RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7786
(252 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 121 bits (304), Expect = 2e-31
Identities = 54/114 (47%), Positives = 74/114 (64%), Gaps = 6/114 (5%)
Query: 124 DIIRRNLRI-LVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGR 182
D IR+ I ++ G++VP SF P+ ++++L+ G +PTPIQVQG P ALSGR
Sbjct: 109 DEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGR 168
Query: 183 DIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL-PGEGPYGLIICPSRELARQ 235
D+IGIA TGSGKTL F+LP ++ Q P L G+GP L++ P+RELA Q
Sbjct: 169 DMIGIAETGSGKTLAFLLPAIVHINAQ----PLLRYGDGPIVLVLAPTRELAEQ 218
Score = 70.2 bits (172), Expect = 7e-14
Identities = 38/94 (40%), Positives = 56/94 (59%), Gaps = 7/94 (7%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFL-PGEGPYGLIICPSRELARQTHDII 66
RD+IGIA TGSGKTL F+LP ++ Q P L G+GP L++ P+RELA Q +
Sbjct: 168 RDMIGIAETGSGKTLAFLLPAIVHINAQ----PLLRYGDGPIVLVLAPTRELAEQIREQC 223
Query: 67 QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
+ A+ I R +A GGVP + +++G++
Sbjct: 224 NKFGASSKI--RNTVAYGGVPKRGQIYALRRGVE 255
>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 = 112 bits (283), Expect = 1e-30
Identities = 44/96 (45%), Positives = 58/96 (60%), Gaps = 6/96 (6%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
F + L L+R + A G +KPTPIQ + IP LSGRD+IG A TGSGKT F++PIL
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPIL-- 58
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
E P +GP LI+ P+RELA Q ++ +
Sbjct: 59 ----EKLDPSPKKDGPQALILAPTRELALQIAEVAR 90
Score = 80.2 bits (199), Expect = 2e-18
Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 8/93 (8%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
RD+IG A TGSGKT F++PIL E P +GP LI+ P+RELA Q ++ +
Sbjct: 37 RDVIGQAQTGSGKTAAFLIPIL------EKLDPSPKKDGPQALILAPTRELALQIAEVAR 90
Query: 68 YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
+ + + GG +++ + +K+G
Sbjct: 91 KLGKHTNL--KVVVIYGGTSIDKQIRKLKRGPH 121
>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 = 112 bits (283), Expect = 1e-28
Identities = 38/104 (36%), Positives = 59/104 (56%), Gaps = 6/104 (5%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
F + L L++AL+ G ++PTPIQ+ IP L+GRD++G A TG+GKT F+LP+L
Sbjct: 30 EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLL- 88
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQYYCAALP 248
+ L + + LI+ P+RELA Q + ++ L
Sbjct: 89 -----QKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLG 127
Score = 85.6 bits (212), Expect = 5e-19
Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 7/96 (7%)
Query: 6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI 65
RD++G A TG+GKT F+LP+L + L + + LI+ P+RELA Q +
Sbjct: 65 AGRDVLGQAQTGTGKTAAFLLPLL------QKILKSVERKYVSALILAPTRELAVQIAEE 118
Query: 66 IQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQY 101
++ L LR + GGV + + ++ +K+G+
Sbjct: 119 LRKLGKNLG-GLRVAVVYGGVSIRKQIEALKRGVDI 153
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 102 bits (255), Expect = 8e-25
Identities = 53/133 (39%), Positives = 72/133 (54%), Gaps = 1/133 (0%)
Query: 116 LSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGI 175
L +++RR L I V+G+ VPP SF LP L+ LE G + PTPIQ+Q I
Sbjct: 93 SGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAI 152
Query: 176 PAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
PAALSGR ++ A TGSGKT F++PI+ C + P P +++ P+REL Q
Sbjct: 153 PAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHP-SEQRNPLAMVLTPTRELCVQ 211
Query: 236 THDIIQYYCAALP 248
D + LP
Sbjct: 212 VEDQAKVLGKGLP 224
Score = 57.5 bits (139), Expect = 1e-09
Identities = 31/93 (33%), Positives = 48/93 (51%), Gaps = 3/93 (3%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
R ++ A TGSGKT F++PI+ C + P P +++ P+REL Q D Q
Sbjct: 159 RSLLVSADTGSGKTASFLVPIISRCCTIRSGHP-SEQRNPLAMVLTPTRELCVQVED--Q 215
Query: 68 YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
+P +T L +GG M Q L I++G++
Sbjct: 216 AKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVE 248
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 90.0 bits (224), Expect = 1e-20
Identities = 42/89 (47%), Positives = 54/89 (60%), Gaps = 6/89 (6%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
L ESL+ AL+ KG +PT IQ + IP AL GRD++G A TG+GKT F+LP L L+
Sbjct: 8 LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFP 67
Query: 211 TKLPFLPGEGPYG-LIICPSRELARQTHD 238
+ GP LI+ P+RELA Q D
Sbjct: 68 RRKS-----GPPRILILTPTRELAMQVAD 91
Score = 50.7 bits (122), Expect = 2e-07
Identities = 32/87 (36%), Positives = 41/87 (47%), Gaps = 13/87 (14%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG-LIICPSRELARQTHDII 66
RD++G A TG+GKT F+LP L L+ + GP LI+ P+RELA Q D
Sbjct: 39 RDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKS-----GPPRILILTPTRELAMQVAD-- 91
Query: 67 QYYCAALPIPLRTCLAI--GGVP-MNQ 90
L +A GGV MN
Sbjct: 92 --QARELAKHTHLDIATITGGVAYMNH 116
>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 = 78.8 bits (195), Expect = 4e-18
Identities = 36/82 (43%), Positives = 50/82 (60%), Gaps = 8/82 (9%)
Query: 168 TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIIC 227
TPIQ Q IPA LSG+D++ A TGSGKTL F+LPIL L ++ GP L++
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKG--------GPQALVLA 52
Query: 228 PSRELARQTHDIIQYYCAALPI 249
P+RELA Q ++ ++ L +
Sbjct: 53 PTRELAEQIYEELKKLFKILGL 74
Score = 73.1 bits (180), Expect = 4e-16
Identities = 40/134 (29%), Positives = 65/134 (48%), Gaps = 29/134 (21%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
+D++ A TGSGKTL F+LPIL L ++ GP L++ P+RELA Q ++ ++
Sbjct: 15 KDVLVQAPTGSGKTLAFLLPILQALLPKKG--------GPQALVLAPTRELAEQIYEELK 66
Query: 68 YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDIIR 127
L + R L GG + + +KKG ++ P ++ D++R
Sbjct: 67 KLFKILGL--RVALLTGGTSLKEQARKLKKG------------KADILVGTPGRLLDLLR 112
Query: 128 R-------NLRILV 134
R NL++LV
Sbjct: 113 RGKLKLLKNLKLLV 126
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 82.2 bits (203), Expect = 6e-18
Identities = 44/108 (40%), Positives = 63/108 (58%), Gaps = 4/108 (3%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
SF + L ++RA+ +G ++PTPIQ Q IPA L GRD++ A TG+GKT F LP+L
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 205 FCLEQETKLPFLPGEGPY-GLIICPSRELARQTHDIIQYYCAALPIGS 251
+ ++ P G P LI+ P+RELA Q + ++ Y L I S
Sbjct: 62 HLITRQ---PHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRS 106
Score = 50.6 bits (121), Expect = 3e-07
Identities = 32/93 (34%), Positives = 51/93 (54%), Gaps = 6/93 (6%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPY-GLIICPSRELARQTHDII 66
RD++ A TG+GKT F LP+L + ++ P G P LI+ P+RELA Q + +
Sbjct: 39 RDLMASAQTGTGKTAGFTLPLLQHLITRQ---PHAKGRRPVRALILTPTRELAAQIGENV 95
Query: 67 QYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGI 99
+ Y L I R+ + GGV +N + ++ G+
Sbjct: 96 RDYSKYLNI--RSLVVFGGVSINPQMMKLRGGV 126
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 74.8 bits (184), Expect = 2e-16
Identities = 33/92 (35%), Positives = 47/92 (51%), Gaps = 10/92 (10%)
Query: 159 LEAKGIKKPTPIQVQGIPAALSG-RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLP 217
+E G + P Q + I A LSG RD+I A TGSGKTL +LP L
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEA---------LKR 51
Query: 218 GEGPYGLIICPSRELARQTHDIIQYYCAALPI 249
G+G L++ P+RELA Q + ++ +L +
Sbjct: 52 GKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83
Score = 62.1 bits (151), Expect = 9e-12
Identities = 28/95 (29%), Positives = 42/95 (44%), Gaps = 11/95 (11%)
Query: 4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 63
RD+I A TGSGKTL +LP L G+G L++ P+RELA Q
Sbjct: 21 LSGLRDVILAAPTGSGKTLAALLPALEA---------LKRGKGGRVLVLVPTRELAEQWA 71
Query: 64 DIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKG 98
+ ++ + L+ GG + L ++ G
Sbjct: 72 EELKKLGP--SLGLKVVGLYGGDSKREQLRKLESG 104
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 73.0 bits (179), Expect = 9e-15
Identities = 39/91 (42%), Positives = 56/91 (61%), Gaps = 8/91 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
+F + L ++ AL G +KP+PIQ + IP L+GRD++G+A TGSGKT F LP L+
Sbjct: 7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLP-LL 65
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQ 235
L+ E K P + L++ P+RELA Q
Sbjct: 66 HNLDPELKAPQI-------LVLAPTRELAVQ 89
Score = 45.6 bits (108), Expect = 1e-05
Identities = 26/56 (46%), Positives = 35/56 (62%), Gaps = 8/56 (14%)
Query: 6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 61
N RD++G+A TGSGKT F LP L+ L+ E K P + L++ P+RELA Q
Sbjct: 42 NGRDVLGMAQTGSGKTAAFSLP-LLHNLDPELKAPQI-------LVLAPTRELAVQ 89
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 68.4 bits (167), Expect = 4e-13
Identities = 39/100 (39%), Positives = 54/100 (54%), Gaps = 1/100 (1%)
Query: 138 DVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
D P +F L +L+ LE+ G + TPIQ +P AL G D+ G A TG+GKTL
Sbjct: 3 DKPLTDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLA 62
Query: 198 FVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 237
F++ ++ L + P E P LI+ P+RELA Q H
Sbjct: 63 FLVAVMNRLLSRPALADRKP-EDPRALILAPTRELAIQIH 101
Score = 49.2 bits (117), Expect = 8e-07
Identities = 32/92 (34%), Positives = 50/92 (54%), Gaps = 3/92 (3%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
D+ G A TG+GKTL F++ ++ L + P E P LI+ P+RELA Q H
Sbjct: 47 GDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKP-EDPRALILAPTRELAIQIHKDAV 105
Query: 68 YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGI 99
+ A L LR L GGV ++ +++++G+
Sbjct: 106 KFGADL--GLRFALVYGGVDYDKQRELLQQGV 135
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 67.9 bits (167), Expect = 5e-13
Identities = 38/94 (40%), Positives = 51/94 (54%), Gaps = 14/94 (14%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
+F + LP +L+ L G + TPIQ Q +PA L+G+D+I A TGSGKT F L +L
Sbjct: 5 AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL- 63
Query: 205 FCLEQETKL---PFLPGEGPYGLIICPSRELARQ 235
KL F L++CP+RELA Q
Sbjct: 64 ------QKLDVKRF----RVQALVLCPTRELADQ 87
Score = 40.6 bits (96), Expect = 5e-04
Identities = 23/59 (38%), Positives = 29/59 (49%), Gaps = 14/59 (23%)
Query: 6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKL---PFLPGEGPYGLIICPSRELARQ 61
+D+I A TGSGKT F L +L KL F L++CP+RELA Q
Sbjct: 40 AGKDVIAQAKTGSGKTAAFGLGLL-------QKLDVKRF----RVQALVLCPTRELADQ 87
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 63.5 bits (155), Expect = 1e-11
Identities = 35/87 (40%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
L +V ALE KG TPIQ +P L+GRD+ G A TG+GKT+ F+ + L
Sbjct: 15 LHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHP 74
Query: 211 TKLPFLPGEGPYGLIICPSRELARQTH 237
+ P LI+ P+RELA Q H
Sbjct: 75 APEDRKVNQ-PRALIMAPTRELAVQIH 100
Score = 41.1 bits (97), Expect = 3e-04
Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI 65
RD+ G A TG+GKT+ F+ + L + P LI+ P+RELA
Sbjct: 44 AGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQ-PRALIMAPTRELA------ 96
Query: 66 IQYYCAALPIP----LRTCLAIGGVPMNQSLDVIKKGI 99
+Q + A P+ L+ LA GG ++ L V++ G+
Sbjct: 97 VQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGV 134
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 59.5 bits (144), Expect = 3e-10
Identities = 36/96 (37%), Positives = 52/96 (54%), Gaps = 8/96 (8%)
Query: 145 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
SF +KL E L+R + + G +KP+ IQ +GI L G D IG A +G+GKT FV+ L
Sbjct: 29 SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAAL- 87
Query: 205 FCLEQETKLPFLPGEGPYGLIICPSRELARQTHDII 240
Q + LI+ P+RELA+Q ++
Sbjct: 88 ----QLIDYDLNACQ---ALILAPTRELAQQIQKVV 116
Score = 37.5 bits (87), Expect = 0.005
Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 31/142 (21%)
Query: 6 NSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDI 65
+ D IG A +G+GKT FV+ L Q + LI+ P+RELA+Q +
Sbjct: 64 DGYDTIGQAQSGTGKTATFVIAAL-----QLIDYDLNACQ---ALILAPTRELAQQIQKV 115
Query: 66 IQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPDQVHDI 125
+ L + C +GG + ++ +K G+ ++ P +V+D+
Sbjct: 116 VLALGDYLKVRCHAC--VGGTVVRDDINKLKAGVHM-------------VVGTPGRVYDM 160
Query: 126 I-RRNLR-------ILVEGDDV 139
I +R+LR IL E D++
Sbjct: 161 IDKRHLRVDDLKLFILDEADEM 182
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 59.2 bits (143), Expect = 3e-10
Identities = 35/90 (38%), Positives = 45/90 (50%), Gaps = 1/90 (1%)
Query: 146 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
F L L+ A+ G TPIQ Q + L+G D IG A TG+GKT F++ I+
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 206 CLEQETKLPFLPGEGPYGLIICPSRELARQ 235
L+ GE P LII P+REL Q
Sbjct: 149 LLQTPPPKERYMGE-PRALIIAPTRELVVQ 177
Score = 38.7 bits (90), Expect = 0.002
Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQ 61
D IG A TG+GKT F++ I+ L+ GE P LII P+REL Q
Sbjct: 125 HDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGE-PRALIIAPTRELVVQ 177
>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 = 55.4 bits (134), Expect = 8e-10
Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 12/93 (12%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 67
RD++ A TGSGKTL +LPIL +G L++ P+RELA Q + ++
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILEL---------LDSLKGGQVLVLAPTRELANQVAERLK 51
Query: 68 YYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQ 100
++ IGG + Q ++
Sbjct: 52 ---ELFGEGIKVGYLIGGTSIKQQEKLLSGKTD 81
Score = 48.5 bits (116), Expect = 2e-07
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 9/60 (15%)
Query: 182 RDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHDIIQ 241
RD++ A TGSGKTL +LPIL +G L++ P+RELA Q + ++
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILEL---------LDSLKGGQVLVLAPTRELANQVAERLK 51
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 56.5 bits (137), Expect = 4e-09
Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQE 210
L + + K TP Q IP SG +++ IA TGSGKT LP++ L
Sbjct: 8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLS-L 65
Query: 211 TKLPFLPGEGPYGLIICPSRELAR 234
K +G Y L I P + L
Sbjct: 66 GKGK--LEDGIYALYISPLKALNN 87
Score = 31.5 bits (72), Expect = 0.48
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 13 IAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR 60
IA TGSGKT LP++ L K +G Y L I P + L
Sbjct: 43 IAPTGSGKTEAAFLPVINELLS-LGKGK--LEDGIYALYISPLKALNN 87
>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 = 54.3 bits (131), Expect = 2e-08
Identities = 25/72 (34%), Positives = 33/72 (45%)
Query: 140 PPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFV 199
P S ESL AL GI++ QV + GR+++ TGSGKT F+
Sbjct: 44 RPGKTSEFPELRDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFL 103
Query: 200 LPILMFCLEQET 211
LPIL L +
Sbjct: 104 LPILDHLLRDPS 115
Score = 37.8 bits (88), Expect = 0.004
Identities = 33/144 (22%), Positives = 56/144 (38%), Gaps = 32/144 (22%)
Query: 1 MVTYRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELAR 60
+ R R+++ TGSGKT F+LPIL L + L++ P+ LA
Sbjct: 79 LRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA---------RALLLYPTNALAN 129
Query: 61 QTHDIIQYYCAALPIPLRTCLAIGGVPMNQSLDVIKKGIQYNDPIKTSWRAPRCILSLPD 120
+ ++ + LP + G P + +I+ P +L+ PD
Sbjct: 130 DQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRN-------------PPDILLTNPD 176
Query: 121 QVHDIIRR----------NLRILV 134
+H ++ R NL+ LV
Sbjct: 177 MLHYLLLRNHDAWLWLLRNLKYLV 200
>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 = 44.3 bits (105), Expect = 3e-05
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 152 PESLVRALEAKGIKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
+V ALEA GI +P Q + A +GR ++ T SGK+L + LP+L
Sbjct: 22 HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVL 73
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 44.0 bits (104), Expect = 4e-05
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 11/89 (12%)
Query: 151 LPESLVRALEAKGIKKPTPIQVQGIPAAL-SGRDIIGIAFTGSGKTLVFVLPILMFCLEQ 209
+PE R L+ +GI++ P+QV + A L G +++ ++ T SGKTL+ L + L
Sbjct: 201 IPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG 260
Query: 210 ETKLPFLPGEGPYGLIICPSRELARQTHD 238
K+ FL P LA Q ++
Sbjct: 261 GKKMLFL----------VPLVALANQKYE 279
>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 = 41.8 bits (99), Expect = 2e-04
Identities = 29/72 (40%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLI 225
P P Q++ AAL GR + IA TGSGKTL LP L+ E P +G + L
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEK-----PKKGLHTLY 67
Query: 226 ICPSRELARQTH 237
I P R LA
Sbjct: 68 ITPLRALAVDIA 79
Score = 36.4 bits (85), Expect = 0.014
Identities = 26/75 (34%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 4 YRNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTH 63
R + IA TGSGKTL LP L+ E P +G + L I P R LA
Sbjct: 25 ALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEK-----PKKGLHTLYITPLRALAVDIA 79
Query: 64 DIIQYYCAALPIPLR 78
+Q L +P+R
Sbjct: 80 RNLQAPIEELGLPIR 94
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 40.4 bits (95), Expect = 6e-04
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 11/88 (12%)
Query: 150 KLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCLE 208
KL + ++ L+ GI + Q + + LS +++ A TGSGKTL+ +L IL LE
Sbjct: 15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE 74
Query: 209 QETKLPFLPGEGPYGLIICPSRELARQT 236
K+ + I P + LA +
Sbjct: 75 GGGKV----------VYIVPLKALAEEK 92
Score = 33.5 bits (77), Expect = 0.11
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 10/47 (21%)
Query: 16 TGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQT 62
TGSGKTL+ +L IL LE K+ + I P + LA +
Sbjct: 56 TGSGKTLIALLAILSTLLEGGGKV----------VYIVPLKALAEEK 92
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 39.6 bits (93), Expect = 0.001
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 171 QVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
Q + I A LSG+D + + TG GK+L + +P L+
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL 56
Score = 30.0 bits (68), Expect = 1.3
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 8 RDIIGIAFTGSGKTLVFVLPILMF 31
+D + + TG GK+L + +P L+
Sbjct: 33 KDTLVVMPTGGGKSLCYQIPALLL 56
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 37.2 bits (87), Expect = 0.007
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 165 KKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL--MFCLEQETKLPFLPGEGPY 222
TP Q IP G++++ + TGSGKTL L I+ +F L +E +L + Y
Sbjct: 31 GTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELE----DKVY 86
Query: 223 GLIICPSRELA 233
L + P R L
Sbjct: 87 CLYVSPLRALN 97
Score = 29.5 bits (67), Expect = 2.1
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 16 TGSGKTLVFVLPIL--MFCLEQETKLPFLPGEGPYGLIICPSRELA 59
TGSGKTL L I+ +F L +E +L + Y L + P R L
Sbjct: 56 TGSGKTLAAFLAIIDELFRLGREGELE----DKVYCLYVSPLRALN 97
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 36.3 bits (84), Expect = 0.013
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 14/64 (21%)
Query: 169 PIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICP 228
P+Q++ I A L GRD + TG GK+L + LP L L+I P
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS--------------DGITLVISP 59
Query: 229 SREL 232
L
Sbjct: 60 LISL 63
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 36.1 bits (84), Expect = 0.016
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 149 MKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLV 197
+ LPE ++ EA+GI++ P Q + + A L G++++ T SGKTL+
Sbjct: 6 LPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLI 55
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 33.2 bits (76), Expect = 0.11
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 19/92 (20%)
Query: 166 KPTPIQVQGIPAALS----GRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGP 221
+ P Q + + A + R + + TG+GKT+V I E K
Sbjct: 36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAI------AELKRST------ 83
Query: 222 YGLIICPSRELARQT-HDIIQYYCAALPIGSF 252
L++ P++EL Q + ++ IG +
Sbjct: 84 --LVLVPTKELLDQWAEALKKFLLLNDEIGIY 113
Score = 31.3 bits (71), Expect = 0.44
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 14/65 (21%)
Query: 5 RNSRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLIICPSRELARQTHD 64
R R + + TG+GKT+V I E K L++ P++EL Q +
Sbjct: 53 RTERRGVIVLPTGAGKTVVAAEAI------AELKRST--------LVLVPTKELLDQWAE 98
Query: 65 IIQYY 69
++ +
Sbjct: 99 ALKKF 103
>gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an
uncharacterized family of the V_Alix_like superfamily.
This domain family is comprised of uncharacterized plant
proteins. It belongs to the V_Alix_like superfamily
which includes the V-shaped (V) domains of Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, mammalian Alix (apoptosis-linked gene-2
interacting protein X), (His-Domain) type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23), and
related domains. Alix, also known as apoptosis-linked
gene-2 interacting protein 1 (AIP1), participates in
membrane remodeling processes during the budding of
enveloped viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), and the abscission
reactions of mammalian cell division. It also functions
in apoptosis. HD-PTP functions in cell migration and
endosomal trafficking, Bro1 in endosomal trafficking,
and Rim20 in the response to the external pH via the
Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. The mammalian Alix
V-domain (belonging to a different family) contains a
binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. In
addition to this V-domain, members of the
V_Alix_Rim20_Bro1_like superfamily also have an
N-terminal Bro1-like domain, which binds components of
the ESCRT-III complex. The Bro1-like domains of Alix and
HD-PTP can also bind to human immunodeficiency virus
type 1 (HIV-1) nucleocapsid. Many members of the
V_Alix_like superfamily also have a proline-rich region
(PRR).
Length = 339
Score = 32.8 bits (75), Expect = 0.13
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 13/71 (18%)
Query: 120 DQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTP---------I 170
+ V ++IR L D A + R M+LPE+L+ AL+ G P +
Sbjct: 13 EMVDELIRTEADRLAAASDE--ARVALREMELPETLI-ALDG-GASLPGDLGLDEEVEAV 68
Query: 171 QVQGIPAALSG 181
Q+ G AAL G
Sbjct: 69 QISGGLAALEG 79
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 32.8 bits (75), Expect = 0.19
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 169 PIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMF 205
P Q + I A LSGRD + + TG GK+L + +P L+
Sbjct: 28 PGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL 64
>gnl|CDD|147901 pfam05992, SbmA_BacA, SbmA/BacA-like family. The Rhizobium
meliloti bacA gene encodes a function that is essential
for bacterial differentiation into bacteroids within
plant cells in the symbiosis between R. meliloti and
alfalfa. An Escherichia coli homolog of BacA, SbmA, is
implicated in the uptake of microcins and bleomycin.
This family is likely to be a subfamily of the ABC
transporter family.
Length = 315
Score = 32.3 bits (74), Expect = 0.21
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 3 TYRNSRDI--IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII 52
T R +R + +G++F S TL+ LP+L + LP G+ P+GL+
Sbjct: 116 TMRFARIMEDLGVSFVRSIMTLIAFLPVLFGLSKHVPVLPIF-GDIPHGLVW 166
Score = 30.4 bits (69), Expect = 0.85
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 185 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII 226
+G++F S TL+ LP+L + LP G+ P+GL+
Sbjct: 126 LGVSFVRSIMTLIAFLPVLFGLSKHVPVLPIF-GDIPHGLVW 166
>gnl|CDD|237060 PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed.
Length = 764
Score = 32.2 bits (74), Expect = 0.23
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 166 KPTPIQVQGIPAALSGRDIIGIAFTGSGKTLV 197
+P +Q+ G L+G D+I +A TG GKTL
Sbjct: 78 RPFDVQLLGALRLLAG-DVIEMA-TGEGKTLA 107
>gnl|CDD|224056 COG1133, SbmA, ABC-type long-chain fatty acid transport system,
fused permease and ATPase components [Lipid metabolism].
Length = 405
Score = 32.1 bits (73), Expect = 0.29
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 3 TYRNSRDI--IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII 52
T R S + +G++F + TL+ LP+L ++LP + G P+ L+
Sbjct: 194 TMRFSSTLENLGVSFINAIMTLIAFLPVLFTLSAHVSELPII-GHIPHALVW 244
Score = 30.5 bits (69), Expect = 0.74
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 185 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII 226
+G++F + TL+ LP+L ++LP + G P+ L+
Sbjct: 204 LGVSFINAIMTLIAFLPVLFTLSAHVSELPII-GHIPHALVW 244
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 31.4 bits (71), Expect = 0.47
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 169 PIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
P Q + I A +SG D+ + TG GK+L + LP L+
Sbjct: 463 PNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALI 498
>gnl|CDD|233212 TIGR00963, secA, preprotein translocase, SecA subunit. The
proteins SecA-F and SecY, not all of which are
necessary, comprise the standard prokaryotic protein
translocation apparatus. Other, specialized
translocation systems also exist but are not as broadly
distributed. This model describes SecA, an essential
member of the apparatus. This model excludes SecA2 of
the accessory secretory system [Protein fate, Protein
and peptide secretion and trafficking].
Length = 745
Score = 30.7 bits (70), Expect = 0.92
Identities = 21/53 (39%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 151 LPESLVRALEA-KGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLP 201
LPE+ EA K + P VQ I AL I + TG GKTL LP
Sbjct: 38 LPEAFAVVREASKRVLGMRPFDVQLIGGIALHKGKIAEMK-TGEGKTLTATLP 89
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 30.4 bits (69), Expect = 0.95
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 169 PIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILM 204
P Q + I L GRD++ + TG GK+L + +P L+
Sbjct: 16 PGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALL 51
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.7 bits (65), Expect = 1.1
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 164 IKKPTPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG 223
+ P Q + I L + + + TGSGKTL L+ L + K
Sbjct: 1 KLELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAA--LIARLAKG-KKKV-------- 49
Query: 224 LIICPSRELARQTHDII 240
L + P ++L Q II
Sbjct: 50 LFVVPRKDLLEQALVII 66
>gnl|CDD|182960 PRK11098, PRK11098, microcin B17 transporter; Reviewed.
Length = 409
Score = 30.0 bits (68), Expect = 1.2
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 11 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII 52
+G++F + TL+ LP+L+ +LP + G PYGL+I
Sbjct: 208 LGVSFINAIMTLIAFLPVLVTLSAHVPELPIV-GHIPYGLVI 248
Score = 30.0 bits (68), Expect = 1.2
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 185 IGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYGLII 226
+G++F + TL+ LP+L+ +LP + G PYGL+I
Sbjct: 208 LGVSFINAIMTLIAFLPVLVTLSAHVPELPIV-GHIPYGLVI 248
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the
Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of species
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1230
Score = 29.7 bits (67), Expect = 1.6
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 168 TPIQVQGIPAALSGRDIIGIAFTGSGKTLVFVLPIL 203
T Q Q I G+DI+ A GSGKT V V I+
Sbjct: 3 TDEQWQAIYT--RGQDILVSASAGSGKTAVLVERII 36
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 29.4 bits (66), Expect = 2.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 14 AFTGSGKTLVFVLPILMF 31
A TG+GKTL ++LP L +
Sbjct: 271 APTGTGKTLGYLLPALYY 288
Score = 29.4 bits (66), Expect = 2.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 188 AFTGSGKTLVFVLPILMF 205
A TG+GKTL ++LP L +
Sbjct: 271 APTGTGKTLGYLLPALYY 288
>gnl|CDD|235708 PRK06131, PRK06131, dihydroxy-acid dehydratase; Validated.
Length = 571
Score = 29.0 bits (66), Expect = 2.4
Identities = 11/21 (52%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 173 QGIPA-ALSGRDIIGIAFTGS 192
QG P GR IIGI T S
Sbjct: 28 QGYPDELFDGRPIIGICNTWS 48
>gnl|CDD|225676 COG3134, COG3134, Predicted outer membrane lipoprotein [Function
unknown].
Length = 179
Score = 28.3 bits (63), Expect = 2.8
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 81 LAIGGVPMNQSLDVIKKGIQYN-----DPIKTSWRAPR 113
A GV SL+V ++G QY PIK + + PR
Sbjct: 14 AAALGVAAVASLNVFERGPQYAQVVSATPIKETVKTPR 51
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 29.0 bits (65), Expect = 2.8
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 149 MKLPESLVRALEAKGIKKPTPIQVQGIPA-ALSGRDIIGIAFTGSGKTLVFVLPILMFCL 207
+++ E + R L+ +GI++ P Q + + + L G++++ T SGKTLV + ++ L
Sbjct: 6 LRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLL 65
Query: 208 EQETKLPFL 216
+ K +L
Sbjct: 66 REGGKAVYL 74
>gnl|CDD|219445 pfam07517, SecA_DEAD, SecA DEAD-like domain. SecA protein binds to
the plasma membrane where it interacts with proOmpA to
support translocation of proOmpA through the membrane.
SecA protein achieves this translocation, in association
with SecY protein, in an ATP dependent manner. This
domain represents the N-terminal ATP-dependent helicase
domain, which is related to the pfam00270.
Length = 381
Score = 28.3 bits (64), Expect = 4.4
Identities = 22/59 (37%), Positives = 27/59 (45%), Gaps = 15/59 (25%)
Query: 151 LPE--SLVRALEA----KGIKKPTPIQVQGIPAALSGRDIIGIA--FTGSGKTLVFVLP 201
LPE +LVR EA G + +Q+ G G+ IA TG GKTL LP
Sbjct: 59 LPEAFALVR--EAAKRVLG-MRHYDVQLIGGLVLHEGK----IAEMKTGEGKTLTATLP 110
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 28.1 bits (63), Expect = 5.6
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 12/72 (16%)
Query: 166 KPTPIQVQGIPA--ALSGRDIIGIAFTGSGKTLVFVLPILMFCLEQETKLPFLPGEGPYG 223
+ Q + I A +GR I+ +A TG+GKTL + L ++ L L
Sbjct: 8 ELRDYQKEAIRAWFKNNGRGILKMA-TGTGKTLTAL--AAASKLYEKIGLLVL------- 57
Query: 224 LIICPSRELARQ 235
L++CP + L Q
Sbjct: 58 LVVCPYQHLVDQ 69
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 28.1 bits (63), Expect = 5.7
Identities = 23/86 (26%), Positives = 34/86 (39%), Gaps = 12/86 (13%)
Query: 119 PDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPES--LVRALEAKGI-KKPTPIQVQGI 175
+ + L D A L E+ LVR + + ++ +Q+ G
Sbjct: 60 EEALRARSLALRARLRARDGFRDAL-------LAEAFALVREASGRVLGQRHFDVQLMGG 112
Query: 176 PAALSGRDIIGIAFTGSGKTLVFVLP 201
A LSGR + + TG GKTL LP
Sbjct: 113 LALLSGR-LAEMQ-TGEGKTLTATLP 136
>gnl|CDD|197251 cd09154, PLDc_SMU_988_like_1, Putative catalytic domain, repeat 1,
of Streptococcus mutans uncharacterized protein SMU_988
and similar proteins. Putative catalytic domain, repeat
1, of Streptococcus mutans uncharacterized protein
SMU_988 and similar proteins. Although SMU_988 and
similar proteins have not been functionally
characterized, members in this subfamily show high
sequence homology to bacterial cardiolipin (CL)
synthases, which catalyze the reversible phosphatidyl
group transfer between two phosphatidylglycerol
molecules to form CL and glycerol. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
may be part of the active site and may be involved in
phosphatidyl group transfer.
Length = 155
Score = 27.1 bits (61), Expect = 5.9
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 18/54 (33%)
Query: 120 DQVHDIIRRNLRILVEGDDVPPACCSFRLM--------KLPESLVRALEAKGIK 165
D + +I++ + EG +V R+M LP+ + LE GIK
Sbjct: 36 DSILEILKEKAK---EGVEV-------RIMYDDFGSITTLPKDYPKELEKIGIK 79
>gnl|CDD|217335 pfam03044, Herpes_UL16, Herpesvirus UL16/UL94 family. This family
groups together HSV-1 UL16, HSV-6 ORF11R, EHV-1 46, HCMV
UL94, EBV BGLF2 and VZV 44. UL16 protein may play a role
in capsid maturation including DNA packaging/cleavage.
In immunofluorescence studies, UL16 was localised to the
nucleus of infected cells in areas containing high
concentrations of HSV capsid proteins. These nuclear
compartments have been described previously as viral
assemblons and are distinct from compartments containing
replicating DNA. Localisation within assemblons argues
for a role of UL16 encoded protein in capsid assembly or
maturation.
Length = 329
Score = 27.7 bits (62), Expect = 6.5
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 117 SLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL 159
++ D + D+I +G++VP ++L++L E L R +
Sbjct: 281 TITDDLSDVIGGVTA---DGEEVPVNSEGWQLVRLSELLSRLI 320
>gnl|CDD|212666 cd07802, FGGY_L-XK, L-xylulose kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial L-xylulose kinases (L-XK, also
known as L-xylulokinase; EC 2.7.1.53), which catalyze
the ATP-dependent phosphorylation of L-xylulose to
produce L-xylulose 5-phosphate and ADP. The presence of
Mg2+ might be required for catalytic activity. Some
uncharacterized sequences are also included in this
subfamily. L-XKs belong 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 = 447
Score = 27.5 bits (62), Expect = 7.6
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 177 AALSGRDIIGIAFTGSGKTLVFV 199
A + DI GI TG G L V
Sbjct: 63 AGVDAEDIAGIGVTGQGDGLWLV 85
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 27.0 bits (61), Expect = 8.7
Identities = 11/15 (73%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 10 IIGIA-FTGSGKTLV 23
IIGIA +GSGKT V
Sbjct: 8 IIGIAGGSGSGKTTV 22
Score = 27.0 bits (61), Expect = 8.7
Identities = 11/15 (73%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 184 IIGIA-FTGSGKTLV 197
IIGIA +GSGKT V
Sbjct: 8 IIGIAGGSGSGKTTV 22
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
0.326 0.145 0.452
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,397,673
Number of extensions: 1305008
Number of successful extensions: 1965
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1924
Number of HSP's successfully gapped: 90
Length of query: 252
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 157
Effective length of database: 6,723,972
Effective search space: 1055663604
Effective search space used: 1055663604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.3 bits)