RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8712
(651 letters)
>gnl|CDD|240453 cd12873, SPRY_DDX1, SPRY domain associated with DEAD box gene DDX1.
This SPRY domain is associated with the DEAD box gene,
DDX1, an RNA-dependent ATPase involved in HIV-1 Rev
function and virus replication. It is suggested that
DDX1 acts as a cellular cofactor by promoting
oligomerization of Rev on the Rev response element
(RRE). DDX1 RNA is overexpressed in breast cancer, data
showing a strong and independent association between
poor prognosis and deregulation of the DEAD box protein
DDX1, thus potentially serving as an effective
prognostic biomarker for early recurrence in primary
breast cancer. DDX1 also interacts with RelA and
enhances nuclear factor kappaB-mediated transcription.
DEAD-box proteins are associated with all levels of RNA
metabolism and function, and have been implicated in
translation initiation, transcription, RNA splicing,
ribosome assembly, RNA transport, and RNA decay.
Length = 155
Score = 302 bits (775), Expect = e-100
Identities = 106/155 (68%), Positives = 129/155 (83%)
Query: 91 LSVWDRDTAMAITPEGLRCQSREQKEWHGCRANKGVYGRGKYYYEATVTDEGLCRVGWST 150
+S +DRD A+AI+P+GL CQSRE+K W GCRA KGV G+GKYYYE TVTDEGLCRVGWST
Sbjct: 1 MSPYDRDAALAISPDGLLCQSREEKGWQGCRATKGVKGKGKYYYEVTVTDEGLCRVGWST 60
Query: 151 SQAVRDLGTDRFGFGFGGTGKKSNNKQFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQH 210
A DLGTD+FGFG+GGTGKKS+ +QF++YGE FG DVIGCLLDLDN T++F+KNG+
Sbjct: 61 EDASLDLGTDKFGFGYGGTGKKSHGRQFEDYGEPFGKGDVIGCLLDLDNGTISFSKNGKD 120
Query: 211 LGLAFNISQQLKNSAFYPAVVLKNAEMSFNFGATP 245
LG+AF+I +L+N A +PAV LKNAE+ FNFG P
Sbjct: 121 LGVAFDIPPKLRNQALFPAVCLKNAEVEFNFGDEP 155
>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 = 176 bits (448), Expect = 3e-48
Identities = 84/292 (28%), Positives = 132/292 (45%), Gaps = 66/292 (22%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
A+I+ P+RELA Q ++ K K + +R ++ GGV+++ Q+ L GVDIV
Sbjct: 97 RKYVSALILAPTRELAVQIAEELRKLGKNL--GGLRVAVVYGGVSIRKQIEALKRGVDIV 154
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
V TPGR+ DLI G L L+ VLDEAD +L G+ + I+++ K +P Q
Sbjct: 155 VATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALP------PDRQT 208
Query: 402 IVCSATLHDFDVKKMAERLM--YFPTWVDLKGEDAVPETVHHVVVKIDPQ---------- 449
++ SAT D++++A R + V ++ + + + ++++ +
Sbjct: 209 LLFSAT-MPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKL 267
Query: 450 -QDETWG-------------RLRSHIQTDGVHA-----------RDN------------- 471
+DE G L ++ G RD
Sbjct: 268 LKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVL 327
Query: 472 ------ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
AR G+DI + +IN LP D +YVHRIGR GRA R G+AIS V+
Sbjct: 328 VATDVAAR-GLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVT 378
Score = 79.8 bits (197), Expect = 1e-15
Identities = 33/88 (37%), Positives = 52/88 (59%), Gaps = 7/88 (7%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
F +G+ PE+ +A++++ + PT +Q AIPLIL G DVL A+TG+GKT AF LP+
Sbjct: 28 PPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPL 87
Query: 61 IQIVCETLKEIQAGKGQGKAKAQVISPT 88
+Q +I + A +++PT
Sbjct: 88 LQ-------KILKSVERKYVSALILAPT 108
>gnl|CDD|240464 cd12884, SPRY_hnRNP, SPRY domain in heterogeneous nuclear
ribonucleoprotein U-like (hnRNP) protein 1. This
domain, consisting of the distinct N-terminal PRY
subdomain followed by the SPRY subdomain, is found at
the C-terminus of heterogeneous nuclear
ribonucleoprotein U-like (hnRNP) protein 1 (also known
as HNRPUL1 ) which is a major constituent of nuclear
matrix or scaffold and binds directly to DNA sequences
through the N-terminal acidic region named serum amyloid
P (SAP). Its function is specifically modulated by
E1B-55kDa in adenovirus-infected cells. HNRPUL1 also
participates in ATR protein kinase signaling pathways
during adenovirus infection. Two transcript variants
encoding different isoforms have been found for this
gene. When associated with bromodomain-containing
protein 7 (BRD7), it activates transcription of
glucocorticoid-responsive promoter in the absence of
ligand-stimulation.
Length = 176
Score = 156 bits (397), Expect = 2e-44
Identities = 57/144 (39%), Positives = 82/144 (56%), Gaps = 16/144 (11%)
Query: 117 WHGCRANKGVYGRGKYYYEATVTDE-------------GLCRVGWSTSQAVRDLGTDRFG 163
W G RA GV GK +E V + + RVGWS + LG ++
Sbjct: 33 WAGARATYGVRK-GKVCFEVKVLENLPVKHLPTEETDPHVVRVGWSVDSSSLQLGEEKLS 91
Query: 164 FGFGGTGKKSNNKQFDNYGEAFGMHDVIGCLLDLDN--MTVAFTKNGQHLGLAFNISQQL 221
+G+G TGKKS N +F++YGE FG DVIGC LDL++ + ++FTKNG+ LG+AF I ++L
Sbjct: 92 YGYGSTGKKSTNGKFEDYGEPFGEGDVIGCYLDLESEPVEISFTKNGKDLGVAFRIDKEL 151
Query: 222 KNSAFYPAVVLKNAEMSFNFGATP 245
+ A +P ++ KN + NFG
Sbjct: 152 EGKALFPHILTKNCAVEVNFGQKE 175
>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 = 135 bits (343), Expect = 1e-36
Identities = 48/139 (34%), Positives = 77/139 (55%), Gaps = 10/139 (7%)
Query: 283 NAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVV 342
+ PQA+I+ P+RELA Q K K ++ ++I GG ++ Q+ L G IVV
Sbjct: 68 DGPQALILAPTRELALQIAEVARKLGKH---TNLKVVVIYGGTSIDKQIRKLKRGPHIVV 124
Query: 343 GTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMI 402
TPGR+ DL+ G L L+ ++ VLDEAD +L G+ + I + K +PK Q +
Sbjct: 125 ATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDR------QTL 178
Query: 403 VCSATLHDFDVKKMAERLM 421
+ SAT+ +V+ +A + +
Sbjct: 179 LFSATMPK-EVRDLARKFL 196
Score = 89.1 bits (222), Expect = 3e-20
Identities = 31/85 (36%), Positives = 52/85 (61%), Gaps = 7/85 (8%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
FEE+G+ PE+ + + + + PT +QA AIP +L G DV+ A+TGSGKT AF +PI++
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILE- 59
Query: 64 VCETLKEIQAGKGQGKAKAQVISPT 88
++ + +A +++PT
Sbjct: 60 ------KLDPSPKKDGPQALILAPT 78
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 129 bits (326), Expect = 4e-32
Identities = 90/297 (30%), Positives = 134/297 (45%), Gaps = 70/297 (23%)
Query: 280 LVNNAPQ--------AIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQM 331
L+ P A+I+ P+RELA Q + + K++ IR L++ GGV++ QM
Sbjct: 63 LITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYL---NIRSLVVFGGVSINPQM 119
Query: 332 SVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPK 391
L GVD++V TPGR+ DL + L VLDEAD +L G+ + I R+ ++P
Sbjct: 120 MKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLP- 178
Query: 392 ITSDGKRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQ- 450
KR Q ++ SAT D D+K +AE+L++ P +++ + E V V +D ++
Sbjct: 179 ----AKR-QNLLFSATFSD-DIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRK 232
Query: 451 ---------DETW-------------GRLRSHIQTDGV-----H---------------- 467
W L + DG+ H
Sbjct: 233 RELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFK 292
Query: 468 --------ARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLV 516
A D A G+DI LP ++N LP+ +YVHRIGR GRA G A+SLV
Sbjct: 293 SGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLV 349
Score = 72.9 bits (179), Expect = 1e-13
Identities = 31/86 (36%), Positives = 55/86 (63%), Gaps = 3/86 (3%)
Query: 3 AFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQ 62
+F+ +G+ P+I +AV E + PT +Q +AIP +L G D++ +A+TG+GKT F LP++Q
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 63 IVCETLKEIQAGKGQGKAKAQVISPT 88
+ + KG+ +A +++PT
Sbjct: 62 HL---ITRQPHAKGRRPVRALILTPT 84
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 120 bits (304), Expect = 4e-29
Identities = 86/287 (29%), Positives = 127/287 (44%), Gaps = 64/287 (22%)
Query: 284 APQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVG 343
QA+++ P+RELA+Q +I + +FI P I+ L + GGV + Q+ L G I+VG
Sbjct: 72 RVQALVLCPTRELADQVAKEIRRLARFI--PNIKVLTLCGGVPMGPQIDSLEHGAHIIVG 129
Query: 344 TPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIV 403
TPGR+ D + G L L VLDEAD +L G+ + ID + +Q P +R Q ++
Sbjct: 130 TPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPA-----RR-QTLL 183
Query: 404 CSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQ-DETWGRLRSH-- 460
SAT + + +++R P V ++ +P + ++ P + RL H
Sbjct: 184 FSATYPE-GIAAISQRFQRDPVEVKVESTHDLP-AIEQRFYEVSPDERLPALQRLLLHHQ 241
Query: 461 --------------------IQTDGVHA-----------RD-------N----------- 471
+ G A RD N
Sbjct: 242 PESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDV 301
Query: 472 -ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
AR G+DI L +IN L D +VHRIGR GRA GLA+SLV+
Sbjct: 302 AAR-GLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVA 347
Score = 57.9 bits (141), Expect = 1e-08
Identities = 25/62 (40%), Positives = 39/62 (62%)
Query: 1 MAAFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPI 60
M AF + + P + + E+ + T +QA+++P IL G DV+ A+TGSGKT AF L +
Sbjct: 3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGL 62
Query: 61 IQ 62
+Q
Sbjct: 63 LQ 64
>gnl|CDD|214669 smart00449, SPRY, Domain in SPla and the RYanodine Receptor.
Domain of unknown function. Distant homologues are
domains in butyrophilin/marenostrin/pyrin homologues.
Length = 122
Score = 104 bits (262), Expect = 1e-26
Identities = 48/123 (39%), Positives = 65/123 (52%), Gaps = 12/123 (9%)
Query: 129 RGKYYYEATVTDEGLCRVGWSTSQAVRD----LGTDRFGFGFGGT-GKKSNNKQFDNYGE 183
G++Y+E + D G RVG +T R LG D+ +G+ G GKK +N YG
Sbjct: 1 SGRHYFEVEIGDGGHWRVGVATKSVPRGYFALLGEDKGSWGYDGDGGKKYHNSTGPEYGL 60
Query: 184 AFGMH-DVIGCLLDLDNMTVAFTKNGQHL-GLAFNISQQLKNS-AFYPAVVLKNAE-MSF 239
DVIGC LDL+ T++F KNG++L GLAF +K S YPA L + +
Sbjct: 61 PLQEPGDVIGCFLDLEAGTISFYKNGKYLHGLAF---FDVKFSGPLYPAFSLGSGNSVRL 117
Query: 240 NFG 242
NFG
Sbjct: 118 NFG 120
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 111 bits (280), Expect = 2e-26
Identities = 86/306 (28%), Positives = 142/306 (46%), Gaps = 68/306 (22%)
Query: 269 ESADVSAGPVKLVN---NAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGV 325
++A ++L++ NA QA+I+ P+RELA+Q ++ ++ K+R +GG
Sbjct: 78 KTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYL---KVRCHACVGGT 134
Query: 326 NVKDQMSVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRM 385
V+D ++ L +GV +VVGTPGR+ D+I HL + + F+LDEAD +L +G+ I +
Sbjct: 135 VVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDV 194
Query: 386 HKQIPKITSDGKRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVV- 444
K++P +Q+ + SAT+ + ++ ++ + M P + +K ++ E + V
Sbjct: 195 FKKLPP------DVQVALFSATMPN-EILELTTKFMRDPKRILVKKDELTLEGIRQFYVA 247
Query: 445 ------KIDPQQD--ETWG----------RLRSHIQTDGVHARDN--------------- 471
K D D ET R + T +H RD
Sbjct: 248 VEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRD 307
Query: 472 --------------------ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGL 511
AR GID+ + +IN LP NY+HRIGR GR R G+
Sbjct: 308 LIMREFRSGSTRVLITTDLLAR-GIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366
Query: 512 AISLVS 517
AI+ V+
Sbjct: 367 AINFVT 372
Score = 36.0 bits (83), Expect = 0.059
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 25 PTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQA 73
P+ +Q I IL G D + A++G+GKT F + +Q++ L QA
Sbjct: 51 PSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQA 99
>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 = 103 bits (260), Expect = 7e-26
Identities = 48/129 (37%), Positives = 73/129 (56%), Gaps = 11/129 (8%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSG-VDI 340
PQA+++ P+RELAEQ + + KK +R L+ GG ++K+Q L G DI
Sbjct: 43 KGGPQALVLAPTRELAEQIYEE---LKKLFKILGLRVALLTGGTSLKEQARKLKKGKADI 99
Query: 341 VVGTPGRMEDLISGGHLSLTH-CRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRL 399
+VGTPGR+ DL+ G L L + VLDEA LL G+G+ ++ + ++P
Sbjct: 100 LVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLP------PDR 153
Query: 400 QMIVCSATL 408
Q+++ SATL
Sbjct: 154 QILLLSATL 162
Score = 67.3 bits (165), Expect = 5e-13
Identities = 30/63 (47%), Positives = 37/63 (58%), Gaps = 9/63 (14%)
Query: 26 TDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQVI 85
T +QA+AIP IL G DVL+ A TGSGKT AF LPI+Q + Q A V+
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQ---------ALVL 51
Query: 86 SPT 88
+PT
Sbjct: 52 APT 54
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 110 bits (276), Expect = 1e-25
Identities = 80/286 (27%), Positives = 124/286 (43%), Gaps = 61/286 (21%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSG-VDIVVG 343
P+A+II P+REL Q K+ + + +GG++ Q+ L + DI+V
Sbjct: 163 PRALIIAPTRELVVQIAKDAAALTKY---TGLNVMTFVGGMDFDKQLKQLEARFCDILVA 219
Query: 344 TPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIV 403
TPGR+ D G + L VLDEAD +L G+ + ++ +Q P+ +R Q ++
Sbjct: 220 TPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPR---KEER-QTLL 275
Query: 404 CSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVH---HVVVKIDPQQ-------DET 453
SAT D DV +A++ P V+++ E+ +TV + V D +
Sbjct: 276 FSATFTD-DVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNP 334
Query: 454 WG-------------RLRSHIQTDGVH-----------------------------ARDN 471
W R+ + DG++ A D
Sbjct: 335 WERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDV 394
Query: 472 ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
A GI I G+ +IN TLP+D +YVHRIGR GRA G++IS
Sbjct: 395 AGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAG 440
Score = 52.2 bits (125), Expect = 6e-07
Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 2/100 (2%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
F + + PE+ A+ ++ + T +QA+ + L G D + A+TG+GKT AF + II
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 64 VCETLKEIQAGKGQGKAKAQVISPTWILSVWDRDTAMAIT 103
+ +T + G+ +A +I+PT L V A A+T
Sbjct: 149 LLQT--PPPKERYMGEPRALIIAPTRELVVQIAKDAAALT 186
>gnl|CDD|240451 cd11709, SPRY, SPRY domain. SPRY domains, first identified in the
SP1A kinase of Dictyostelium and rabbit Ryanodine
receptor (hence the name), are homologous to B30.2. SPRY
domains have been identified in at least 11 protein
families, covering a wide range of functions, including
regulation of cytokine signaling (SOCS), RNA metabolism
(DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha),
intracellular calcium release (ryanodine receptors or
RyR) and regulatory and developmental processes (HERC1
and Ash2L). B30.2 also contains residues in the
N-terminus that form a distinct PRY domain structure;
i.e. B30.2 domain consists of PRY and SPRY subdomains.
B30.2 domains comprise the C-terminus of three protein
families: BTNs (receptor glycoproteins of immunoglobulin
superfamily); several TRIM proteins (composed of
RING/B-box/coiled-coil or RBCC core); Stonutoxin
(secreted poisonous protein of the stonefish Synanceia
horrida). While SPRY domains are evolutionarily ancient,
B30.2 domains are a more recent adaptation where the
SPRY/PRY combination is a possible component of immune
defense. Mutations found in the SPRY-containing proteins
have shown to cause Mediterranean fever and Opitz
syndrome.
Length = 118
Score = 100 bits (252), Expect = 2e-25
Identities = 43/119 (36%), Positives = 61/119 (51%), Gaps = 9/119 (7%)
Query: 130 GKYYYEATV--TDEGLCRVGWSTSQAVRD----LGTDRFGFGFGGTGKKSNNKQ-FDNYG 182
GK+YYE V + GL +VGW+T D +G D +GF G+ + + + G
Sbjct: 1 GKWYYEVRVDSGNGGLIQVGWATKSFSLDGERGVGDDEGSWGFDGSRLRKGHGGSSEPGG 60
Query: 183 EAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVVL-KNAEMSFN 240
+ DV+GCLLDLD T++F+ NG LG+AF K YPAV L ++ N
Sbjct: 61 RPWKSGDVVGCLLDLDAGTLSFSLNGVDLGVAFENL-FRKGGPLYPAVSLGSGQGVTIN 118
>gnl|CDD|216029 pfam00622, SPRY, SPRY domain. SPRY Domain is named from SPla and
the RYanodine Receptor. Domain of unknown function.
Distant homologues are domains in
butyrophilin/marenostrin/pyrin homologues.
Length = 125
Score = 100 bits (252), Expect = 2e-25
Identities = 47/127 (37%), Positives = 62/127 (48%), Gaps = 12/127 (9%)
Query: 129 RGKYYYEATVTD--EGLCRVGWSTSQAVRD----LGTDRFGFGFGGT-GKKSNNKQFDNY 181
GK+Y+E V G RVGW+T + LG D +G+ G+ G K +N + + Y
Sbjct: 1 SGKHYFEVEVDTGGGGHVRVGWATKSVKKPGFRLLGDDEGSWGYDGSGGSKYHNGESEPY 60
Query: 182 GEAFGMHDVIGCLLDLDNMTVAFTKNGQHL-GLAFNISQQLKNSAFYPAVVLK--NAEMS 238
G F DVIGC LDL+ ++FTKNG+ L G F YPAV L +
Sbjct: 61 GLKFQEGDVIGCFLDLEEGEISFTKNGKDLGGYTF--RNVEFGGPLYPAVSLGSTGEAVQ 118
Query: 239 FNFGATP 245
FNFG
Sbjct: 119 FNFGQLK 125
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 99.1 bits (247), Expect = 1e-23
Identities = 46/162 (28%), Positives = 85/162 (52%), Gaps = 13/162 (8%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGV-DI 340
+ +++ P+RELAEQ + KK ++ + + GG + ++Q+ L SG DI
Sbjct: 52 GKGGRVLVLVPTRELAEQWAEE---LKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDI 108
Query: 341 VVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQ 400
+V TPGR+ DL+ LSL++ +LDEA LL G+G+ ++++ K +P K +Q
Sbjct: 109 LVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLP------KNVQ 162
Query: 401 MIVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHV 442
+++ SAT + +++ + E + P V + E +
Sbjct: 163 LLLLSATPPE-EIENLLELFLNDP--VFIDVGFTPLEPIEQF 201
Score = 54.8 bits (132), Expect = 1e-08
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 17 VEEMDWLLPTDVQAEAIPLIL-GGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGK 75
+E+ + Q EAI +L G DV++AA TGSGKT A LP ++A K
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPA----------LEALK 50
Query: 76 GQGKAKAQVISPT 88
+ V+ PT
Sbjct: 51 RGKGGRVLVLVPT 63
>gnl|CDD|240452 cd12872, SPRY_Ash2, SPRY domain in Ash2. This SPRY domain is found
at the C-terminus of Ash2 (absent, small, or homeotic
discs 2) -like proteins, core components of all
mixed-lineage leukemia (MLL) family histone
methyltransferases. Ash2 is a member of the trithorax
group of transcriptional regulators of the Hox genes.
Recent studies show that the SPRY domain of Ash2
mediates the interaction with RbBP5 and has an important
role in regulating the methyltransferase activity of MLL
complexes. In yeast, Ash2 is involved in histone
methylation and is required for the earliest stages of
embryogenesis.
Length = 149
Score = 95.3 bits (238), Expect = 5e-23
Identities = 50/145 (34%), Positives = 72/145 (49%), Gaps = 16/145 (11%)
Query: 108 RCQSREQKEWHGCRANKGVYGRGKYYYEATVTDEGL----CRVGWSTSQAVRD--LGTDR 161
R +K + RAN GV GK+Y+E + + G RVGWS +A +G D+
Sbjct: 7 RLTVTGEKGYRMARANHGVR-EGKWYFEVKILEGGGETGHVRVGWSRREASLQAPVGYDK 65
Query: 162 FGFGFGG-TGKKSNNKQFDNYGE-AFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAF-NIS 218
+ + + G+K + + YGE F DVIGCL+ L + F KNG+ G+AF +I
Sbjct: 66 YSYAYRDKDGEKFHLSRGKPYGEPGFKEGDVIGCLITLP--KIEFFKNGKSQGVAFEDIY 123
Query: 219 QQLKNSAFYPAVVL-KNAEMSFNFG 242
+YPAV L A + NFG
Sbjct: 124 GTG---GYYPAVSLYMGATVRLNFG 145
>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 = 88.2 bits (219), Expect = 1e-20
Identities = 45/127 (35%), Positives = 68/127 (53%), Gaps = 10/127 (7%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
Q +++ P+RELA Q ++ K + I+ +IGG ++K Q +LS DIV
Sbjct: 28 LKGGQVLVLAPTRELANQVAERL----KELFGEGIKVGYLIGGTSIKQQEKLLSGKTDIV 83
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
VGTPGR+ D + LSL +LDEA LL QG+G L ++ ++PK Q+
Sbjct: 84 VGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKD------RQV 137
Query: 402 IVCSATL 408
++ SAT
Sbjct: 138 LLLSATP 144
Score = 44.6 bits (106), Expect = 2e-05
Identities = 24/95 (25%), Positives = 33/95 (34%), Gaps = 25/95 (26%)
Query: 41 DVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQVISPTWILSVWDRDTAM 100
DVL+AA TGSGKT A LPI ++ + V++PT L+
Sbjct: 2 DVLLAAPTGSGKTLAALLPI----------LELLDSLKGGQVLVLAPTRELANQ------ 45
Query: 101 AITPEGLRCQSREQKEWHGCRANKGVYGRGKYYYE 135
+ KE G G G +
Sbjct: 46 ---------VAERLKELFGEGIKVGYLIGGTSIKQ 71
>gnl|CDD|240465 cd12885, SPRY_RanBP_like, SPRY domain in Ran binding proteins,
SSH4, HECT E3 and SPRYD3. This family includes SPRY
domains found in Ran binding proteins (RBP or RanBPM) 9
and 10, SSH4 (suppressor of SHR3 null mutation protein
4), SPRY domain-containing protein 3 (SPRYD3) as well as
HECT, a C-terminal catalytic domain of a subclass of
ubiquitin-protein ligase (E3). RanBP9 and RanBP10 act as
androgen receptor (AR) coactivators. Both consist of the
N-terminal proline- and glutamine-rich regions, the SPRY
domain, and LisH-CTLH and CRA motifs. The SPRY domain in
SSH4 may be involved in cargo recognition, either
directly or by combination with other adaptors, possibly
leading to a higher selectivity. SPRYD3 is highly
expressed in most tissues in humans, possibly involved
in important cellular processes. HECT E3 mediates the
direct transfer of ubiquitin from E2 to substrate.
Length = 132
Score = 85.8 bits (213), Expect = 6e-20
Identities = 40/132 (30%), Positives = 64/132 (48%), Gaps = 13/132 (9%)
Query: 121 RANKGV-YGRGKYYYEATVTD---EGLCRVGWSTS--QAVRDLGTDRFGFGF-GGTGKK- 172
RA+ + +Y+E T+ D +G+ +G+ TS R G + +G+ G G+
Sbjct: 4 RADHPIPPKVPVFYFEVTILDLGEKGIVSIGFCTSGFPLNRMPGWEDGSYGYHGDDGRVY 63
Query: 173 SNNKQFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVVL 232
+ +NYG FG DV+GC ++ + FTKNG+ LG AF + + YP V L
Sbjct: 64 LGGGEGENYGPPFGTGDVVGCGINFKTGEIFFTKNGELLGTAF---ENVVKGRLYPTVGL 120
Query: 233 --KNAEMSFNFG 242
++ NFG
Sbjct: 121 GSPGVKVRVNFG 132
>gnl|CDD|240462 cd12882, SPRY_RNF123, SPRY domain at N-terminus of ring finger
protein 123. This SPRY domain is found at the
N-terminus of RING finger protein 123 domain (also known
as E3 ubiquitin-protein ligase RNF123). The ring finger
domain motif is present in a variety of functionally
distinct proteins and known to be involved in
protein-protein and protein-DNA interactions. RNF123
displays E3 ubiquitin ligase activity toward the
cyclin-dependent kinase inhibitor p27 (Kip1).
Length = 128
Score = 82.7 bits (205), Expect = 7e-19
Identities = 45/127 (35%), Positives = 68/127 (53%), Gaps = 6/127 (4%)
Query: 121 RANKGVYGRGKYYYEATVTDEGLCRVGWSTSQ----AVRDLGTDRFGFGFGGTGKKSNNK 176
RAN VY GK+ YE T+ +G+ ++GW+T +G + + G + N
Sbjct: 3 RANACVYK-GKWMYEVTLGTKGIMQIGWATISCRFTQEEGVGDTPDSYAYDGNRVRKWNV 61
Query: 177 QFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVVLKNAE 236
YGE + DVIGC +DLD T++F +NG+ LG+AF+ ++ A++PAV L E
Sbjct: 62 STQKYGEPWVAGDVIGCCIDLDEGTISFYRNGRSLGVAFDNVRRGPGLAYFPAVSLSFGE 121
Query: 237 M-SFNFG 242
NFG
Sbjct: 122 SVELNFG 128
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 79.6 bits (197), Expect = 1e-15
Identities = 48/145 (33%), Positives = 68/145 (46%), Gaps = 9/145 (6%)
Query: 284 APQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVG 343
P+ +I+ P+RELA Q +Q + K T I I GGV + V S DIVV
Sbjct: 73 PPRILILTPTRELAMQVADQARELAKH-THLDI--ATITGGVAYMNHAEVFSENQDIVVA 129
Query: 344 TPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIV 403
TPGR+ I + +LDEAD +L G+ I+ + + R Q ++
Sbjct: 130 TPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETR------WRKQTLL 183
Query: 404 CSATLHDFDVKKMAERLMYFPTWVD 428
SATL V+ AERL+ P V+
Sbjct: 184 FSATLEGDAVQDFAERLLNDPVEVE 208
Score = 67.7 bits (166), Expect = 7e-12
Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQ 62
F E+ + + +A+++ + PT +QAEAIP L G DVL +A TG+GKT AF LP +Q
Sbjct: 3 FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61
Score = 55.7 bits (135), Expect = 3e-08
Identities = 30/62 (48%), Positives = 36/62 (58%), Gaps = 6/62 (9%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAIS 514
GR+ + TD V AR GIDI + +IN +P Y+HRIGR GRA R G AIS
Sbjct: 294 GRVNVLVATD-VAAR-----GIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAIS 347
Query: 515 LV 516
LV
Sbjct: 348 LV 349
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 76.2 bits (188), Expect = 1e-14
Identities = 50/150 (33%), Positives = 79/150 (52%), Gaps = 8/150 (5%)
Query: 283 NAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVV 342
N P+A+I+ P+RELA Q + ++ L GG Q+ VL SGVDI++
Sbjct: 82 NQPRALIMAPTRELAVQIHADA---EPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILI 138
Query: 343 GTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMI 402
GT GR+ D H++L + VLDEAD + G+ I + +++P RL M+
Sbjct: 139 GTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPANQ---RLNML 195
Query: 403 VCSATLHDFDVKKMAERLMYFPTWVDLKGE 432
SATL + V+++A M P +V+++ E
Sbjct: 196 F-SATL-SYRVRELAFEHMNNPEYVEVEPE 223
Score = 54.2 bits (131), Expect = 1e-07
Identities = 24/48 (50%), Positives = 29/48 (60%)
Query: 468 ARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISL 515
A D A G+ I + + N LPDD +YVHRIGR GRA G +ISL
Sbjct: 311 ATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
Score = 45.3 bits (108), Expect = 6e-05
Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAF 56
F + + P++ +A+E+ + T +QA A+PL L G DV A+TG+GKT AF
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAF 62
>gnl|CDD|240489 cd12909, SPRY_RanBP9_10, SPRY domain in Ran binding proteins 9 and
10. This family includes SPRY domain in Ran binding
protein (RBP or RanBPM) 9 and 10, and similar proteins.
RanBP9 (also known as RanBPM), a binding partner of Ran,
is a small Ras-like GTPase that exerts multiple
functions via interactions with various proteins. RanBP9
and RanBP10 also act as androgen receptor (AR)
coactivators. Both consist of the N-terminal proline-
and glutamine-rich regions, the SPRY domain, and
LisH-CTLH and CRA motifs. SPRY domain of RanBPM forms a
complex with CD39, a prototypic member of the NTPDase
family, thus down-regulating activity substantially.
RanBP10 enhances the transcriptional activity of AR in a
ligand-dependent manner and exhibits a protein
expression pattern different from RanBPM in various cell
lines. RanBP10 is highly expressed in AR-positive
prostate cancer LNCaP cells, while RanBPM is abundant in
WI-38 and MCF-7 cells.
Length = 153
Score = 70.3 bits (173), Expect = 2e-14
Identities = 41/132 (31%), Positives = 56/132 (42%), Gaps = 32/132 (24%)
Query: 130 GKYYYEATVTD---EGLCRVGWSTSQAVRDL--------------GTDRFGFGFGGTGKK 172
G YY+E + +G +G ST +L G D F GTGK
Sbjct: 34 GIYYFEVKILSKGRDGYIGIGLSTKGV--NLNRLPGWEKHSWGYHGDDGHSFSSSGTGKP 91
Query: 173 SNNKQFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVVL 232
YG F DVIGC ++ + T+ +TKNG +LG AF + L + YP V L
Sbjct: 92 --------YGPTFTTGDVIGCGINFVDNTIFYTKNGVNLGTAF---RDLPDKNLYPTVGL 140
Query: 233 K--NAEMSFNFG 242
+ + NFG
Sbjct: 141 RTPGEHVEANFG 152
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 75.4 bits (185), Expect = 3e-14
Identities = 44/125 (35%), Positives = 69/125 (55%), Gaps = 8/125 (6%)
Query: 285 PQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGT 344
P+A+I+ P+RELA Q +KF D +R L+ GGV+ Q +L GVD+++ T
Sbjct: 85 PRALILAPTRELAIQIHKDAVKFG---ADLGLRFALVYGGVDYDKQRELLQQGVDVIIAT 141
Query: 345 PGRMEDLISGGH-LSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQMIV 403
PGR+ D + +SL C VLDEAD + G+ I + +++P+ + Q ++
Sbjct: 142 PGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTR----QTLL 197
Query: 404 CSATL 408
SATL
Sbjct: 198 FSATL 202
Score = 44.6 bits (105), Expect = 1e-04
Identities = 22/48 (45%), Positives = 27/48 (56%)
Query: 468 ARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISL 515
A D A G+ I G+ ++ N LP D +YVHRIGR R G AIS
Sbjct: 313 ATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360
Score = 38.8 bits (90), Expect = 0.009
Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII 61
F + P + +E + T +QA +P+ L GGDV A+TG+GKT AF + ++
Sbjct: 11 FSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVM 68
>gnl|CDD|240458 cd12878, SPRY2_RyR, SPRY domain 2 (SPRY2) of ryanodine receptor
(RyR). This SPRY domain (SPRY2) is the second of three
structural repeats in all three isoforms of the
ryanodine receptor (RyR), which are the major Ca2+
release channels in the membranes of sarcoplasmic
reticulum (SR). There are three RyR genes in mammals;
the skeletal RyR1, the cardiac RyR2 and the brain RyR3.
The three SPRY domains are located in the N-terminal
part of the cytoplasmic region of the RyRs, The SPRY2
domain has been shown to bind to the dihydropryidine
receptor (DHPR) II-III loop and the ASI region of RyR1.
Length = 133
Score = 68.5 bits (168), Expect = 7e-14
Identities = 30/86 (34%), Positives = 50/86 (58%), Gaps = 4/86 (4%)
Query: 129 RGKYYYEATVTDEGLCRVGWS--TSQAVRDLGTDRFGFGFGG-TGKKSNNKQFDNYGEAF 185
GK+Y+E V G RVGW+ + +LG+D + F G +K + +++G+ +
Sbjct: 13 SGKWYFEFEVLTSGYMRVGWARPGFRPDLELGSDDLSYAFDGFLARKWHQGS-ESFGKQW 71
Query: 186 GMHDVIGCLLDLDNMTVAFTKNGQHL 211
DV+GC+LDL + T++FT NG+ L
Sbjct: 72 QPGDVVGCMLDLVDRTISFTLNGELL 97
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 74.1 bits (182), Expect = 1e-13
Identities = 51/164 (31%), Positives = 82/164 (50%), Gaps = 15/164 (9%)
Query: 270 SADVSAGPVKLVNN------APQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIG 323
S +A + L++N APQ +++ P+RELA Q + F K + + + + G
Sbjct: 54 SGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHM--RGVNVVALYG 111
Query: 324 GVNVKDQMSVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLID 383
G Q+ L G IVVGTPGR+ D + G L L+ VLDEAD +L+ G+ ++
Sbjct: 112 GQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVE 171
Query: 384 RMHKQIPKITSDGKRLQMIVCSATLHDFDVKKMAERLMYFPTWV 427
+ QIP + Q + SAT+ + ++++ R M P V
Sbjct: 172 TIMAQIP------EGHQTALFSATMPE-AIRRITRRFMKEPQEV 208
Score = 63.3 bits (154), Expect = 2e-10
Identities = 34/91 (37%), Positives = 52/91 (57%), Gaps = 9/91 (9%)
Query: 3 AFEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQ 62
F ++G+ I +A+ ++ + P+ +QAE IP +L G DVL A+TGSGKT AF LP++
Sbjct: 7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLH 66
Query: 63 IVCETLKEIQAGKGQGKAKAQVISPTWILSV 93
+ LK Q V++PT L+V
Sbjct: 67 NLDPELKAPQ---------ILVLAPTRELAV 88
Score = 52.5 bits (126), Expect = 5e-07
Identities = 28/62 (45%), Positives = 36/62 (58%), Gaps = 6/62 (9%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAIS 514
GRL I TD V AR G+D+ + ++N +P D +YVHRIGR GRA R G A+
Sbjct: 294 GRLDILIATD-VAAR-----GLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALL 347
Query: 515 LV 516
V
Sbjct: 348 FV 349
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 72.1 bits (177), Expect = 3e-13
Identities = 44/169 (26%), Positives = 85/169 (50%), Gaps = 11/169 (6%)
Query: 282 NNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIV 341
P A+++ P+REL Q +Q K + + L++GG + Q+ + GV+++
Sbjct: 194 QRNPLAMVLTPTRELCVQVEDQAKVLGKGL---PFKTALVVGGDAMPQQLYRIQQGVELI 250
Query: 342 VGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGKRLQM 401
VGTPGR+ DL+S + L + VLDE D +L++G+ Q+ +I + Q+
Sbjct: 251 VGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGF-------RDQVMQIFQALSQPQV 303
Query: 402 IVCSATLHDFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQ 450
++ SAT+ +V+K A L + + + + V + + ++ +Q
Sbjct: 304 LLFSATVSP-EVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQ 351
Score = 58.6 bits (142), Expect = 5e-09
Identities = 34/96 (35%), Positives = 49/96 (51%), Gaps = 2/96 (2%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQI 63
F G+ P++ +E + PT +Q +AIP L G +L++A+TGSGKT +F +PII
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182
Query: 64 VCETLKEIQAGKGQGKAKAQVISPTWILSVWDRDTA 99
C Q A V++PT L V D A
Sbjct: 183 CCTI--RSGHPSEQRNPLAMVLTPTRELCVQVEDQA 216
Score = 29.8 bits (67), Expect = 4.9
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLV 516
G+D+ + +I +P+ Y+H+IGR R G AI V
Sbjct: 431 GVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFV 472
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 71.3 bits (175), Expect = 6e-13
Identities = 40/117 (34%), Positives = 62/117 (52%), Gaps = 3/117 (2%)
Query: 273 VSAGPVKLVNNAPQAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMS 332
++A P+ + P +++ P+RELAEQ Q KF KIR + GGV + Q+
Sbjct: 192 INAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFG---ASSKIRNTVAYGGVPKRGQIY 248
Query: 333 VLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGLLKQGYGNLIDRMHKQI 389
L GV+I++ PGR+ D + +L + VLDEAD +L G+ I ++ QI
Sbjct: 249 ALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQI 305
Score = 47.8 bits (114), Expect = 1e-05
Identities = 24/58 (41%), Positives = 33/58 (56%)
Query: 4 FEEMGVLPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII 61
FE I K+++ + PT +Q + P+ L G D++ AETGSGKT AF LP I
Sbjct: 132 FEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAI 189
Score = 46.7 bits (111), Expect = 3e-05
Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 16/84 (19%)
Query: 447 DPQQDE-TW-------GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDKANYVH 498
D +Q+E TW G+ I TD V +R G+D+ + ++IN P+ +YVH
Sbjct: 410 DKKQEERTWVLNEFKTGKSPIMIATD-VASR-----GLDVKDVKYVINFDFPNQIEDYVH 463
Query: 499 RIGRVGRAERMGLAISLVSTVPEK 522
RIGR GRA G + + ++ P+K
Sbjct: 464 RIGRTGRAGAKGASYTFLT--PDK 485
>gnl|CDD|240463 cd12883, SPRY_RING, SPRY domain at N-terminus of Really Interesting
New Gene (RING) finger domain. This SPRY domain is
found at the N-terminus of RING finger domains which are
present in a variety of functionally distinct proteins
and known to be involved in protein-protein and
protein-DNA interactions. RING-finger domain is a type
of Zn-finger that binds two Zn atoms and is identified
in proteins with a wide range of functions such as viral
replication, signal transduction, and development.
Length = 121
Score = 62.3 bits (152), Expect = 7e-12
Identities = 37/128 (28%), Positives = 53/128 (41%), Gaps = 22/128 (17%)
Query: 130 GKYYYEATVTDEGLCRVGWSTSQAV------RDLGTDRFGFGFGGTGKKSNNKQFDNYGE 183
G +YYE TV G+ ++GW+T + +G D + F + G +Q Y
Sbjct: 1 GVWYYEVTVLTSGVMQIGWATKDSKFLNHEGYGIGDDEYSFAYDGC------RQLIWYNA 54
Query: 184 AFGMH--------DVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVVLKNA 235
H DV+GCLLDLD + F+ NG L S F+ A +
Sbjct: 55 ESRPHTHPRWKPGDVVGCLLDLDKKQMIFSLNGNRLPPERLPFTSAS-SGFFAAASFMSF 113
Query: 236 EM-SFNFG 242
+ FNFG
Sbjct: 114 QQCEFNFG 121
>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 = 53.0 bits (128), Expect = 2e-08
Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISL 515
GID+ + +IN LP ++Y+ RIGR GRA + G AI L
Sbjct: 91 GIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|240466 cd12886, SPRY_like, SPRY domain-like in bacteria. This family
contains SPRY-like domains that are found only in
bacterial and are mostly uncharacterized. SPRY domains,
first identified in the SP1A kinase of Dictyostelium and
rabbit Ryanodine receptor (hence the name), are
homologous to B30.2. SPRY domains have been identified
in at least 11 eukaryotic protein families, covering a
wide range of functions, including regulation of
cytokine signaling (SOCS), RNA metabolism (DDX1 and
hnRNP), immunity to retroviruses (TRIM5alpha),
intracellular calcium release (ryanodine receptors or
RyR) and regulatory and developmental processes (HERC1
and Ash2L).
Length = 128
Score = 51.3 bits (123), Expect = 6e-08
Identities = 35/128 (27%), Positives = 49/128 (38%), Gaps = 15/128 (11%)
Query: 130 GKYYYEATVTDEGL---CRVGWSTSQAVRDLGTDRFGFGFG-GTGKKSNNKQFDN----- 180
GK+Y+E TV +G + + + G +G G S N
Sbjct: 1 GKWYWEVTVVSSTSSSAAGIGVAPAAVTLNNGLGIELSSYGYSLGVSSGNTYSGGSTVAS 60
Query: 181 YGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLG---LAFNISQQLKNSAFYPAVVLKNA-- 235
+G F DVIG LDLD + F KNG G A + + YPAV ++
Sbjct: 61 FGAGFTAGDVIGVALDLDAGKIWFYKNGVWQGSGSPAPGTNPAFAGTQVYPAVTGGSSTG 120
Query: 236 -EMSFNFG 242
+ NFG
Sbjct: 121 GSFTANFG 128
>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 = 49.4 bits (119), Expect = 1e-07
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGRA 506
GID+ + +IN LP + A+Y+ RIGR GRA
Sbjct: 46 GIDLPDVNLVINYDLPWNPASYIQRIGRAGRA 77
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 55.0 bits (133), Expect = 1e-07
Identities = 27/63 (42%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 25 PTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQV 84
T Q AIP I G +VL+ A TGSGKT A LP+I L + GK + A
Sbjct: 23 LTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVIN----ELLSLGKGKLEDGIYALY 78
Query: 85 ISP 87
ISP
Sbjct: 79 ISP 81
>gnl|CDD|240456 cd12876, SPRY_SOCS3, SPRY domain in the suppressor of cytokine
signaling 3 (SOCS3) family. The SPRY domain-containing
SOCS box protein family (SPSB1-4, also known as SSB-1 to
-4) is composed of a central SPRY protein interaction
domain and a C-terminal SOCS box. All four SPSB proteins
interact with c-Met, the hepatocyte growth factor
receptor, but SOCS3 regulates cellular response to a
variety of cytokines such as leukemia inhibitory factor
(LIF) and interleukin 6. SOCS3, along with SOCS1, are
expressed by immune cells and cells of the central
nervous system (CNS) and have the potential to impact
immune processes within the CNS. In non-small cell lung
cancer (NSCLC), SOCS3 is silenced and proline-rich
tyrosine kinase 2 (Pyk2) is over-expressed; it has been
suggested that SOCS3 could be an effective way to
prevent the progression of NSCLC due to its role in
regulating Pyk2 expression.
Length = 187
Score = 52.2 bits (126), Expect = 1e-07
Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 157 LGTDRFGFGFGGTGKKSNNKQFDNYGEAFG-MHDVIGCLLDLDNMTVAFTKNGQHLGLAF 215
LG D +G G +N + Y E FG +IG LD+ + T+ F KNG+ LG+AF
Sbjct: 84 LGLDEESWGLSYKGLLWHNGESRPYTEKFGNQGTIIGVHLDMWSGTLTFYKNGKPLGVAF 143
Query: 216 -NISQQLKNSAFYPAV 230
+ Q YP V
Sbjct: 144 TGL--QNDGKKLYPMV 157
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 45.7 bits (109), Expect = 2e-06
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGRA 506
G+D+ G+ +I LP A+Y+ RIGR GRA
Sbjct: 50 GLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81
>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 = 47.4 bits (113), Expect = 2e-05
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 10/60 (16%)
Query: 29 QAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEIQAGKGQGKAKAQVISPT 88
Q +A+ LI G +V++ TGSGKT +F LPI+ L+ A+A ++ PT
Sbjct: 75 QVDALRLIREGRNVVVTTGTGSGKTESFLLPILD---HLLR-------DPSARALLLYPT 124
Score = 38.5 bits (90), Expect = 0.012
Identities = 38/184 (20%), Positives = 79/184 (42%), Gaps = 23/184 (12%)
Query: 286 QAIIIEPSRELAEQTFNQIIKFKKFITD--PKIRELLIIGGVNVKDQMSVLSSGVDIVVG 343
+A+++ P+ LA +Q + ++ I+D K+ G +++ +++ + DI++
Sbjct: 117 RALLLYPTNALA---NDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLT 173
Query: 344 TPGRMEDLISGGHLS----LTHCRFFVLDEA---DGLLKQGYGNLIDRMHKQIPKITSDG 396
P + L+ H + L + ++ V+DE G+ L+ R+ + + G
Sbjct: 174 NPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRL-LRR--LRRYG 230
Query: 397 KRLQMIVCSATLHD--FDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQDETW 454
LQ+I SATL + +++ R P ED P + + V +P E
Sbjct: 231 SPLQIICTSATLANPGEFAEELFGRDFEVPVD-----EDGSPRGLRYFVR-REPPIRELA 284
Query: 455 GRLR 458
+R
Sbjct: 285 ESIR 288
Score = 31.6 bits (72), Expect = 1.6
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 455 GRLRSHIQTDGVHARDNARPGIDISGLPFIINMTLPDDK-ANYVHRIGRVGRAERMGLAI 513
G L I T+ + GIDI L +I P ++ R GR GR + L +
Sbjct: 363 GELLGVIATNALEL------GIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVL 416
Query: 514 SLVSTVP 520
++ + P
Sbjct: 417 VVLRSDP 423
>gnl|CDD|240457 cd12877, SPRY1_RyR, SPRY domain 1 (SPRY1) of ryanodine receptor
(RyR). This SPRY domain is the first of three
structural repeats in all three isoforms of the
ryanodine receptor (RyR), which are the major Ca2+
release channels in the membranes of sarcoplasmic
reticulum (SR). There are three RyR genes in mammals;
the skeletal RyR1, the cardiac RyR2 and the brain RyR3.
The three SPRY domains are located in the N-terminal
part of the cytoplasmic region of the RyRs, but no
specific function has been found for this first SPRY
domain of the RyRs.
Length = 151
Score = 43.8 bits (104), Expect = 4e-05
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 26/114 (22%)
Query: 119 GCRANKGVYGRGKYYYEATVT--DEGLC-----RVGWSTSQAVRD------------LGT 159
G Y K+Y+E V ++ RVGW+ + +G
Sbjct: 9 GVVEGSAQYK--KWYFEVEVDHVEQFTHQPAHLRVGWANTSGYVPYPGGGEGWGGNGVGD 66
Query: 160 DRFGFGFGG----TGKKSNNKQFDNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQ 209
D + +GF G TG +S DV+GC LDL +++F NG+
Sbjct: 67 DLYSYGFDGLHLWTGGRSRRVTSGTQ-HLLKKGDVVGCCLDLSVPSISFRVNGR 119
>gnl|CDD|240469 cd12889, SPRY_PRY_TRIM67_9, PRY/SPRY domain in tripartite
motif-containing proteins, TRIM9 and TRIM67. This
domain, consisting of the distinct N-terminal PRY
subdomain followed by the SPRY subdomain, is found at
the C-terminus of TRIM9 proteins. TRIM9 protein is
expressed mainly in the cerebral cortex, and functions
as an E3 ubiquitin ligase. It has been shown that TRIM9
is localized to the neurons in the normal human brain
and its immunoreactivity in affected brain areas in
Parkinson's disease and dementia with Lewy bodies is
severely decreased, possibly playing an important role
in the regulation of neuronal function and participating
in pathological process of Lewy body disease through its
ligase. TRIM67 negatively regulates Ras activity via
degradation of 80K-H , leading to neural
differentiation, including neuritogenesis.
Length = 172
Score = 39.9 bits (94), Expect = 0.001
Identities = 33/117 (28%), Positives = 48/117 (41%), Gaps = 16/117 (13%)
Query: 129 RGKYYYEATV---TDEGLCRVGWSTSQAVRD--LGTDRFGFGFGGTGKKS----NNKQFD 179
RG +Y+E T+ G + + +D LG D G+ +S NN+ +
Sbjct: 48 RGVHYWEVTIDRYDGHPDPAFGVARADVAKDKMLGKDDKGWAMYIDSNRSWFLHNNEHSN 107
Query: 180 NYGEAFGMHDVIGCLLDLDNMTVAFTKNG-QHLGLAF-NISQQLKNSAFYPAVVLKN 234
+ VIG LLDLD T++F N +AF N+ FYPA L
Sbjct: 108 RTEGGITVGSVIGVLLDLDRGTLSFYVNDEPQGPVAFTNLPG-----LFYPAFSLNR 159
>gnl|CDD|240486 cd12906, SPRY_SOCS1-2-4, SPRY domain in the suppressor of cytokine
signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4). The
SPRY domain-containing SOCS box protein family (SPSB1-4,
also known as SSB-1 to -4) is composed of a central SPRY
protein interaction domain and a C-terminal SOCS box.
All four SPSB proteins interact with c-Met, the
hepatocyte growth factor receptor, but only SPSB1,
SPSB2, and SPSB4 interact with prostate apoptosis
response protein 4 (Par-4). They are negative regulators
that recruit the ECS E3 ubiquitin ligase complex to
polyubiquitinate inducible nitric-oxide synthase (iNOS),
resulting in its proteasomal degradation, thus
contributing to protection against the cytotoxic effect
of iNOS in activated macrophages. It has been shown that
SPSB1 and SPSB4 induce the degradation of iNOS more
strongly than SPSB2. The Drosophila melanogaster SPSB1
homolog, GUSTAVUS, interacts with the DEAD box RNA
helicase Vasa. Suppressor of cytokine signaling (SOCS)
proteins negatively regulate signaling from
JAK-associated cytokine receptor complexes, and play key
roles in the regulation of immune homeostasis.
Length = 174
Score = 40.0 bits (94), Expect = 0.001
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 182 GEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV 230
E F + D +LD+D T++F +GQ+LG+AF + LK YP V
Sbjct: 115 DENFVVPDKFLVVLDMDEGTLSFVVDGQYLGVAF---RGLKGKTLYPIV 160
>gnl|CDD|240455 cd12875, SPRY_SOCS_Fbox, SPRY domain in Fbxo45 and suppressors of
cytokine signaling (SOCS) proteins. This family
consists of the SPRY domain-containing SOCS box protein
family (SPSB1-4, also known as SSB-1 to -4) as well as
F-box protein 45 (Fbxo45), a novel synaptic E3 and
ubiquitin ligase. The SPSB protein is composed of a
central SPRY protein interaction domain and a C-terminal
SOCS box. SPSB1, SPSB2, and SPSB4 interact with prostate
apoptosis response protein 4 (Par-4) and are negative
regulators that recruit the ECS E3 ubiquitin ligase
complex to polyubiquitinate inducible nitric-oxide
synthase (iNOS), resulting in its proteasomal
degradation. Fbxo45 is related to this family; it is
located N-terminal to the SPRY domain, and known to
induce the degradation of a synaptic vesicle-priming
factor, Munc13-1, via the SPRY domain, thus playing an
important role in the regulation of neurotransmission by
modulating Munc13-1 at the synapse. Suppressor of
cytokine signaling (SOCS) proteins negatively regulate
signaling from JAK-associated cytokine receptor
complexes, and play key roles in the regulation of
immune homeostasis.
Length = 171
Score = 39.7 bits (93), Expect = 0.001
Identities = 43/142 (30%), Positives = 63/142 (44%), Gaps = 28/142 (19%)
Query: 119 GCRANKGVYGRGKYYYEATVTDEGLCR-----VGWSTSQA-------VRDLGTDRFGFGF 166
R G Y RG + +E V EG R VG +T A V LG+D +G+
Sbjct: 32 AIRGKIG-YSRGLHAWE--VKWEGRQRGSHAVVGVATKDAPLQCDGYVALLGSDSESWGW 88
Query: 167 G-GTGK-----KSNNKQF--DNYGEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAFNIS 218
T K K + + E + + D + +LD+++ T+AF NG++LG+AF
Sbjct: 89 DLSTNKLYHDGKVVIGSYPAGSATENYSVPDRVLVILDMEDGTLAFEANGEYLGVAFR-- 146
Query: 219 QQLKNSAFYPAV--VLKNAEMS 238
L YPAV V N E+
Sbjct: 147 -GLPGKLLYPAVSAVYGNCEIR 167
>gnl|CDD|240461 cd12881, SPRY_HERC1, SPRY domain in HERC1. This SPRY domain is
found in the HERC1, a large protein related to
chromosome condensation regulator RCC1. It is widely
expressed in many tissues, playing an important role in
intracellular membrane trafficking in the cytoplasm as
well as Golgi apparatus. HERC1 also interacts with
tuberous sclerosis 2 (TSC2, tuberin), which suppresses
cell growth, and results in the destabilization of TSC2.
However, the biological function of HERC1 has yet to be
defined.
Length = 160
Score = 39.2 bits (92), Expect = 0.002
Identities = 16/43 (37%), Positives = 28/43 (65%), Gaps = 3/43 (6%)
Query: 189 DVIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAVV 231
D I C+LD++ T++F KNG+ G+AF + + ++ YP V+
Sbjct: 106 DYITCVLDMEERTLSFGKNGEEPGVAF---EDVDSTELYPCVM 145
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 40.6 bits (96), Expect = 0.003
Identities = 20/36 (55%), Positives = 24/36 (66%)
Query: 26 TDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPII 61
T Q AIPLI G +VL+++ TGSGKT A L II
Sbjct: 34 TPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAII 69
>gnl|CDD|240492 cd13734, SPRY_PRY_C-I, PRY/SPRY domain in tripartite
motif-containing proteins 1, 9, 18, 36, 46, 67,76
(TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67, TRIM76).
This domain, consisting of the distinct N-terminal PRY
subdomain followed by the SPRY subdomain, is found at
the C-terminus of several Class I TRIM proteins,
including TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67
and TRIM76. TRIM1 (also known as MID2) and its close
homolog, TRIM18 (also known as MID1), both contain a
B30.2-like domain at their C-terminus and a single
fibronectin type III (FN3) motif between it and their
N-terminal RBCC domain. Their coiled-coil motifs mediate
both homo- and heterodimerization, a prerequisite for
association of the rapamycin-sensitive PP2A regulatory
subunit Alpha 4 with microtubules. Mutations in TRIM18
have shown to cause Opitz syndrome, a disorder causing
congenital anomalies such as cleft lip and palate as
well as heart defects. TRIM9 is expressed mainly in the
cerebral cortex, and functions as an E3 ubiquitin
ligase. Its immunoreactivity is severely decreased in
affected brain areas in Parkinson's disease and dementia
with Lewy bodies, possibly playing an important role in
the regulation of neuronal function and participating in
pathological process of Lewy body disease through its
ligase. TRIM36 interacts with centromere protein-H, one
of the kinetochore proteins and possibly associates with
chromosome segregation; an excess of TRIM36 may cause
chromosomal instability. TRIM46 has not yet been
characterized. TRIM67 negatively regulates Ras activity
via degradation of 80K-H, leading to neural
differentiation, including neuritogenesis. TRIM76 (also
known as cardiomyopathy-associated protein 5 or CMYA5)
is a muscle-specific member of the TRIM superfamily, but
lacks the RING domain. It is possibly involved in
protein kinase A signaling as well as vesicular
trafficking. It has also been implicated in Duchenne
muscular dystrophy and cardiac disease.
Length = 169
Score = 36.5 bits (85), Expect = 0.015
Identities = 30/124 (24%), Positives = 43/124 (34%), Gaps = 38/124 (30%)
Query: 129 RGKYYYEATVTDEGLCRVGWSTSQAVRD--LGTDRFGFGFGGTGKKSNNKQFD---NYGE 183
G++Y+E +V RVG + RD LG N+ +
Sbjct: 54 SGRHYWEVSVDRSTSYRVGVAYKSVPRDEDLG--------------KNSTSWCLRRTNNR 99
Query: 184 AFGMHDV-------------IGCLLDLDNMTVAF--TKNGQHLGLAFNISQQLKNSAFYP 228
HD IG LLD D T++F ++ QHL F++ YP
Sbjct: 100 YSARHDGKVVDLTVTPHPRRIGVLLDYDRGTLSFYDAESKQHL-HTFHVD---FEEPVYP 155
Query: 229 AVVL 232
A L
Sbjct: 156 AFSL 159
>gnl|CDD|240487 cd12907, SPRY_Fbox, SPRY domain in the F-box family Fbxo45. Fbxo45
is a novel synaptic E3 and ubiquitin ligase, related to
the suppressor of cytokine signaling (SOCS) proteins and
located N-terminal to a SPRY (SPla and the ryanodine
receptor) domain. Fbxo45 induces the degradation of a
synaptic vesicle-priming factor, Munc13-1, via the SPRY
domain, thus playing an important role in the regulation
of neurotransmission by modulating Munc13-1 at the
synapse. F-box motifs are found in proteins that
function as the substrate recognition component of SCF
E3 complexes.
Length = 175
Score = 35.2 bits (81), Expect = 0.052
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 191 IGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV--VLKNAEMSFNFGATP 245
I +LD+++ T+AF + + LG+AF L YPAV V N E++ + P
Sbjct: 119 IRVILDMEDNTLAFERGYEFLGVAFR---GLPKVCLYPAVSAVYGNTEVTMVYLGPP 172
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 35.7 bits (83), Expect = 0.071
Identities = 16/43 (37%), Positives = 20/43 (46%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAISLVS 517
GID + F+I+ LP +Y GR GR AI L S
Sbjct: 293 GIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYS 335
>gnl|CDD|240490 cd12910, SPRY_SSH4_like, SPRY domain in SSH4 and similar proteins.
This family includes SPRY domain in SSH4 (suppressor of
SHR3 null mutation protein 4) and similar proteins. SSH4
is a component of the endosome-vacuole trafficking
pathway that regulates nutrient transport and may be
involved in processes determining whether plasma
membrane proteins are degraded or routed to the plasma
membrane. The SPRY domain in SSH4 may be involved in
cargo recognition, either directly or by combination
with other adaptors, possibly leading to a higher
selectivity. In yeast, SSH4 and the homologous protein
EAR1 (endosomal adapter of RSP5) recruit Rsp5p, an
essential ubiquitin ligase of the Nedd4 family, and
assist it in its function at multivesicular bodies by
directing the ubiquitylation of specific cargoes.
Length = 191
Score = 34.2 bits (79), Expect = 0.10
Identities = 29/133 (21%), Positives = 46/133 (34%), Gaps = 21/133 (15%)
Query: 131 KYYYEATVTD----EGLCRVGWSTSQ--AVRDLGTDRFGFG-FGGTGKKSNNKQF--DNY 181
Y+E + D + +G++T R G R G + N F ++
Sbjct: 56 TIYFEVKIYDLPRDDTSVAIGFATKPYPPFRLPGWHRGSLAVHSDDGHRYINDPFGGKDF 115
Query: 182 GEAFGMHDVIGCLLDLDNMTVAFTKNGQHLGLAF----------NISQQLKNSAFYPAVV 231
F D IG + TV FT+NG+ LG ++ YPA+
Sbjct: 116 TPPFREGDTIGIGYKFSSGTVFFTRNGKKLGEWDLGEELDAEDDGVTGLEGFHDLYPAIG 175
Query: 232 LKN--AEMSFNFG 242
+ E+ N G
Sbjct: 176 VFGGECEVHVNPG 188
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 35.4 bits (82), Expect = 0.11
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 29 QAEAI-PLILGGGDVLMAAETGSGKT 53
Q EA+ +L +VL++A TGSGKT
Sbjct: 36 QQEAVEKGLLSDENVLISAPTGSGKT 61
>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 = 34.3 bits (79), Expect = 0.25
Identities = 29/113 (25%), Positives = 46/113 (40%), Gaps = 16/113 (14%)
Query: 11 PEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKE 70
P++ A+E P QA A L G V++A T SGK+ A+ LP+
Sbjct: 23 PDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPV---------- 72
Query: 71 IQAGKGQGKAKAQVISPTWILSVWDRDTAMAITPEGLRCQ------SREQKEW 117
+ A +A A ++PT L+ +T G+R E++ W
Sbjct: 73 LSALADDPRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRW 125
Score = 29.7 bits (67), Expect = 6.6
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGRAERMGLAI 513
G+DISGL ++ P +A+ + GR GR + L +
Sbjct: 342 GVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVV 380
>gnl|CDD|149722 pfam08750, CNP1, CNP1-like family. This family of proteins are
likely to be lipoproteins. CNP1 (cryptic neisserial
protein) has been expressed in E. coli and shown to be
localised periplasmicly.
Length = 139
Score = 32.3 bits (74), Expect = 0.34
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 14/73 (19%)
Query: 99 AMAITPEGLRCQSREQK---------EWHGCRAN--KGVYGRGKYYYEATVTDEGLCR-- 145
A ++ EG+RC + E+K W R + + Y A + + C
Sbjct: 65 ARNVSYEGIRCDTFERKIYATGRNDGRWSRARRAEWQRIEDGAPNRYHAALAQDYFCPGG 124
Query: 146 -VGWSTSQAVRDL 157
++AVR L
Sbjct: 125 SPAGDAAEAVRRL 137
>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 = 32.0 bits (73), Expect = 1.2
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 26 TDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIV 64
TD Q +AI G D+L++A GSGKT II+ +
Sbjct: 3 TDEQWQAI--YTRGQDILVSASAGSGKTAVLVERIIRKI 39
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 31.8 bits (72), Expect = 1.4
Identities = 22/52 (42%), Positives = 31/52 (59%), Gaps = 11/52 (21%)
Query: 376 QGYGNLIDR---MHKQI-----PKITSDGKRLQM--IVCSATLHDFDVKKMA 417
+GY L++R +HKQ PK+ DGK +Q+ +VCSA DFD +MA
Sbjct: 1806 EGYPVLLNRAPTLHKQSIQAFHPKLI-DGKAIQLHPLVCSAFNADFDGDQMA 1856
>gnl|CDD|203913 pfam08336, P4Ha_N, Prolyl 4-Hydroxylase alpha-subunit, N-terminal
region. The members of this family are eukaryotic
proteins, and include all three isoforms of the prolyl
4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2)
is important in the post-translational modification of
collagen, as it catalyzes the formation of
4-hydroxyproline. In vertebrates, the complete enzyme is
an alpha2-beta2 tetramer; the beta-subunit is identical
to protein disulphide isomerase. The function of the
N-terminal region featured in this family does not seem
to be known.
Length = 134
Score = 29.9 bits (68), Expect = 1.8
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 381 LIDRMHKQIPKITSDGKRLQMIVCSATLHDFDVKKMAERLMYFPTWVDLKG 431
LI R+H +D +L+ + + +K + E PT DL+G
Sbjct: 65 LIKRLH-------TDWPKLENYMEKDVGEEL-IKNLEELRKSLPTDEDLEG 107
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 31.2 bits (71), Expect = 2.0
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 21/75 (28%)
Query: 334 LSSGVDIVVGTPG----RMEDLISGGHLSLTH------------CRFFVLDEADGLL--- 374
L++G++I PG + L+SGG SLT F+VLDE D L
Sbjct: 1046 LTAGIEISARPPGKKLQSLS-LLSGGEKSLTALALLFAIQKYRPAPFYVLDEVDAALDDA 1104
Query: 375 -KQGYGNLIDRMHKQ 388
+ LI M K+
Sbjct: 1105 NVERVARLIKEMSKE 1119
>gnl|CDD|107088 PHA01818, PHA01818, hypothetical protein.
Length = 458
Score = 30.8 bits (69), Expect = 2.7
Identities = 22/82 (26%), Positives = 32/82 (39%), Gaps = 10/82 (12%)
Query: 314 PKIRELLIIGGVNVKDQMSVLSSGVDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEADGL 373
P + +I G N+ D + S GV V+G G M +S G L L +D D
Sbjct: 148 PSNKNAVISGT-NILD---IASPGVYFVMGMTGGMPSGVSSGFLDL------SVDANDNR 197
Query: 374 LKQGYGNLIDRMHKQIPKITSD 395
L + + + I K T
Sbjct: 198 LARLTDAETGKEYTSIKKPTGT 219
>gnl|CDD|128778 smart00502, BBC, B-Box C-terminal domain. Coiled coil region
C-terminal to (some) B-Box domains.
Length = 127
Score = 29.2 bits (66), Expect = 2.9
Identities = 9/52 (17%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 569 DEKRMLGEIEEHLN---VTIQQVDDKLEIPADEFDGKVVYGQKRVNMGSSYE 617
+K++L ++EE ++Q + L ++ + + ++ +N G E
Sbjct: 58 RKKQLLEDLEEQKENKLKVLEQQLESLTQKQEKLSHAINFTEEALNSGDPTE 109
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains separated
by a hinge in the middle. The eukaryotic SMC proteins
form two kind of heterodimers: the SMC1/SMC3 and the
SMC2/SMC4 types. These heterodimers constitute an
essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 30.7 bits (69), Expect = 2.9
Identities = 23/101 (22%), Positives = 37/101 (36%), Gaps = 15/101 (14%)
Query: 286 QAIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVLSSGVDIVVGTP 345
+ II E + E + + EL + ++D S G++I P
Sbjct: 1010 REIIEETCQRFKEFLELFVSINRGLNKVFFYLELGGSAELRLEDSDDPFSGGIEISARPP 1069
Query: 346 G---RMEDLISGGHLSLT---------HCR---FFVLDEAD 371
G + D +SGG +L R F++LDE D
Sbjct: 1070 GKGVKNLDNLSGGEKTLVALALIFAIQKYRPAPFYLLDEID 1110
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.4 bits (69), Expect = 3.4
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 15/99 (15%)
Query: 287 AIIIEPSRELAEQTFNQIIKFKKFITDPKIRELLIIGGVNVKDQMSVL----SSGVDIVV 342
II P+ L Q + ++ KF + + ++ + K++ L S DI++
Sbjct: 128 VYIIVPTTTLVRQVYERLKKFAEDAGSLDVL-VVYHSALPTKEKEEALERIESGDFDILI 186
Query: 343 GT----PGRMEDLISGGHLSLTHCRFFVLDEADGLLKQG 377
T R E+L F +D+ D +LK
Sbjct: 187 TTSQFLSKRFEELSK------LKFDFIFVDDVDAILKAS 219
>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 = 30.4 bits (69), Expect = 3.8
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 31/103 (30%)
Query: 294 RELAEQTFNQIIK-FKKFITDPKIRELLIIGG------VNVKDQMSVLSSGVDIVVGTPG 346
RE + TF+Q+ + F++ L GG + +D +L +G++I PG
Sbjct: 1031 RERFKDTFDQVNENFQRVFPK------LFGGGEAELRLTDPED---LLEAGIEIFAQPPG 1081
Query: 347 -RMED--LISGGHLSLT---------HCR---FFVLDEADGLL 374
+ ++ L+SGG +LT + F +LDE D L
Sbjct: 1082 KKNQNLSLLSGGEKALTALALLFAIFKVKPAPFCILDEVDAPL 1124
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.3 bits (64), Expect = 3.8
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 25 PTDVQAEAIPLILGGGDVLMAAETGSGKT 53
Q EAI +L L+ TGSGKT
Sbjct: 4 LRPYQEEAIERLLEKKRGLIVMATGSGKT 32
>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 = 30.4 bits (69), Expect = 3.9
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 278 VKLVNNAPQAIIIEPSRELAEQTFNQIIK-FKKFITDPKIRELL--IIGGVNVKDQMSVL 334
K V + Q ++ P+ LA+Q F + F F P ELL + + L
Sbjct: 494 FKAVLDGKQVAVLVPTTLLAQQHFETFKERFANF---PVTIELLSRFRSAKEQNEILKEL 550
Query: 335 SSG-VDIVVGT 344
+SG +DI++GT
Sbjct: 551 ASGKIDILIGT 561
>gnl|CDD|219138 pfam06690, DUF1188, Protein of unknown function (DUF1188). This
family consists of several hypothetical archaeal
proteins of around 260 residues in length which seem to
be specific to Methanobacterium, Methanococcus and
Methanopyrus species. The function of this family is
unknown.
Length = 252
Score = 29.7 bits (67), Expect = 4.1
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 288 IIIEPSRELAEQTFNQIIKFKKFITDPKIRELLII-----GGVNVKDQMSVLSSGVDIVV 342
+++ L E N+ IKF + I LI+ GGV+ +++S L+ V IV
Sbjct: 68 TVVDIHPHLKE-ILNEGIKFMESINGTPGNPDLIVDLTGLGGVS-PEELSKLNPKVLIVE 125
Query: 343 GTPGRMED 350
G D
Sbjct: 126 DPKGDGSD 133
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 30.2 bits (68), Expect = 4.4
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 30 AEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEI 71
+ GG +L+ A TG+GKT A+ LP + E K++
Sbjct: 25 EAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV 66
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 30.1 bits (68), Expect = 4.9
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 25 PTDVQAEAIPLILGGGDVLMAAETGSGKT 53
Q EAI ++ G VL+ A T SGKT
Sbjct: 120 LDPFQQEAIAILERGESVLVCAPTSSGKT 148
>gnl|CDD|189009 cd09602, M1_APN_3, Peptidase M1 family containing Aminopeptidase N.
This family contains bacterial and eukaryotic
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 438
Score = 29.9 bits (68), Expect = 5.2
Identities = 18/105 (17%), Positives = 32/105 (30%), Gaps = 16/105 (15%)
Query: 410 DFDVKKMAERLMYFPTWVDLKGEDAVPETVHHVVVKIDPQQDETWGRLRSHIQTDGVHAR 469
FD++K ++D KG V V + +P +T+ R + +
Sbjct: 30 TFDLRKNGG-----DLFIDFKGG-----QVLSVSLNGNPVDPDTFEDGRIPLPGLELKNG 79
Query: 470 DN-----ARPGIDISGLPFIINMTLPDDKANYVHRIGRVGRAERM 509
N G + P D Y++ A R+
Sbjct: 80 RNEVVIDFTNPYSNDGEG-LHRFVDPADGKTYLYTQFEPDDARRV 123
>gnl|CDD|180668 PRK06719, PRK06719, precorrin-2 dehydrogenase; Validated.
Length = 157
Score = 28.8 bits (64), Expect = 5.7
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 35 LILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLKEI 71
+I+GGG + +G TGAF + +C+ +KE+
Sbjct: 17 VIIGGGKIAYRKASGLKDTGAFVTVVSPEICKEMKEL 53
>gnl|CDD|99733 cd00378, SHMT, Serine-glycine hydroxymethyltransferase (SHMT). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). SHMT
carries out interconversion of serine and glycine; it
catalyzes the transfer of hydroxymethyl group of N5,
N10-methylene tetrahydrofolate to glycine resulting in
the formation of serine and tetrahydrofolate. Both
eukaryotic and prokaryotic SHMT enzymes form tight
obligate homodimers; the mammalian enzyme forms a
homotetramer comprising four pyridoxal phosphate-bound
active sites.
Length = 402
Score = 29.5 bits (67), Expect = 5.9
Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 25/84 (29%)
Query: 350 DLISGGHLS------------LTHCRFFVLDEADGLLKQGYGNLIDRMHKQIPKITSDGK 397
DL GGHL+ L + +D GL+ D + K +
Sbjct: 112 DLSHGGHLTHGSFTKVSASGKLFESVPYGVDPETGLID------YDALEKMALE-----F 160
Query: 398 RLQMIVCSATLH--DFDVKKMAER 419
+ ++IV A+ + D K+ E
Sbjct: 161 KPKLIVAGASAYPRPIDFKRFREI 184
>gnl|CDD|240459 cd12879, SPRY3_RyR, SPRY domain 3 (SPRY3) of ryanodine receptor
(RyR). This SPRY domain (SPRY3) is the third of three
structural repeats in all three isoforms of the
ryanodine receptor (RyR), which are the major Ca2+
release channels in the membranes of sarcoplasmic
reticulum (SR). There are three RyR genes in mammals;
the skeletal RyR1, the cardiac RyR2 and the brain RyR3.
The three SPRY domains are located in the N-terminal
part of the cytoplasmic region of the RyRs, but no
specific function has been found for this third SPRY
domain of the RyRs.
Length = 151
Score = 28.4 bits (64), Expect = 6.0
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 190 VIGCLLDLDNMTVAFTKNGQHLGLAFNISQQLKNSAFYPAV 230
+IGCL+D + FT NG+ G F + K +PAV
Sbjct: 99 LIGCLIDTATGLLTFTANGKETGTRFQVEPGTK---LFPAV 136
>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 = 29.0 bits (65), Expect = 8.3
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 475 GIDISGLPFIINMTLPDDKANYVHRIGRVGR 505
GI+ + F+I+ +LP +Y GR GR
Sbjct: 289 GINKPDVRFVIHYSLPKSMESYYQESGRAGR 319
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 29.2 bits (66), Expect = 8.9
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 8/93 (8%)
Query: 280 LVNNAPQAIIIEPSRELAEQTFNQIIKFKKF--ITDPKIRELLIIGGVNVKDQMSVLSSG 337
L + + + P++ L Q +K I + +I L G V +++ + +
Sbjct: 54 LRWFGGKVLFLAPTKPLVLQ---HAEFCRKVTGIPEDEIAALT--GEVRPEEREELWAKK 108
Query: 338 VDIVVGTPGRMEDLISGGHLSLTHCRFFVLDEA 370
+ V TP +E+ + G + L + DEA
Sbjct: 109 -KVFVATPQVVENDLKAGRIDLDDVSLLIFDEA 140
>gnl|CDD|153349 cd07665, BAR_SNX1, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 1. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX1 is a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi. The retromer consists of a cargo-recognition
subcomplex and a subcomplex formed by a dimer of sorting
nexins (SNX1 and/or SNX2), which ensures effcient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. SNX1 is localized to a
microdomain in early endosomes where it regulates
cation-independent mannose-6-phosphate receptor
retrieval to the trans Golgi network. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 234
Score = 28.5 bits (63), Expect = 9.5
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 566 IWFDEKRMLGEIEEHLNVTIQQVDDKLEIPADEFDGKVVYGQKRVNM-GSSYENHVTQME 624
+WF+EK E EE + V + L E K + M GSS +N T +
Sbjct: 22 VWFEEKLQEVECEEQRLRKLHAVVETLVNHRKELALNTALFAKSLAMLGSSEDN--TALS 79
Query: 625 PSVNKLSKLESKAQLIY 641
++++L+++E K + ++
Sbjct: 80 RALSQLAEVEEKIEQLH 96
>gnl|CDD|131112 TIGR02057, PAPS_reductase, phosphoadenosine phosphosulfate
reductase, thioredoxin dependent. Requiring thioredoxin
as an electron donor, phosphoadenosine phosphosulfate
reductase catalyzes the reduction of
3'-phosphoadenylylsulfate (PAPS) to sulfite and
phospho-adenosine-phosphate (PAP). Found in
enterobacteria, cyanobacteria, and yeast, PAPS reductase
is related to a group of plant (TIGR00424) and bacterial
(TIGR02055) enzymes preferring 5'-adenylylsulfate (APS)
over PAPS as a substrate for reduction to sulfite
[Central intermediary metabolism, Sulfur metabolism].
Length = 226
Score = 28.6 bits (64), Expect = 9.9
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 12/85 (14%)
Query: 572 RMLGEIEEHLNVTIQ-QVDDKLEIPADEFDGKVVYG----QKRVNMGSSYENHVTQMEPS 626
+ E+ + T+ D E AD F+ K YG QK + Y +++ ++EP
Sbjct: 69 TLKDELTKKYYQTLNLYKYDGCESEAD-FEAK--YGKLLWQKDI---EKY-DYIAKVEPM 121
Query: 627 VNKLSKLESKAQLIYLKHHQAKQRA 651
L +L + A + Q RA
Sbjct: 122 QRALKELNASAWFTGRRRDQGSARA 146
>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
Length = 355
Score = 28.8 bits (64), Expect = 10.0
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 10 LPEIGKAVEEMDWLLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPIIQIVCETLK 69
LP G + DWL D A A+ + G V G G L +++ +CE L+
Sbjct: 214 LPVYGNGQQIRDWLYVED-HARALYCVATTGKVGETYNIG-GHNERKNLDVVETICELLE 271
Query: 70 EIQAGKGQGKA 80
E+ K QG A
Sbjct: 272 ELAPNKPQGVA 282
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
0.319 0.136 0.412
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,557,003
Number of extensions: 3318589
Number of successful extensions: 2889
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2845
Number of HSP's successfully gapped: 102
Length of query: 651
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 548
Effective length of database: 6,369,140
Effective search space: 3490288720
Effective search space used: 3490288720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.6 bits)