKDEEEEEEEEEEDEDFDDD 192
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 26.6 bits (59), Expect = 9.8
Identities = 19/88 (21%), Positives = 31/88 (35%)
Query: 66 VNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLE 125
+LE + E ++ D + + L L + +LE E E
Sbjct: 315 ERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRL 374
Query: 126 EEAEEVLEELEEESANTTEFVKKTRNKL 153
EE EE LE L + A + N++
Sbjct: 375 EELEEQLETLRSKVAQLELQIASLNNEI 402
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
0.309 0.130 0.347
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,824,032
Number of extensions: 841064
Number of successful extensions: 2265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2184
Number of HSP's successfully gapped: 207
Length of query: 167
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 77
Effective length of database: 6,945,742
Effective search space: 534822134
Effective search space used: 534822134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (24.7 bits)