RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12466
(680 letters)
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 248 bits (636), Expect = 3e-77
Identities = 109/313 (34%), Positives = 161/313 (51%), Gaps = 32/313 (10%)
Query: 377 HQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVL 436
+Q +GV++L + G ILADEMGLGKTLQ IAL+ T L++G L
Sbjct: 1 YQLEGVNWLISLESNGL-----GGILADEMGLGKTLQTIALLATYLKEGKD---RRGPTL 52
Query: 437 IVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAED----YVYSRVSPVLIISYEMLIR 492
+V P S NW +EF+KW R+ YH + + +++ V+I +YE+L +
Sbjct: 53 VVCPLSTLHNWLNEFEKWAPALRVVVYHGDGRERSKLRQSMAKRLDTYDVVITTYEVLRK 112
Query: 493 AYQTIVDT----EFDLLICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEFF 548
+ ++ E+D ++ DE HRLKN KSKLY+ + L R R+LL+GTP+QN+L+E +
Sbjct: 113 -DKKLLSLLNKVEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQNNLEELW 171
Query: 549 YLNDFANPGVLGSLREFRKNFEEPILESRSPNSTEAQKSLGELRSSQLAKRTAGFILRRT 608
L +F PG GS + F + F PI + ++ G+ ++L K F+LRRT
Sbjct: 172 ALLNFLRPGPFGSFKVFEEWFNIPIA--NTADNKNKNLEKGKEGINRLHKLLKPFLLRRT 229
Query: 609 -SDVQASLLNSKRETLLVCRATPLQQSLYLRCVEYWDA---RASRDSHLSVTHA------ 658
DV+ SL K E +L C + Q+ LY + + A +V A
Sbjct: 230 KDDVEKSLPP-KTEHVLYCNLSDEQRKLYKKLLTKRRLALSFAVEGGEKNVGIASLLNLI 288
Query: 659 --LRKICNHPGLV 669
LRKICNHP L
Sbjct: 289 MQLRKICNHPYLF 301
Score = 65.5 bits (160), Expect = 2e-11
Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 12/95 (12%)
Query: 183 HQEKNRRSYILRVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAED----YVYSR 238
+ K+RR L+V P S NW +EF+KW R+ YH + + +++
Sbjct: 42 KEGKDRRG---PTLVVCPLSTLHNWLNEFEKWAPALRVVVYHGDGRERSKLRQSMAKRLD 98
Query: 239 VSPVLIISYEMLIRAYQTIVDT----EFDLLICDE 269
V+I +YE+L + + ++ E+D ++ DE
Sbjct: 99 TYDVVITTYEVLRK-DKKLLSLLNKVEWDRVVLDE 132
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 182 bits (462), Expect = 3e-48
Identities = 152/547 (27%), Positives = 229/547 (41%), Gaps = 82/547 (14%)
Query: 188 RRSYILRVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAEDYVYS-------RVS 240
R I RVLI+ P +L + W E + V K +
Sbjct: 129 LRGEIKRVLILVPKTLRAQWVVELLEKFN----IRLAVLDKEGLRYLLKQYDAYNPFSTE 184
Query: 241 PVLIISYEMLIRAYQTIVD-------TEFDLLICDEKSLLKPPSGNSPGNDSGIP----- 288
+++IS ++ R+ + E DLL+ DE L G
Sbjct: 185 DLVLISLDLAKRSDSKRREALLEAEWGERDLLVIDEAHNLGSSEGTRKLAPLETLEYELL 244
Query: 289 -SLPRKSDSGIGSLPCKRPLEESTAETLQCNQINSHLSVTHALR----------KICNHP 337
L K S + L K L +T E L+ + + L + LR +
Sbjct: 245 KQLAEKIPSKLLDL--KVLLLSATPEQLKEEDLFARLRLLDPLRLADLSQILEKFVRETL 302
Query: 338 GLVQQPDVMEEEGQWKHNPSGKPLVDVTVDGFLSRVLKPHQRQGVSFLYERVCDLASLDL 397
L + E + + L++ LS L+P+Q +GV++L E L S +L
Sbjct: 303 KLSARDLKDELKELLAELRLSEDLLNAPEPVDLSAELRPYQLEGVNWLSEL---LRS-NL 358
Query: 398 EGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPSSLTSNWNDEFKKWLGL 457
G ILAD+MGLGKT+Q IAL+ +LL + LIV P+SL SNW EF+K+
Sbjct: 359 LGGILADDMGLGKTVQTIALLLSLLESIKVYLG---PALIVVPASLLSNWKREFEKFAPD 415
Query: 458 TRMCPYHVNQKNKAE----------DYVYSRVSPVLIISYEMLIRAYQTIV---DTEFDL 504
R+ + +K++ + + V+I +YE+L R E+D
Sbjct: 416 LRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDR 475
Query: 505 LICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEFFYLND-FANPGVLG-SL 562
++ DE HR+KN +S + + L R+ L+GTPL+N L E + L F NPG+LG S
Sbjct: 476 VVLDEAHRIKNDQSSEGKALQFLKALNRLDLTGTPLENRLGELWSLLQEFLNPGLLGTSF 535
Query: 563 REFRKNFEEPILESRSPNSTEAQKSLGELRSSQLAKRTAGFILRRT-SDVQ-ASLLNSKR 620
F + FE+PI EA+ EL L K + FILRRT DV+ L K
Sbjct: 536 AIFTRLFEKPIQAEEDIGPLEAR----ELGIELLRKLLSPFILRRTKEDVEVLKELPPKI 591
Query: 621 ETLLVCRATPLQQSLY----------LRCVEY-------WDARASRDSH-LSVTHALRKI 662
E +L C + Q+ LY + +E + + + L++ LR+I
Sbjct: 592 EKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLTRLRQI 651
Query: 663 CNHPGLV 669
CNHP LV
Sbjct: 652 CNHPALV 658
Score = 46.7 bits (110), Expect = 4e-05
Identities = 25/101 (24%), Positives = 45/101 (44%), Gaps = 13/101 (12%)
Query: 182 DHQEKNRRSYILRVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAE--------- 232
++ + Y+ LIV P+SL SNW EF+K+ R+ + +K++ +
Sbjct: 380 LSLLESIKVYLGPALIVVPASLLSNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRDL 439
Query: 233 -DYVYSRVSPVLIISYEMLIRAYQTIV---DTEFDLLICDE 269
+ V+I +YE+L R E+D ++ DE
Sbjct: 440 LKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDE 480
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 142 bits (359), Expect = 5e-35
Identities = 92/282 (32%), Positives = 140/282 (49%), Gaps = 33/282 (11%)
Query: 401 ILADEMGLGKTLQCIALIWTLLR----QGPYGMPVIRKVLIVTPSSLTSNWNDEFKKWLG 456
ILADEMGLGKTLQ I+L+ L GP+ ++V P S NW +E +++
Sbjct: 192 ILADEMGLGKTLQTISLLGYLHEYRGITGPH--------MVVAPKSTLGNWMNEIRRFCP 243
Query: 457 LTRMCPYHVNQKNKA---EDYVYSRVSPVLIISYEMLIRAYQTIVDTEFDLLICDEGHRL 513
+ R +H N + +A E+ + + V + S+EM I+ + + +I DE HR+
Sbjct: 244 VLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRI 303
Query: 514 KNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEFFYLNDFANPGVLGSLREFRKNFEEPI 573
KN S L + M + R+L++GTPLQN+L E + L +F P + S F + F+
Sbjct: 304 KNENSLLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQ--- 360
Query: 574 LESRSPNSTEAQKSLGELRSSQLAKRTAGFILRR-TSDVQASLLNSKRETLLVCRATPLQ 632
S E + E+ QL K F+LRR SDV+ L K+ET+L + +Q
Sbjct: 361 ------ISGENDQ--QEV-VQQLHKVLRPFLLRRLKSDVEKG-LPPKKETILKVGMSQMQ 410
Query: 633 QSLYLRC----VEYWDARASRDSHLSVTHALRKICNHPGLVQ 670
+ Y ++ +A R L++ LRK CNHP L Q
Sbjct: 411 KQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQ 452
Score = 40.9 bits (96), Expect = 0.002
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 196 LIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKA---EDYVYSRVSPVLIISYEMLIR 252
++V P S NW +E +++ + R +H N + +A E+ + + V + S+EM I+
Sbjct: 223 MVVAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIK 282
Query: 253 AYQTIVDTEFDLLICDEKSLLK 274
+ + +I DE +K
Sbjct: 283 EKTALKRFSWRYIIIDEAHRIK 304
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 107 bits (270), Expect = 9e-27
Identities = 51/196 (26%), Positives = 88/196 (44%), Gaps = 27/196 (13%)
Query: 366 VDGFLSRVLKPHQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQ-CIALIWTLLRQ 424
++ F L+P+Q++ + L + D+ ILA G GKTL + + L R
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDV--------ILAAPTGSGKTLAALLPALEALKRG 52
Query: 425 GPYGMPVIRKVLIVTP-SSLTSNWNDEFKKWL---GLTRMCPYHVNQKNKAEDYVYSRVS 480
+VL++ P L W +E KK GL + Y + K + + S +
Sbjct: 53 KG------GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKT 106
Query: 481 PVLIISYEMLIRAYQ--TIVDTEFDLLICDEGHRLKNG--KSKLYELMTGLN-IRKRILL 535
+L+ + L+ + + + DL+I DE HRL +G +L +L+ L + +LL
Sbjct: 107 DILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLL 166
Query: 536 SGTP---LQNDLQEFF 548
S TP ++N L+ F
Sbjct: 167 SATPPEEIENLLELFL 182
Score = 53.6 bits (129), Expect = 4e-08
Identities = 26/108 (24%), Positives = 46/108 (42%), Gaps = 13/108 (12%)
Query: 168 KTEVNPLILPKPIVDHQEKNRRSYILRVLIVTPS-SLTSNWNDEFKKWL---GLTRMCPY 223
KT L P ++ +R RVL++ P+ L W +E KK GL + Y
Sbjct: 37 KT----LAALLPALEA---LKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLY 89
Query: 224 HVNQKNKAEDYVYSRVSPVLIISYEMLIRAYQ--TIVDTEFDLLICDE 269
+ K + + S + +L+ + L+ + + + DL+I DE
Sbjct: 90 GGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDE 137
>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 = 91.2 bits (227), Expect = 1e-21
Identities = 39/149 (26%), Positives = 64/149 (42%), Gaps = 12/149 (8%)
Query: 398 EGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPSSLTSNW-NDEFKKWLG 456
+LA G GKTL + I LL G +VL++ P+ +N + K+ G
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGG-----QVLVLAPTRELANQVAERLKELFG 55
Query: 457 L-TRMCPYHVNQKNKAEDYVYSRVSPVLIISYEMLIRAYQTIVD--TEFDLLICDEGHRL 513
++ K ++ + S + +++ + L+ + + + DLLI DE HRL
Sbjct: 56 EGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRL 115
Query: 514 KNGKSKLYELMTGLNIRK---RILLSGTP 539
N L L L + K +LLS TP
Sbjct: 116 LNQGFGLLGLKILLKLPKDRQVLLLSATP 144
Score = 43.5 bits (103), Expect = 4e-05
Identities = 20/106 (18%), Positives = 45/106 (42%), Gaps = 11/106 (10%)
Query: 168 KTEVNPLILPKPIVDHQEKNRRSYILRVLIVTPSSLTSNW-NDEFKKWLGL-TRMCPYHV 225
KT L PI++ + + +VL++ P+ +N + K+ G ++
Sbjct: 13 KT----LAALLPILELLDSLKG---GQVLVLAPTRELANQVAERLKELFGEGIKVGYLIG 65
Query: 226 NQKNKAEDYVYSRVSPVLIISYEMLIRAYQTIVD--TEFDLLICDE 269
K ++ + S + +++ + L+ + + + DLLI DE
Sbjct: 66 GTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDE 111
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 52.4 bits (126), Expect = 5e-07
Identities = 44/207 (21%), Positives = 70/207 (33%), Gaps = 42/207 (20%)
Query: 373 VLKPHQRQGVSFLYERVCDLASLDLEGAILADEMGL-------GKTLQCIALIWTLLRQG 425
L+P+Q + + L + G+ GKT+ I L
Sbjct: 36 ELRPYQEEALD------------ALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL---- 79
Query: 426 PYGMPVIRKVLIVTPSS-LTSNWNDEFKKWLGLTR-MCPYHVNQKNKAEDYVYSRVSPVL 483
R L++ P+ L W + KK+L L + Y +K + V
Sbjct: 80 ------KRSTLVLVPTKELLDQWAEALKKFLLLNDEIGIYGGGEKE-------LEPAKVT 126
Query: 484 IISYEMLIR--AYQTIVDTEFDLLICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTPLQ 541
+ + + L R + EF L+I DE H L + + R+ L+ TP +
Sbjct: 127 VATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLS-AAYPRLGLTATPER 185
Query: 542 NDLQEFFYLNDFANPGVLG-SLREFRK 567
D L D P V SL+E
Sbjct: 186 EDGGRIGDLFDLIGPIVYEVSLKELID 212
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 42.0 bits (99), Expect = 0.001
Identities = 37/159 (23%), Positives = 64/159 (40%), Gaps = 26/159 (16%)
Query: 363 DVTVDGFLSRVLKPHQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLL 422
+D + + +Q + RV + S A+L G GKT IA+I L+
Sbjct: 155 LAYIDIDSAIGPRYYQIIAIR----RVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLI 210
Query: 423 RQGPYGMPVIRKVL-IVTPSSLTSNWNDEFKKWL-GLTRMCPYHVNQKNKAEDYVYSRVS 480
+ G +++VL + ++L F+ +L T+M NK ED S
Sbjct: 211 KSG-----WVKRVLFLADRNALVDQAYGAFEDFLPFGTKM--------NKIEDKKGDTSS 257
Query: 481 PVLIISYEMLIRAYQTIVDT-------EFDLLICDEGHR 512
+ + +Y+ + + D FDL++ DE HR
Sbjct: 258 EIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR 296
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 40.2 bits (95), Expect = 0.004
Identities = 44/155 (28%), Positives = 69/155 (44%), Gaps = 26/155 (16%)
Query: 402 LADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPSSLTSNWNDEFKKWLGL---- 457
LADE+GLGKT++ +I + +Q G +VLI+ P +L W E + L
Sbjct: 174 LADEVGLGKTIEA-GMI--IHQQLLTGR--AERVLILVPETLQHQWLVEMLRRFNLRFSL 228
Query: 458 ---TRMCPYHVNQKNKAEDYVYSRVSPVLIISYEMLIR---AYQTIVDTEFDLLICDEGH 511
R + N E ++I S + L R + + E+DLL+ DE H
Sbjct: 229 FDEERYAEAQHDADNPFET------EQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAH 282
Query: 512 RL---KNGKSKLYELMTGL--NIRKRILLSGTPLQ 541
L + S+ Y+++ L I +LL+ TP Q
Sbjct: 283 HLVWSEEAPSREYQVVEQLAEVIPGVLLLTATPEQ 317
>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 = 36.5 bits (85), Expect = 0.017
Identities = 32/143 (22%), Positives = 55/143 (38%), Gaps = 14/143 (9%)
Query: 407 GLGKTLQCIALIWTLLRQGPYGMPVIRKVLIVTPS-SLTSNWNDEFKKWLGLTRM--CPY 463
G GKTL L+ L P + L++ P+ L +E KK + +
Sbjct: 24 GSGKTL--AFLLPILQALLPKKGGP--QALVLAPTRELAEQIYEELKKLFKILGLRVALL 79
Query: 464 H-VNQKNKAEDYVYSRVSPVLIISYEML---IRAYQTIVDTEFDLLICDEGHRL--KNGK 517
+ + + +L+ + L +R + + LL+ DE HRL
Sbjct: 80 TGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFG 139
Query: 518 SKLYELMTGL-NIRKRILLSGTP 539
L E+++ L R+ +LLS T
Sbjct: 140 DDLEEILSRLPPDRQILLLSATL 162
>gnl|CDD|227444 COG5113, UFD2, Ubiquitin fusion degradation protein 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 929
Score = 32.3 bits (73), Expect = 1.1
Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 4/114 (3%)
Query: 35 YVYPEPGGTEVSEAQNSNHATSVTRIFNVVYGKPSAKKHKSWEQDGVLE--ISGTMAILK 92
Y+ E G N + + + Y +PS + S +D L + +L
Sbjct: 596 YIEIESTGQSTQFYDKFNIRFIICMMKDFEYKQPSYSEGLSSIKDTNLPFFVKFDAKMLN 655
Query: 93 DTLGKVIDSKVKILDEIKPGTSSLQSSPR-LNASDNVQSSTVNAQTSSVNAQTS 145
D L +++D +K L E S L + N S+ + + + A+ S
Sbjct: 656 D-LTRLLDEALKELVEEHNIQSLLADAISNSNISERIGELQKSLAFAKRQARNS 708
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 31.8 bits (73), Expect = 1.2
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 502 FDLLICDEGHRLKNGKSKLYELMTGLN 528
D++I DE HRL KS LY +G N
Sbjct: 80 EDVVIVDEAHRLWT-KSDLYFNFSGPN 105
>gnl|CDD|132814 cd07281, PX_SNX1, The phosphoinositide binding Phox Homology domain
of Sorting Nexin 1. The PX domain is a phosphoinositide
(PI) binding module present in many proteins with
diverse functions. Sorting nexins (SNXs) make up the
largest group among PX domain containing proteins. They
are involved in regulating membrane traffic and protein
sorting in the endosomal system. The PX domain of SNXs
binds PIs and targets the protein to PI-enriched
membranes. SNXs differ from each other in PI-binding
specificity and affinity, and the presence of other
protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX1 is both membrane
associated and a cytosolic protein that exists as a
tetramer in protein complexes. It can associate
reversibly with membranes of the endosomal compartment,
thereby coating these vesicles. 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 efficient cargo sorting by facilitating proper
membrane localization of the cargo-recognition
subcomplex. SNX1 contains a Bin/Amphiphysin/Rvs (BAR)
domain C-terminal to the PX domain. The PX domain of
SNX1 specifically binds phosphatidylinositol-3-phosphate
(PI3P) and PI(3,5)P2, while the BAR domain detects
membrane curvature. Both domains help determine the
specific membrane-targeting of SNX1, which is localized
to a microdomain in early endosomes where it regulates
cation-independent mannose-6-phosphate receptor
retrieval to the trans Golgi network.
Length = 124
Score = 30.4 bits (68), Expect = 1.2
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 287 IPSLPRKSDSGIGSLPCKRPLEESTAETLQCNQINSHLSVTHALRKICNHPGLVQQPDVM 346
+P P KS G+ + + + S+AE L+ ++ L++I +HP L+Q PDV
Sbjct: 64 VPPPPEKSLIGMTKVKVGKE-DSSSAEFLE----RRRAALERYLQRIVSHPSLLQDPDVR 118
Query: 347 E 347
E
Sbjct: 119 E 119
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 31.7 bits (72), Expect = 1.3
Identities = 28/148 (18%), Positives = 52/148 (35%), Gaps = 25/148 (16%)
Query: 450 EFKKWLGLTRMCPYHVNQKNKAEDYVY-----SRVSPVLIISYEMLIRA----YQTIVDT 500
K L CPY+ E + + + + +++ ++ +L+ I+
Sbjct: 166 TDDKDSCLGEDCPYY------TECFYFPARKEAENADLVVTNHALLLADVALEESRILLP 219
Query: 501 EFDLLICDEGHRL----KNGKSKLYELMTGLNIRKRILLSGTPLQNDLQEF----FYLND 552
E D+++ DE H L ++ S T + K I G L+ DL+ L
Sbjct: 220 ENDVVVFDEAHNLPDIARSALSIRLSERTLERLLKEIQALGETLEKDLKRLEDLADRLEK 279
Query: 553 FA--NPGVLGSLREFRKNFEEPILESRS 578
+L + N E + E S
Sbjct: 280 ALEDLRELLIFDVDELGNLRERLREQLS 307
>gnl|CDD|217941 pfam04178, Got1, Got1/Sft2-like family. Traffic through the yeast
Golgi complex depends on a member of the syntaxin family
of SNARE proteins, Sed5, present in early Golgi
cisternae. Got1 is thought to facilitate Sed5-dependent
fusion events. This is a family of sequences derived
from eukaryotic proteins. They are similar to a region
of a SNARE-like protein required for traffic through the
Golgi complex, SFT2 protein. This is a conserved protein
with four putative transmembrane helices, thought to be
involved in vesicular transport in later Golgi
compartments.
Length = 116
Score = 29.8 bits (68), Expect = 1.4
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 392 LASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVIRKVL 436
+L L+ L L Q +ALIW LL P G P ++KVL
Sbjct: 73 YFALILKSYGLT---LLFSIFQILALIWYLLSYIPGGRPGVKKVL 114
>gnl|CDD|192561 pfam10382, DUF2439, Protein of unknown function (DUF2439).
Proteins in this family have been implicated in telomere
maintenance in Saccharomyces cerevisiae and in meiotic
chromosome segregation in Schizosaccharomyces pombe.
Length = 83
Score = 29.1 bits (66), Expect = 1.7
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 61 FNVVYGKPSAKKHKSWEQDGVLEIS--GTMAILKDTLGKVIDSK-VKILDEIKPG 112
+ +Y +K K W DG L+ +L D G +I S ++ E+ G
Sbjct: 4 YECLYTHQKRQKQKKW-HDGKLKFHTFNNRIMLYDEDGVLIGSDFLRNSSELVDG 57
>gnl|CDD|197257 cd09160, PLDc_SMU_988_like_2, Putative catalytic domain, repeat 2,
of Streptococcus mutans uncharacterized protein SMU_988
and similar proteins. Putative catalytic domain, repeat
2, of Streptococcus mutans uncharacterized protein
SMU_988 and similar proteins. Although SMU_988 and
similar proteins have not been functionally
characterized, members in this subfamily show high
sequence homology to bacterial cardiolipin (CL)
synthases, which catalyze the reversible phosphatidyl
group transfer between two phosphatidylglycerol
molecules to form CL and glycerol. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
may be part of the active site and may be involved in
phosphatidyl group transfer.
Length = 176
Score = 30.2 bits (69), Expect = 2.4
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 229 NKAEDYVYSRVSPVLIISYEM---LIRAYQTIVD 259
N+A+DYVY +P LI+ EM L A + VD
Sbjct: 21 NQAKDYVYI-TTPYLILDDEMLDALCLAAKRGVD 53
Score = 30.2 bits (69), Expect = 2.4
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 469 NKAEDYVYSRVSPVLIISYEM---LIRAYQTIVD 499
N+A+DYVY +P LI+ EM L A + VD
Sbjct: 21 NQAKDYVYI-TTPYLILDDEMLDALCLAAKRGVD 53
>gnl|CDD|176781 cd08803, Death_ank3, Death domain of Ankyrin-3. Death Domain (DD)
of the human protein ankyrin-3 (ANK-3) and related
proteins. Ankyrins are modular proteins comprising three
conserved domains, an N-terminal membrane-binding domain
containing ANK repeats, a spectrin-binding domain and a
C-terminal DD. ANK-3, also called anykyrin-G (for
general or giant), is found in neurons and at least one
splice variant has been shown to be essential for
propagation of action potentials as a binding partner to
neurofascin and voltage-gated sodium channels. It is
required for maintaining axo-dendritic polarity, and may
be a genetic risk factor associated with bipolar
disorder. ANK-3 may also play roles in other cell types.
Mutations affecting ANK-3 pathways for Na channel
localization are associated with Brugada syndrome, a
potentially fata arrythmia. In general, DDs are
protein-protein interaction domains found in a variety
of domain architectures. Their common feature is that
they form homodimers by self-association or heterodimers
by associating with other members of the DD superfamily
including CARD (Caspase activation and recruitment
domain), DED (Death Effector Domain), and PYRIN. They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 84
Score = 28.5 bits (63), Expect = 2.9
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 396 DLEGAILADEMGLGKTLQCIALIWT-LLRQGPYGMPVIRKVLIVTPSSLTSNWNDEFKKW 454
D+ AI+AD +GL WT L R+ + + I ++ + P+SL + KKW
Sbjct: 4 DIRMAIVADHLGLS---------WTELARELNFSVDEINQIRVENPNSLIAQSFMLLKKW 54
Query: 455 L 455
+
Sbjct: 55 V 55
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 30.6 bits (69), Expect = 3.5
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 501 EFDLLICDEGHRL------KNGKSKLYELMTGLNIR--KRILLSGTP 539
EFDL+ICDE HR + KS + + NI+ KR+ ++ TP
Sbjct: 304 EFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKAAKRLYMTATP 350
>gnl|CDD|225237 COG2362, DppA, D-aminopeptidase [Amino acid transport and
metabolism].
Length = 274
Score = 30.1 bits (68), Expect = 3.5
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 143 QTSSVSASSSLPWRPVKKS-----RLSLHAKTEVNPLILPKPIV 181
+ SS SA+ SL +K+ R ++ K + PL PIV
Sbjct: 176 EASSRSAAISLSPAKAEKAIREAVRAAVQRKLSLAPLRPADPIV 219
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.3 bits (64), Expect = 3.7
Identities = 9/36 (25%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 504 LLICDEGHRLKNGKSKLYELMTGLNIRKRILLSGTP 539
++I DE H + K+K +++ + L+ TP
Sbjct: 64 VIIIDEAHHS-SAKTKYRKILEKFKPAFLLGLTATP 98
Score = 28.0 bits (63), Expect = 5.0
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 21/84 (25%)
Query: 373 VLKPHQRQGVSFLYERVCDLASLDLEGAILADEMGLGKTLQCIALIWTLLRQGPYGMPVI 432
L+P+Q + + ER+ L+ + ++ G GKTL ALI L +
Sbjct: 3 ELRPYQEEAI----ERL-----LEKKRGLIVMATGSGKTLTAAALIARLAKG-------K 46
Query: 433 RKVLIVTPS-SLTSNW----NDEF 451
+KVL V P L DE
Sbjct: 47 KKVLFVVPRKDLLEQALVIIIDEA 70
>gnl|CDD|165311 PHA03011, PHA03011, hypothetical protein; Provisional.
Length = 120
Score = 28.8 bits (64), Expect = 4.3
Identities = 24/104 (23%), Positives = 39/104 (37%), Gaps = 5/104 (4%)
Query: 431 VIRKVLIVTPSSLTSNWNDEFKKWLGLTRMCPYHVNQKNKAEDYVYSRVSPVLIISYEML 490
+I +I P ++ N ++L P + + + + LI Y L
Sbjct: 17 IILYKIINIPPYESNILNKFDDEYLANLIFEPEQIFDFKEGDINAIIEILDELIAQYNEL 76
Query: 491 IRAYQTIVDTEFDLLIC-----DEGHRLKNGKSKLYELMTGLNI 529
+ Y I + DL I DE H L+ KL E + L+I
Sbjct: 77 LDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENIANLSI 120
>gnl|CDD|232784 TIGR00018, panC, pantoate--beta-alanine ligase. This family is
pantoate--beta-alanine ligase, the last enzyme of
pantothenate biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Pantothenate and
coenzyme A].
Length = 282
Score = 29.7 bits (67), Expect = 4.3
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 30 KENHNYVYPEPGGTEVSE-AQNSNH----ATSVTRIFNVV 64
E H V G +EV E A H AT VT++FN+V
Sbjct: 103 TEQHTTVDVPLGLSEVLEGASRPGHFRGVATIVTKLFNLV 142
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.4 bits (64), Expect = 6.3
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 488 EMLIRAYQTIVDTEFDLLICDEGHRLKNGKSKLYELMTGLNIRK---RILLSGTP 539
E+L + LLI DE L L EL ++ + +++L GTP
Sbjct: 66 ELLEAILDALKRRGRPLLIIDEAQHLS--LEALEELRDLYDLSEKGIQVILVGTP 118
>gnl|CDD|185258 PRK15360, PRK15360, pathogenicity island 2 effector protein SseE;
Provisional.
Length = 137
Score = 27.9 bits (62), Expect = 8.2
Identities = 11/52 (21%), Positives = 23/52 (44%)
Query: 483 LIISYEMLIRAYQTIVDTEFDLLICDEGHRLKNGKSKLYELMTGLNIRKRIL 534
+++ + ++ Y I E +I E RL G+ + +L L + + I
Sbjct: 25 ILLGQQFILSPYLVIYRIEAKEMIICEFRRLTPGQPRPQQLFHLLGLLRGIF 76
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
0.315 0.132 0.384
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,774,435
Number of extensions: 3247071
Number of successful extensions: 2325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2293
Number of HSP's successfully gapped: 45
Length of query: 680
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 577
Effective length of database: 6,369,140
Effective search space: 3674993780
Effective search space used: 3674993780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.8 bits)