RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4494
(234 letters)
>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 = 183 bits (467), Expect = 1e-55
Identities = 84/238 (35%), Positives = 122/238 (51%), Gaps = 46/238 (19%)
Query: 25 FGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTT 84
F D+PN+ Y+VR K L++L + + F+ +SGIIY
Sbjct: 192 FCTSFDRPNLY--------------YEVRRKTP---KILEDLLRFIRKEFKGKSGIIYCP 234
Query: 85 SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPN 126
S K+ E + L+N G+ AYHA LE + ++AFG+GI+KP+
Sbjct: 235 SRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPD 294
Query: 127 VRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFD-----QQTGL 181
VRFVIH+ L KSME++YQESGRAGRDG + C L+Y D+ +L ++ + Q+T
Sbjct: 295 VRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQQRTYK 354
Query: 182 ANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTE-----CRGMCDHCRGGRRDAKRVDV 234
LY ++ YCL+ + CRR I+ S+F E + CD+C R D K DV
Sbjct: 355 LKLYEMMEYCLNSSTCRRLILLSHFGEKQLNKSFGIMGTEKCCDNCC-KRLDYKTKDV 411
Score = 62.1 bits (151), Expect = 3e-11
Identities = 20/30 (66%), Positives = 28/30 (93%)
Query: 22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
++AFG+GI+KP+VRFVIH+ L KSME++YQ
Sbjct: 283 TVAFGMGINKPDVRFVIHYSLPKSMESYYQ 312
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 151 bits (383), Expect = 2e-42
Identities = 73/236 (30%), Positives = 106/236 (44%), Gaps = 42/236 (17%)
Query: 26 GLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSR-RFRNQSGIIYTT 84
LG+ N+ F +V K + D+LA L + ++SGIIY
Sbjct: 187 QLGLQDANI-FRGSFDRP---NLALKVVEKG----EPSDQLAFLATVLPQLSKSGIIYCL 238
Query: 85 SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPN 126
+ K+ E+L E LR G+ AYHA L + + AFG+GIDKP+
Sbjct: 239 TRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPD 298
Query: 127 VRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYN 186
VRFVIH+ L S+E++YQE+GRAGRDG A IL Y D+ ++ +Q
Sbjct: 299 VRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLI-EQSKPDEEQKQ 357
Query: 187 I--------VSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV 234
I ++YC + CRR ++ YF E + C +C K+ D
Sbjct: 358 IELAKLRQMIAYC-ETQTCRRLVLLKYFGE-----DEPEPCGNCDNCLDTPKQFDG 407
Score = 60.4 bits (147), Expect = 1e-10
Identities = 19/29 (65%), Positives = 25/29 (86%)
Query: 23 IAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
AFG+GIDKP+VRFVIH+ L S+E++YQ
Sbjct: 288 NAFGMGIDKPDVRFVIHYDLPGSIESYYQ 316
>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 = 143 bits (363), Expect = 1e-39
Identities = 79/199 (39%), Positives = 105/199 (52%), Gaps = 33/199 (16%)
Query: 49 FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
+ V K QK LD L ++ R QSGIIY +S K+ E+L E L ++G+ AYHA
Sbjct: 202 RFSVVKKNNKQKFLLDYL-----KKHRGQSGIIYASSRKKVEELAERLESQGISALAYHA 256
Query: 109 KLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
L + V + AFG+GIDKPNVRFVIH+ + ++E++YQE+GRAG
Sbjct: 257 GLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAG 316
Query: 151 RDGQIAHCILYYRLPDV------FKLSSMVFD-QQTGLANLYNIVSYCLDQTRCRRAIIA 203
RDG A IL Y D+ + S D +Q L +++YC QT CRRA I
Sbjct: 317 RDGLPAEAILLYSPADIALLKRRIEQSEADDDYKQIEREKLRAMIAYCETQT-CRRAYIL 375
Query: 204 SYFDEAWSDTECRGMCDHC 222
YF E C G CD+C
Sbjct: 376 RYFGEN-EVEPC-GNCDNC 392
Score = 54.7 bits (132), Expect = 1e-08
Identities = 18/30 (60%), Positives = 26/30 (86%)
Query: 22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
+ AFG+GIDKPNVRFVIH+ + ++E++YQ
Sbjct: 281 TNAFGMGIDKPNVRFVIHYDMPGNLESYYQ 310
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 134 bits (338), Expect = 6e-36
Identities = 70/202 (34%), Positives = 106/202 (52%), Gaps = 39/202 (19%)
Query: 60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYH------------ 107
K CL+++ + ++ GIIY S +CE + E L+ G + + YH
Sbjct: 664 KKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQ 723
Query: 108 ---AKLESNV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY 161
+K E N+ ++AFG+GI+KP+VRFVIHH L KS+E ++QE GRAGRDGQ + C+LY
Sbjct: 724 KQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLY 783
Query: 162 YRLPDVFKLSSMV----FDQ-----------------QTGLANLYNIVSYCLDQTRCRRA 200
Y D ++ M+ +Q +T NL +VSYC ++ CRR
Sbjct: 784 YSYSDYIRVKHMISQGGVEQSPMAMGYNRMASSGRILETNTENLLRMVSYCENEVDCRRF 843
Query: 201 IIASYFDEAWSDTECRGMCDHC 222
+ +F E + T C+ CD+C
Sbjct: 844 LQLVHFGEKFDSTNCKKTCDNC 865
Score = 54.5 bits (131), Expect = 1e-08
Identities = 19/30 (63%), Positives = 27/30 (90%)
Query: 22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
++AFG+GI+KP+VRFVIHH L KS+E ++Q
Sbjct: 737 TVAFGMGINKPDVRFVIHHSLPKSIEGYHQ 766
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 123 bits (311), Expect = 1e-32
Identities = 74/219 (33%), Positives = 115/219 (52%), Gaps = 50/219 (22%)
Query: 30 DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC 89
D+PN+R+ + +E F KP LD+L + + R +SGIIY S +
Sbjct: 209 DRPNIRYTL-------VEKF-----KP------LDQLMRYVQEQ-RGKSGIIYCNSRAKV 249
Query: 90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVI 131
ED L++RG+ +AYHA L+++V ++AFG+GI+KPNVRFV+
Sbjct: 250 EDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 132 HHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYC 191
H + +++E++YQE+GRAGRDG A +L+Y D+ L + ++ G +I +
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAG--QQQDIERHK 367
Query: 192 LD--------QTRCRRAIIASYFDEAWSDTECRGMCDHC 222
L+ QT CRR ++ +YF E C G CD C
Sbjct: 368 LNAMGAFAEAQT-CRRLVLLNYFGE-GRQEPC-GNCDIC 403
Score = 48.6 bits (116), Expect = 1e-06
Identities = 16/30 (53%), Positives = 27/30 (90%)
Query: 22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
++AFG+GI+KPNVRFV+H + +++E++YQ
Sbjct: 293 TVAFGMGINKPNVRFVVHFDIPRNIESYYQ 322
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 83.4 bits (207), Expect = 1e-20
Identities = 39/131 (29%), Positives = 54/131 (41%), Gaps = 20/131 (15%)
Query: 49 FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
V + + L EL L + +I+ S K ++L E LR G++V+A H
Sbjct: 3 KQYVLPVEDEKLEALLEL--LKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 109 KL---------------ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
E V +A GID PNV VI++ L S ++ Q GRAG
Sbjct: 61 DGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAG 120
Query: 151 RDGQIAHCILY 161
R GQ IL
Sbjct: 121 RAGQKGTAILL 131
Score = 33.0 bits (76), Expect = 0.043
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 11 LNLWRTSFYQVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ 51
L +R V +A GID PNV VI++ L S ++ Q
Sbjct: 71 LKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQ 114
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 56.8 bits (138), Expect = 4e-11
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 18/78 (23%)
Query: 94 EELRNRGLRVSAYHAKLESN-----------------VSI-AFGLGIDKPNVRFVIHHCL 135
+ LR G++V+ H L V+ G GID P+V VI++ L
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 136 SKSMENFYQESGRAGRDG 153
+ ++ Q GRAGR G
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
Score = 36.7 bits (86), Expect = 8e-04
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 24 AFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
G GID P+V VI++ L + ++ Q
Sbjct: 42 VAGRGIDLPDVNLVINYDLPWNPASYIQ 69
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 56.8 bits (138), Expect = 5e-11
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 18/82 (21%)
Query: 90 EDLREELRNRGLRVSAYHAKLESN-----------------VSI-AFGLGIDKPNVRFVI 131
E+L E L+ G++V+ H L V+ G+D P V VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 132 HHCLSKSMENFYQESGRAGRDG 153
+ L S ++ Q GRAGR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
Score = 34.5 bits (80), Expect = 0.006
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 24 AFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
G+D P V VI + L S ++ Q
Sbjct: 46 VAERGLDLPGVDLVIIYDLPWSPASYIQ 73
>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 = 52.1 bits (125), Expect = 8e-08
Identities = 42/208 (20%), Positives = 78/208 (37%), Gaps = 25/208 (12%)
Query: 44 KSMENFYQVRIKPAAQK-DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR 102
K ++ FY + ++ +K + L +L I++ + + E+L E LR RG +
Sbjct: 245 KKIKQFY-LEVESEEEKLELLLKLLKDE----DEGRVIVFVRTKRLVEELAESLRKRGFK 299
Query: 103 VSAYHAKL---------------ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ 144
V+A H L E V +A G+D P+V VI++ L E++
Sbjct: 300 VAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVH 359
Query: 145 ESGRAGRDGQIAHCI-LYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIA 203
GR GR G+ I +V KL + + L + + + + +
Sbjct: 360 RIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRP 419
Query: 204 SYFDEAWSDTECRGMCDHCRGGRRDAKR 231
+E+ E + + + R
Sbjct: 420 GLEEESDISDEIKKLKSSKKALLRGLGV 447
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 44.4 bits (105), Expect = 2e-05
Identities = 30/106 (28%), Positives = 46/106 (43%), Gaps = 25/106 (23%)
Query: 71 SRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN----------------- 113
S+ +R Q+ I++T S + C +L + L +GL+ + YHA L
Sbjct: 436 SKGYRGQT-IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAV 494
Query: 114 -VSIAFGLGIDKPNVRFVIHHCLSK-----SMENFYQESGRAGRDG 153
+ A G+D P + VI L+ S+ F Q GRAGR
Sbjct: 495 VTTAALAAGVDFPASQ-VIFESLAMGIEWLSVREFQQMLGRAGRPD 539
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 39.0 bits (91), Expect = 0.001
Identities = 34/129 (26%), Positives = 54/129 (41%), Gaps = 19/129 (14%)
Query: 63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE----------- 111
D L DL Q+ IIY + ++ + L +++ R VS H ++
Sbjct: 255 FDTLCDLYETLTITQA-IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREF 313
Query: 112 ----SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRL 164
+ V I L GID V VI++ L S EN+ GR+GR G+ I +
Sbjct: 314 RSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTP 373
Query: 165 PDVFKLSSM 173
D+ +L +
Sbjct: 374 DDIEQLKEI 382
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 33.6 bits (78), Expect = 0.071
Identities = 31/126 (24%), Positives = 52/126 (41%), Gaps = 28/126 (22%)
Query: 49 FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
FY+V + + L L L+ + +S +++ + KEC+++ + L +G A H
Sbjct: 221 FYEV-----SPDERLPALQRLLLH-HQPESCVVFCNTKKECQEVADALNAQGFSALALHG 274
Query: 109 KLE-----------SNVSI---------AFGLGIDKPNVRFVIHHCLSKSMENFYQESGR 148
LE +N S A GL I + VI++ L++ E GR
Sbjct: 275 DLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIK--ALEAVINYELARDPEVHVHRIGR 332
Query: 149 AGRDGQ 154
GR G
Sbjct: 333 TGRAGS 338
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 31.9 bits (73), Expect = 0.27
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 11/67 (16%)
Query: 51 QVRIKPAA-QKDCLDELADLMS----RRFRNQSGIIYTTSIKECEDLREELRNRGLRVSA 105
++ ++P Q D DL+S R RN+ ++ T + K EDL + L+ G++V
Sbjct: 418 EIEVRPTDGQVD------DLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRY 471
Query: 106 YHAKLES 112
H+++++
Sbjct: 472 LHSEIDT 478
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 31.2 bits (71), Expect = 0.53
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 121 GIDKPNVR-FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYR 163
GID PN +I + YQ GR GR + A+ L Y
Sbjct: 725 GIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYP 768
>gnl|CDD|235910 PRK07024, PRK07024, short chain dehydrogenase; Provisional.
Length = 257
Score = 30.7 bits (70), Expect = 0.58
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 11/40 (27%)
Query: 86 IKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKP 125
IK E LR ELR G+RV V+IA G I P
Sbjct: 159 IKYLESLRVELRPAGVRV----------VTIAPGY-IRTP 187
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain
of RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains
of mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23),
RhoA-binding protein Rhophilin-2, Brox, Bro1 and Rim20
(also known as PalA) from Saccharomyces cerevisiae,
Ustilago maydis Rim23 (also known as PalC), and related
domains. Rhophilin-1 binds both GDP- and GTP-bound
RhoA. Bro1-like domains are boomerang-shaped, and part
of the domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped
(V) domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 30.6 bits (69), Expect = 0.66
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 54 IKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELR 97
+K + D L +L+S F + G Y I+E EDLR+ +R
Sbjct: 6 LKETKELDLPTPLKELISEHF-GEDGTSYEAEIRELEDLRQAMR 48
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 30.5 bits (69), Expect = 0.77
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAH-CILYYRLPDVFKLSS 172
G+D +V++VI+ +E++ GR GR G A + PD ++L+
Sbjct: 440 GLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAG--AKGASYTFLTPDKYRLAR 490
>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 = 30.5 bits (69), Expect = 0.84
Identities = 36/140 (25%), Positives = 56/140 (40%), Gaps = 25/140 (17%)
Query: 47 ENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGI-----IYTTSIKECEDLREELRNRGL 101
EN VR +A + D LADL++ R + + + L E +
Sbjct: 247 ENGAPVR--RSASAEAADLLADLVAEGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAE 304
Query: 102 RVSAYHA--------KLESNVSI----------AFGLGIDKPNVRFVIHHCLSKSMENFY 143
RV+AY A +LE + A LG+D + V+ + + +
Sbjct: 305 RVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLW 364
Query: 144 QESGRAGRDGQIAHCILYYR 163
Q++GRAGR GQ A +L R
Sbjct: 365 QQAGRAGRRGQGALVVLVAR 384
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.0 bits (68), Expect = 1.4
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 21/74 (28%)
Query: 79 GIIYTTS---IKECEDLREELRNRGLRVSAYHAKLESN--------VSIAFGL------- 120
G+I+ ++ E+L E LR+ G+ HA+ E V + G+
Sbjct: 338 GLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKEEALEDFEEGEVDVLVGVASYYGVL 397
Query: 121 --GIDKPN-VRFVI 131
G+D P+ +R+ +
Sbjct: 398 VRGLDLPHRIRYAV 411
>gnl|CDD|221043 pfam11246, Phage_gp53, Base plate wedge protein 53. The baseplate
of bacteriophage T4 controls host cell recognition,
attachment, tail sheath contraction and viral DNA
ejection. The structure of the baseplate suggests a
mechanism of baseplate structural transition during the
initial stages of T4 infection. The baseplate is
assembled from six identical wedges that surround the
central hub. Gp53, along with other T4 gene products,
combine sequentially to assemble a wedge.
Length = 193
Score = 28.9 bits (65), Expect = 1.7
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 1/66 (1%)
Query: 38 IHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELR 97
+HH E +Y + P D+ R G + S E E LR E
Sbjct: 109 VHHHEDVEGEKYYNLVEDPEGPIVWYDKRDGDSDNRTLQYEGALRPVSNYEYETLRNE-S 167
Query: 98 NRGLRV 103
R +++
Sbjct: 168 KRVIKI 173
>gnl|CDD|236949 PRK11655, ubiC, chorismate pyruvate lyase; Provisional.
Length = 169
Score = 28.0 bits (63), Expect = 2.8
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 56 PAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREEL 96
P D L E D M++RF Q + T I+E ++EL
Sbjct: 22 PPQLLDWLMEE-DSMTKRFEQQCKRVSVTLIREGFVTQDEL 61
>gnl|CDD|212139 cd11532, NTP-PPase_COG4997, Nucleoside Triphosphate
Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found
in a group of uncharacterized proteins from archaea and
bacteria. The family includes some uncharacterized
hypothetical proteins from archaea and bacteria.
Although their biological roles remain unclear, the
family members show significant sequence similarity to
the dimeric 2-deoxyuridine 5'-triphosphate
nucleotidohydrolase (dUTP pyrophosphatase or dUTPase)
and NTP-PPase MazG proteins. However, unlike typical
tandem-domain MazG proteins, the family contains a
single MazG-like domain.
Length = 95
Score = 27.1 bits (61), Expect = 3.3
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 57 AAQKDCLDELADLMS--RRFRNQSGIIYTTSIKECEDLREE-LRNRG 100
A +D L+ELADL+ GI S++E E +RE+ RG
Sbjct: 48 AKTEDSLEELADLLEVIYAIAEAHGI----SLEELEKVREKKREERG 90
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 28.5 bits (64), Expect = 3.5
Identities = 29/96 (30%), Positives = 42/96 (43%), Gaps = 27/96 (28%)
Query: 43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIY--TTSIK---------ECED 91
+S+E +Q R P A LD L L+S GI Y T +K E+
Sbjct: 194 CQSLETLFQERF-PQA----LDNLEKLVS-------GISYDFDTDLKLPRFNRDRPAVEE 241
Query: 92 LREE----LRNRGLRVSAYHAKLESNVSIAFGLGID 123
LRE L+ +GL S Y +L+ +S+ +G D
Sbjct: 242 LRELAELGLKEKGLWSSPYQERLDKELSVIHDMGFD 277
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 28.6 bits (64), Expect = 3.6
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 15/94 (15%)
Query: 17 SFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCL-DELADLMSRRFR 75
FY + ++ + + PN+RF + +V A + D + +E+A++
Sbjct: 379 QFYDLGVSV-IPPNTPNIRF----------DEADRVYATAAEKNDAIVEEIAEVHKT--- 424
Query: 76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAK 109
Q ++ T + E E+L E L G+ + +AK
Sbjct: 425 GQPVLVGTQDVAESEELAEALLEAGVPCNVLNAK 458
>gnl|CDD|203656 pfam07503, zf-HYPF, HypF finger. The HypF family of proteins are
involved in the maturation and regulation of
hydrogenase. In the N-terminus they appear to have two
Zinc finger domains, as modelled by this family.
Length = 35
Score = 25.5 bits (57), Expect = 3.8
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 60 KDCLDELADLMSRRFRNQ 77
+CL E D ++RRF Q
Sbjct: 3 PECLKEYFDPLNRRFHAQ 20
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 28.3 bits (64), Expect = 3.9
Identities = 36/138 (26%), Positives = 60/138 (43%), Gaps = 35/138 (25%)
Query: 52 VRIKPAA-QKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL 110
+ ++P Q D D L+++ R +N+ ++ T + K EDL E L+ G++V H+ +
Sbjct: 423 IEVRPTKGQVD--DLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDI 480
Query: 111 ES---------------NVSIAFGL---GIDKPNVRFVIHHCLSKSMENFY-------QE 145
++ +V + L G+D P V V L E F Q
Sbjct: 481 DTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVA--ILDADKEGFLRSERSLIQT 538
Query: 146 SGRAGR--DGQIAHCILY 161
GRA R +G++ ILY
Sbjct: 539 IGRAARNVNGKV---ILY 553
>gnl|CDD|148147 pfam06369, Anemone_cytotox, Sea anemone cytotoxic protein. Sea
anemones are a rich source of cytotoxic proteins.
Cytolysins comprise a group of more than 30 highly basic
proteins with molecular masses of about 20 kDa.
Cytolysins isolated from the sea anemone, Heteractis
magnifica, include magnificalysin I (HMg I),
magnificalysin II (HMg II) and Heteractis magnifica
toxin (HMgtxn). These are highly homologous at their
N-terminals. HMg I and II have molecular masses of
approximately 19 kDa, and pI values of 9.4 and 10.0,
respectively. Cytolysins isolated from other sea
anemones Actinia tenebrosa (Tenebrosin-C, TN-C), Actinia
equina (Equinatoxin, EqT) and Stichodactyla helianthus
(ShC) exhibit pore-forming, haemolytic, cytotoxic, and
heart stimulatory activities.
Length = 176
Score = 27.6 bits (61), Expect = 4.9
Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 48 NFYQVRIKPAAQKDCLDELADL-MSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAY 106
N++ V+I ++ AD M + I + E +L L+ RG S
Sbjct: 113 NWWNVKIYDGKRR------ADQKMYEELYYNNNPIRGDNGWEKRNLGYGLKLRGFMTSNG 166
Query: 107 HAKLESNVS 115
AKL ++
Sbjct: 167 DAKLVIHIE 175
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 28.0 bits (63), Expect = 5.1
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 121 GIDKPNVR-FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYR 163
GID PN +I + YQ GR GR + A+ Y
Sbjct: 868 GIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYP 911
>gnl|CDD|114908 pfam06216, RTBV_P46, Rice tungro bacilliform virus P46 protein.
This family consists of several Rice tungro bacilliform
virus P46 proteins. The function of this family is
unknown.
Length = 392
Score = 27.7 bits (61), Expect = 5.2
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 8/78 (10%)
Query: 88 ECEDLREELRNRGLRVSAYHAKLESNVSIAFGL--GIDKP------NVRFVIHHCLSKSM 139
ECE L +++ + + A++ I GL + KP C +SM
Sbjct: 79 ECEKLNDQVSHLKKQNEELKAQIAEMKDIIEGLREPLKKPIYTTQDKEALRNFFCEERSM 138
Query: 140 ENFYQESGRAGRDGQIAH 157
E Y R ++ +H
Sbjct: 139 EYIYHHIKRLAQESYYSH 156
>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 = 28.1 bits (63), Expect = 5.3
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 91 DLREELRNRGLRVSAYHAKLESNVSI-AFGLGIDKPNVRFVIHHCL-SKSMENFYQESGR 148
L E R R +L ++ A LGID ++ VI + S+ +F Q +GR
Sbjct: 347 GLHREERRRIEAEFK-EGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGR 405
Query: 149 AGRDGQ 154
AGR GQ
Sbjct: 406 AGRRGQ 411
>gnl|CDD|133910 PHA00540, PHA00540, hypothetical protein.
Length = 715
Score = 28.1 bits (62), Expect = 5.5
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 14 WRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQV-RIKPAAQKDCLDELADLM 70
W F Q S + G+ DKP+ F+ ++ S++N Y V + +++ L++L D +
Sbjct: 90 WYLDFLQDSYSTGVVYDKPSESFLNYYHQWHSLKNTYMVEKFYDVKKENFLNDLTDFI 147
>gnl|CDD|234910 PRK01158, PRK01158, phosphoglycolate phosphatase; Provisional.
Length = 230
Score = 27.6 bits (62), Expect = 5.6
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 73 RFRNQSGIIYTTSIKECEDLREELRNR 99
I+ I+ECE EL+ R
Sbjct: 72 SVGFDGKRIFLGDIEECEKAYSELKKR 98
>gnl|CDD|129395 TIGR00294, TIGR00294, GTP cyclohydrolase, MptA/FolE2 family. This
family includes type I GTP cyclohydrolases involved in
methanopterin in archaea (MptA) and de novo
tetrahydrofolate biosynthesis in bacteria (FolE2)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 308
Score = 27.1 bits (60), Expect = 7.5
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 3/45 (6%)
Query: 70 MSRRFRNQSGIIYT---TSIKECEDLREELRNRGLRVSAYHAKLE 111
MSR + ++ T+ E L E+ N+ L+ Y E
Sbjct: 56 MSRNPEVITSVLEEAEETTAANFEMLCNEIVNQLLKKHRYATLAE 100
>gnl|CDD|181507 PRK08626, PRK08626, fumarate reductase flavoprotein subunit;
Provisional.
Length = 657
Score = 27.2 bits (61), Expect = 8.0
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 9/65 (13%)
Query: 47 ENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAY 106
EN ++++ ++ + E + FRN + ++KE ++L E +N GL+
Sbjct: 462 ENVFEIK---NEMQEIMMEKVGI----FRNGPEL--EKAVKELQELLERSKNIGLKSKKR 512
Query: 107 HAKLE 111
A E
Sbjct: 513 GANPE 517
>gnl|CDD|217762 pfam03851, UvdE, UV-endonuclease UvdE.
Length = 275
Score = 27.1 bits (60), Expect = 8.9
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 93 REELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIH 132
R E+ +R AYH +L + +A ++P+ +IH
Sbjct: 116 RPEVTESAIRDMAYHYRLLDGMGLA-----ERPDAVLIIH 150
>gnl|CDD|226953 COG4587, COG4587, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 268
Score = 27.0 bits (60), Expect = 9.1
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 1 MFALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVI 38
+FALLY L + Y +A L +RF+I
Sbjct: 129 IFALLYGAILQFLSPWTLYLFVLALALLF---LLRFLI 163
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 26.8 bits (60), Expect = 9.7
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 79 GIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVS 115
I Y +S + E++ EEL+ G++ +VS
Sbjct: 26 IITYRSSEEGAEEVVEELKAYGVKALGV----VCDVS 58
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
0.327 0.139 0.432
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,913,703
Number of extensions: 1096454
Number of successful extensions: 1616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1601
Number of HSP's successfully gapped: 66
Length of query: 234
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 140
Effective length of database: 6,768,326
Effective search space: 947565640
Effective search space used: 947565640
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 (21.7 bits)
S2: 57 (25.7 bits)