RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5647
(755 letters)
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 345 bits (885), Expect = e-106
Identities = 200/644 (31%), Positives = 311/644 (48%), Gaps = 56/644 (8%)
Query: 47 DEPNSKLPMTKEEMSEHENLIRQILAKPFKVPILNYTGGGYSTKALGVRREGARKALHDP 106
D L T E++ E + R L P ++ L+ + + L + + L +
Sbjct: 257 DLKVLLLSATPEQLKEEDLFARLRLLDPLRLADLSQILEKFVRETLKLSARDLKDELKEL 316
Query: 107 TAPNALVLYTPPQLSAHDLLKIDKDKIQVHVVVDPVLSNILRPHQREGVKFMYECVTGVR 166
A L DL LRP+Q EGV ++ E +
Sbjct: 317 LAELRLSEDLLNAPEPVDLSAE------------------LRPYQLEGVNWLSE----LL 354
Query: 167 IEDAYGCIMADEMGLGKTLQCITLMWTLLRQGPLAKPLIDKAIIVAPSSLVKNWCNEITK 226
+ G I+AD+MGLGKT+Q I L+ +LL + A+IV P+SL+ NW E K
Sbjct: 355 RSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLG---PALIVVPASLLSNWKREFEK 411
Query: 227 WLGGRVAALPIDGGSKAEIDNKLNSFMQ--TYGRRPVNPILVISYETFRSHA---SVLHK 281
+ L G K+E+D K + + +++ +YE R L K
Sbjct: 412 FAPDLRLVLVYHG-EKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKK 470
Query: 282 NEVGLVLCDEGHRLKNCESQTYQALMGLKAKRRVLLSGTPIQNDLLEYFSLV-HFVNQGI 340
E V+ DE HR+KN +S +AL LKA R+ L+GTP++N L E +SL+ F+N G+
Sbjct: 471 IEWDRVVLDEAHRIKNDQSSEGKALQFLKALNRLDLTGTPLENRLGELWSLLQEFLNPGL 530
Query: 341 LGTA-QEFRKQYETPILRGQDSCASDAERTKANERLEQLIGIVNRCLIRRTSA--LLSKY 397
LGT+ F + +E PI +D +A +E L +++ ++RRT + K
Sbjct: 531 LGTSFAIFTRLFEKPIQAEEDIGPLEAR----ELGIELLRKLLSPFILRRTKEDVEVLKE 586
Query: 398 LPVKTEQVVCIKMTDLQKELYTNLIKS-----DAVRRTMKGGENTK----LGMTALSSIT 448
LP K E+V+ ++++ Q+ELY L++ + K + + L+ +T
Sbjct: 587 LPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRIGDSELNILALLT 646
Query: 449 SLKKLCNHPDLVMDKIQTGADGFENAMNILPTGYAASYKSGKLLIELS-AKLMVLDTML- 506
L+++CNHP LV + ++ D + K LI+LS KL LD +L
Sbjct: 647 RLRQICNHPALVDEGLEATFDRIVLLLRED----KDFDYLKKPLIQLSKGKLQALDELLL 702
Query: 507 AVIKMT-TDDKIVLVSNYTQTLDLFERLSKLRGYKYVRLDGSMTIKKRAKVVETFNKTSN 565
+ K+++ S +T LDL E K G KYVRLDGS K+R ++++ FN
Sbjct: 703 DKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEE 762
Query: 566 EFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDDQAMARVWRDGQKKPCFVYRFLSTG 625
E +F+LS KAGG GLNL GA+ +++FDP WNPA + QA+ R R GQK+P VYR ++ G
Sbjct: 763 EKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRG 822
Query: 626 SIEEKMMQRQAHKKALSSCVVD-CEEDVARHFSMSELRSLFQLE 668
+IEEK+++ Q K+ L ++D E S+ +L LF L
Sbjct: 823 TIEEKILELQEKKQELLDSLIDAEGEKELSKLSIEDLLDLFSLG 866
>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 = 285 bits (732), Expect = 1e-90
Identities = 109/317 (34%), Positives = 170/317 (53%), Gaps = 22/317 (6%)
Query: 150 HQREGVKFMYECVTGVRIEDAYGCIMADEMGLGKTLQCITLMWTLLRQGPLAKPLIDKAI 209
+Q EGV ++ + G I+ADEMGLGKTLQ I L+ T L++G K +
Sbjct: 1 YQLEGVNWLISLESN-----GLGGILADEMGLGKTLQTIALLATYLKEG---KDRRGPTL 52
Query: 210 IVAPSSLVKNWCNEITKWLGG-RVAALPIDGGSKAEIDNKLNSFMQTYGRRPVNPILVIS 268
+V P S + NW NE KW RV DG ++++ + + TY +++ +
Sbjct: 53 VVCPLSTLHNWLNEFEKWAPALRVVVYHGDGRERSKLRQSMAKRLDTYD------VVITT 106
Query: 269 YET---FRSHASVLHKNEVGLVLCDEGHRLKNCESQTYQALMGLKAKRRVLLSGTPIQND 325
YE + S+L+K E V+ DE HRLKN +S+ Y+AL LK + R+LL+GTPIQN+
Sbjct: 107 YEVLRKDKKLLSLLNKVEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQNN 166
Query: 326 LLEYFSLVHFVNQGILGTAQEFRKQYETPILRGQDSCASDAERTKANERLEQLIGIVNRC 385
L E ++L++F+ G G+ + F + + PI D + K E + +L ++
Sbjct: 167 LEELWALLNFLRPGPFGSFKVFEEWFNIPIANTAD--NKNKNLEKGKEGINRLHKLLKPF 224
Query: 386 LIRRTSALLSKYLPVKTEQVVCIKMTDLQKELYTNLIKSD--AVRRTMKGGENTKLGMTA 443
L+RRT + K LP KTE V+ ++D Q++LY L+ A+ ++GGE +
Sbjct: 225 LLRRTKDDVEKSLPPKTEHVLYCNLSDEQRKLYKKLLTKRRLALSFAVEGGEKNVGIASL 284
Query: 444 LSSITSLKKLCNHPDLV 460
L+ I L+K+CNHP L
Sbjct: 285 LNLIMQLRKICNHPYLF 301
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 238 bits (609), Expect = 1e-66
Identities = 163/537 (30%), Positives = 272/537 (50%), Gaps = 70/537 (13%)
Query: 123 HDLLKIDKDKIQVH----VVVDP-VLSNILRPHQREGVKFMYECVTGVRI-EDAYGCIMA 176
+ LK ++D + ++V P + +R +Q G+ ++ +R+ E+ I+A
Sbjct: 141 EEYLKEEEDGLGGSGGTRLLVQPSCIKGKMRDYQLAGLNWL------IRLYENGINGILA 194
Query: 177 DEMGLGKTLQCITLMWTLLRQGPLAKPLIDKAIIVAPSSLVKNWCNEITKWLGGRVAALP 236
DEMGLGKTLQ I+L+ L + P ++VAP S + NW NEI ++ P
Sbjct: 195 DEMGLGKTLQTISLLGYLHEYRGITGP----HMVVAPKSTLGNWMNEIRRFC-------P 243
Query: 237 IDGGSK----AEIDNKLNSFMQTYGRRPVNPILVISYETFRSHASVLHKNEVGLVLCDEG 292
+ K E + G+ V V S+E + L + ++ DE
Sbjct: 244 VLRAVKFHGNPEERAHQREELLVAGKFDV---CVTSFEMAIKEKTALKRFSWRYIIIDEA 300
Query: 293 HRLKNCESQTYQALMGLKAKRRVLLSGTPIQNDLLEYFSLVHFVNQGILGTAQEFRKQYE 352
HR+KN S + + R+L++GTP+QN+L E ++L++F+ I +A+ F + ++
Sbjct: 301 HRIKNENSLLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQ 360
Query: 353 TPILRGQDSCASDAERTKANERLEQLIGIVNRCLIRRTSALLSKYLPVKTEQVVCIKMTD 412
+ E ++QL ++ L+RR + + K LP K E ++ + M+
Sbjct: 361 I------------SGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGLPPKKETILKVGMSQ 408
Query: 413 LQKELYTNLIKSD--AVRRTMKGGENTKLGMTALSSITSLKKLCNHPDLVMDKIQTGADG 470
+QK+ Y L++ D V GGE +L L+ L+K CNHP L
Sbjct: 409 MQKQYYKALLQKDLDVVNA---GGERKRL----LNIAMQLRKCCNHPYL----------- 450
Query: 471 FENAMNILPTGYAASYKSGKLLIELSAKLMVLDTMLAVIKMTTDDKIVLVSNYTQTLDLF 530
F+ A P Y +G+ L+E S K+++LD +L +K D ++++ S T+ LD+
Sbjct: 451 FQGAEPGPP------YTTGEHLVENSGKMVLLDKLLPKLK-ERDSRVLIFSQMTRLLDIL 503
Query: 531 ERLSKLRGYKYVRLDGSMTIKKRAKVVETFNKTSNE-FIFMLSSKAGGCGLNLIGANRLV 589
E RGY+Y R+DG+ + R ++ FNK +E F+F+LS++AGG G+NL A+ ++
Sbjct: 504 EDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVI 563
Query: 590 MFDPDWNPANDDQAMARVWRDGQKKPCFVYRFLSTGSIEEKMMQRQAHKKALSSCVV 646
++D DWNP D QA R R GQKK V+RF + +IEEK+++R K AL + V+
Sbjct: 564 LYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 101 bits (252), Expect = 3e-24
Identities = 59/218 (27%), Positives = 89/218 (40%), Gaps = 38/218 (17%)
Query: 147 LRPHQREGVKFMYECVTGVRIEDAYGCIMADEMGLGKTLQ-CITLMWTLLRQGPLAKPLI 205
LRP+Q+E ++ + + V I+A G GKTL + + L R
Sbjct: 9 LRPYQKEAIEALLSGLRDV--------ILAAPTGSGKTLAALLPALEALKRGKG------ 54
Query: 206 DKAIIVAP-SSLVKNWCNEITKWL---GGRVAALPIDGGSKAEIDNKLNSFMQTYGRRPV 261
+ +++ P L + W E+ K G +V L G SK E KL S
Sbjct: 55 GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGL-YGGDSKREQLRKLES--------GK 105
Query: 262 NPILVISYETFRSHAS--VLHKNEVGLVLCDEGHRLKNC--ESQTYQALMGL-KAKRRVL 316
ILV + L + V LV+ DE HRL + Q + L L K + +L
Sbjct: 106 TDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165
Query: 317 LSGTP---IQNDLLEYFSLVHFVNQGILGTAQEFRKQY 351
LS TP I+N L + + F++ G T E +Q+
Sbjct: 166 LSATPPEEIENLLELFLNDPVFIDVGF--TPLEPIEQF 201
>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 = 98.5 bits (246), Expect = 3e-24
Identities = 27/124 (21%), Positives = 56/124 (45%), Gaps = 3/124 (2%)
Query: 496 SAKLMVLDTMLAVIKMTTDDKIVLVSNYTQTLDLFERLSKLRGYKYVRLDGSMTIKKRAK 555
KL L +L K+++ + LD L + G K L G + ++R +
Sbjct: 11 DEKLEALLELLKEHL-KKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREE 69
Query: 556 VVETFNKTSNEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDDQAMARVWRDGQKKP 615
V++ F + E + ++++ G++L + ++ +D W+P++ Q + R R GQK
Sbjct: 70 VLKDFRE--GEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGT 127
Query: 616 CFVY 619
+
Sbjct: 128 AILL 131
>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 = 87.6 bits (218), Expect = 4e-21
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 535 KLRGYKYVRLDGSMTIKKRAKVVETFNKTSNEFIFMLSSKAGGCGLNLIGANRLVMFDPD 594
+ G K RL G ++ ++R +++E F + + ++++ G G++L N ++ +D
Sbjct: 4 RKPGIKVARLHGGLSQEEREEILEDFR--NGKSKVLVATDVAGRGIDLPDVNLVINYDLP 61
Query: 595 WNPANDDQAMARVWRDG 611
WNPA+ Q + R R G
Sbjct: 62 WNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 83.0 bits (206), Expect = 2e-19
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 528 DLFERLSKLRGYKYVRLDGSMTIKKRAKVVETFNKTSNEFIFMLSSKAGGCGLNLIGANR 587
+ L K G K RL G ++ ++R ++++ FN + ++++ GL+L G +
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNN--GKIKVLVATDVAERGLDLPGVDL 58
Query: 588 LVMFDPDWNPANDDQAMARVWRDG 611
++++D W+PA+ Q + R R G
Sbjct: 59 VIIYDLPWSPASYIQRIGRAGRAG 82
>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 = 77.0 bits (190), Expect = 1e-16
Identities = 34/156 (21%), Positives = 58/156 (37%), Gaps = 19/156 (12%)
Query: 172 GCIMADEMGLGKTLQCITLMWTLLRQGPLAKPLIDKAIIVAP-SSLVKNWCNEITKWLGG 230
++A G GKTL + + LL + +++AP L + + G
Sbjct: 2 DVLLAAPTGSGKTLAALLPILELLDSLK-----GGQVLVLAPTRELANQVAERLKELFGE 56
Query: 231 RVAALPIDGGSKAEIDNKLNSFMQTYGRRPVNPILVISYETFRSHA--SVLHKNEVGLVL 288
+ + GG+ + KL S + I+V + L ++ L++
Sbjct: 57 GIKVGYLIGGTSIKQQEKLLS------GKTD--IVVGTPGRLLDELERLKLSLKKLDLLI 108
Query: 289 CDEGHRLKNCESQTYQALMGLKAK---RRVLLSGTP 321
DE HRL N + LK + +LLS TP
Sbjct: 109 LDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2
and 3. This family of class II histone deacetylase
complex subunits HDA2 and HDA3 is found in fungi, The
member from S. pombe is referred to as Ccq1. These
proteins associate with HDA1 to generate the activity of
the HDA1 histone deacetylase complex. HDA1 interacts
with itself and with the HDA2-HDA3 subcomplex to form a
probable tetramer and these interactions are necessary
for catalytic activity. The HDA1 histone deacetylase
complex is responsible for the deacetylation of lysine
residues on the N-terminal part of the core histones
(H2A, H2B, H3 and H4). Histone deacetylation gives a tag
for epigenetic repression and plays an important role in
transcriptional regulation, cell cycle progression and
developmental events. HDA2 and HDA3 have a conserved
coiled-coil domain towards their C-terminus.
Length = 279
Score = 59.3 bits (144), Expect = 2e-09
Identities = 51/247 (20%), Positives = 92/247 (37%), Gaps = 35/247 (14%)
Query: 410 MTDLQKELYTNLIKSDA------VRRTMKGGENTKLGMTALSSITS----LKKLCNHPDL 459
MT LQK+L ++ + + KL SI L + HP L
Sbjct: 12 MTSLQKDLTEQIVSLHYSDILKFCETSSSKEDIIKLLEDLTESIKLLFENLSLVATHPYL 71
Query: 460 VMDKIQTGADGFENAMNILPTGYAASYKSGKLLIELSAKLMVLDTML-AVIKMTTDDKIV 518
++D + +P + + L E S K +VL+ ++ +I+ D ++
Sbjct: 72 LID-------------HYMPKSLLLK-EPPEHLAETSGKFLVLNDLINLLIRSERDLHVL 117
Query: 519 LVSNYTQTLDLFERLSKLRGYKYVRLDGSMTIKKRAKVVETFNKTSNEFIFMLSSKAG-- 576
++S +TLDL E L +G Y RL G ++ KV + K S L++ G
Sbjct: 118 IISRSVKTLDLVEALLLGKGLNYKRLSGESLYEENHKV--SDKKGSLSLWIHLTTSDGLT 175
Query: 577 ---GCGLNLIGANRLVMFDPDWNPANDD-QAMARVWRDGQKKPCFVYRFLSTGSIEEKMM 632
L+ + ++ FDP + + +++ R + R + SIE +
Sbjct: 176 NTDSSLLSNYKFDLIISFDPSLDTSLPSIESLRTQNRR--GNLTPIIRLVVVNSIEHVEL 233
Query: 633 QRQAHKK 639
Sbjct: 234 CFPKKYP 240
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 47.8 bits (114), Expect = 1e-05
Identities = 44/194 (22%), Positives = 68/194 (35%), Gaps = 39/194 (20%)
Query: 147 LRPHQREGVKFMYECVTGVRIEDAYGCIMADEMGLGKTLQCITLMWTLLRQGPLAKPLID 206
LRP+Q E + V R E ++ G GKT+ + L R
Sbjct: 37 LRPYQEEALD---ALVKNRRTERRGVIVLP--TGAGKTVVAAEAIAELKR---------- 81
Query: 207 KAIIVAPSS-LVKNWCNEITKWLGGRVAALPIDGGSKAEIDNKLNSFMQTYGRRPVNPIL 265
+++ P+ L+ W + K+L GG K K +
Sbjct: 82 STLVLVPTKELLDQWAEALKKFLLLNDEIGIYGGGEKELEPAK---------------VT 126
Query: 266 VISYETF--RSHASVLHKNEVGLVLCDEGHRLKNCESQTYQALMGLKAKRRVL-LSGTPI 322
V + +T R NE GL++ DE H L + L L A L L+ TP
Sbjct: 127 VATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILEL--LSAAYPRLGLTATPE 184
Query: 323 QND---LLEYFSLV 333
+ D + + F L+
Sbjct: 185 REDGGRIGDLFDLI 198
>gnl|CDD|219956 pfam08658, Rad54_N, Rad54 N terminal. This is the N terminal of
the DNA repair protein Rad54.
Length = 191
Score = 45.4 bits (108), Expect = 2e-05
Identities = 36/135 (26%), Positives = 51/135 (37%), Gaps = 33/135 (24%)
Query: 14 PEDSPGI--KTFPPPVKKEKRSCTSRKPL----------GSVDNEDEPNSKLPMTKEE-- 59
DS K F P + S +P G+ +D+ NS P T +
Sbjct: 7 VTDSLDRLTKPFKVP-GSATPTRESDRPARKRRRKVNYAGADGEDDDNNSDKPYTNKRRL 65
Query: 60 -MSEHENLIRQ---------ILAKPFKVPILNYTGGGYSTK----ALGVRREGAR---KA 102
++ + K F VP++N GY + LG+RR GA +
Sbjct: 66 ALATRDVNRFPVFRLKDKETTFKKSFSVPLINKKSKGYVPRRPPPTLGMRR-GAVFVPRP 124
Query: 103 LHDPTAPNALVLYTP 117
LHDPT A+VLY P
Sbjct: 125 LHDPTGEFAIVLYDP 139
>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 = 37.8 bits (88), Expect = 0.018
Identities = 21/124 (16%), Positives = 54/124 (43%), Gaps = 13/124 (10%)
Query: 502 LDTMLAVIKMTTDDKIVLVSNYTQTLDLFERLSKLRGYKYVRLDGSMTIKKRAKVVETFN 561
L+ +L ++K + ++++ + ++ + RG+K L G + ++R + +E F
Sbjct: 261 LELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFK 320
Query: 562 KTSNEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDDQAMARVWRDGQKKPCFVYRF 621
E ++++ GL++ + ++ +D P + + + R+ R G R
Sbjct: 321 D--GELRVLVATDVAARGLDIPDVSHVINYDL---PLDPEDYVHRIGRTG--------RA 367
Query: 622 LSTG 625
G
Sbjct: 368 GRKG 371
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 34.4 bits (79), Expect = 0.27
Identities = 55/255 (21%), Positives = 91/255 (35%), Gaps = 52/255 (20%)
Query: 99 ARKALHDPTAPNALVLYTPPQLSAHDLLKIDKDKIQVHVVV-DPVLSNILRPHQREGVKF 157
A KA+ +P + + S D D ++Q ++ + P RPHQ+ +
Sbjct: 116 AEKAIEQQRSPGMRIGLSEIAESPIDWDIFDPTELQDNLPLKKP---KKPRPHQQTAIDA 172
Query: 158 MYECVTGVRIEDAYGCIMADEMGLGKTLQCITLMWTLLRQGPLAKPLIDKAIIVAPSSLV 217
E G D IMA G GKT + + L A+ L I S +
Sbjct: 173 AKE---GFSDNDRGKLIMA--CGTGKTFTSLKISEALAA----ARILFLVPSISLLSQTL 223
Query: 218 KNWCNEITKWLGGRVAALPIDGG-SKAEIDNK-----------LNSFMQTYGRRPVNPIL 265
+ W + K L R +A+ D S++ D K L + R L
Sbjct: 224 REWTAQ--KELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGL 281
Query: 266 VISYETFRSHASVLHK------NEVGLVLCDEGHR-------------LKNCESQTYQAL 306
+ + T++S + + +E L++CDE HR S
Sbjct: 282 TVVFSTYQS-LPRIKEAQEAGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQN--- 337
Query: 307 MGLKAKRRVLLSGTP 321
+KA +R+ ++ TP
Sbjct: 338 --IKAAKRLYMTATP 350
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 32.2 bits (74), Expect = 1.4
Identities = 34/134 (25%), Positives = 55/134 (41%), Gaps = 21/134 (15%)
Query: 71 LAKPFKVPILNYTGGGYSTKALGVRREGARKA------LHDPT-APNALV-LYTPPQLSA 122
+KVP + +ST ++ K+ + PT P AL +TP L
Sbjct: 337 SGGRYKVPFV------FSTNGRPYLKQLKTKSGIWFRDVRKPTNHPRALQGWHTPEGLL- 389
Query: 123 HDLLKIDKDKIQVHVVVDPVLSNI-LRPHQREGVKFMYECVTGVRIEDAYGCIMADEMGL 181
DLL+ D + + +P + LR +Q + + + V +E ++A G
Sbjct: 390 -DLLESDIEAANQWLADEPFDYGLGLRYYQEDAI----QAVEKAIVEGQREILLAMATGT 444
Query: 182 GKTLQCITLMWTLL 195
GKT I LM+ LL
Sbjct: 445 GKTRTAIALMYRLL 458
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 31.1 bits (71), Expect = 2.4
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 8/56 (14%)
Query: 227 WLGGRVAALPIDGGSKAEIDNKLNSFMQTYGRRPVNPILVISYETFRS--HASVLH 280
+L G V GG K+ + L ++ Y + I + S H LH
Sbjct: 82 YLLGPV------GGGKSSLVECLKRGLEEYSKTDEGRIYTFKWNGEESPMHEDPLH 131
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 30.8 bits (69), Expect = 2.5
Identities = 40/173 (23%), Positives = 70/173 (40%), Gaps = 31/173 (17%)
Query: 441 MTALSSITSLKKLCNHPDLVMDKIQTGADGFENAMNILPTGYAASYKSGKLLIELSAKLM 500
MT + SIT+ +K + P + + G + NI+P+ A+ GK+L L+ KL
Sbjct: 179 MTTVHSITATQKTVDGPSM-----KDWRGGRAASFNIIPSSTGAAKAVGKVLPSLNGKL- 232
Query: 501 VLDTMLAVIKMTTDDKIVLVSNYTQTLDLFERLSKLRGYKYVRLDGSMTIKKRAKVVETF 560
T ++ T D +V DL RL K Y ++ ++ + K+
Sbjct: 233 ---TGMSFRVPTVDVSVV---------DLTVRLEKAATYDEIK--KAIKEESEGKLKGIL 278
Query: 561 NKTSNEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDDQAMARV-WRDGQ 612
T ++ + + +G NR +FD A D+ + V W D +
Sbjct: 279 GYTEDDVV----------STDFVGDNRSSIFDAKAGIALSDKFVKLVSWYDNE 321
>gnl|CDD|234775 PRK00476, aspS, aspartyl-tRNA synthetase; Validated.
Length = 588
Score = 31.2 bits (72), Expect = 2.6
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 5/33 (15%)
Query: 229 GGRVAALPIDGG----SKAEIDNKLNSFMQTYG 257
GGRV A+ + GG S+ +ID +L F + YG
Sbjct: 318 GGRVKAIRVPGGAAQLSRKQID-ELTEFAKIYG 349
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 30.5 bits (69), Expect = 3.4
Identities = 37/245 (15%), Positives = 77/245 (31%), Gaps = 30/245 (12%)
Query: 65 NLIRQILAKPFKVPILNYTGGGYSTKALGVRREGARKALHDPTAPNALVLYTPPQLSAHD 124
L ++LA+ +V +++ G YS A + E + N L ++ + +
Sbjct: 20 LLALRLLARGGRVIVID-PKGEYSGLARALGGEVIDLGPGSGISLNPLDIFPTGEDAEEL 78
Query: 125 LLKIDKDKIQVHVVVDPVLSNILRPHQREGVKFMYECVTGVR--IEDAYGCIMADEMGLG 182
K+ + L +L G T + + Y G
Sbjct: 79 EADAHARKLDL-------LLALLELAALLGRDLTPREETALDRALRALYE-------EEG 124
Query: 183 KTLQCITLMWTLLRQGPLAKPLID---KAIIVAPSSLVKNWCNEITKWLGGRVAALPIDG 239
+ LL L + A++ + + + L G + L DG
Sbjct: 125 IDRDAYPTLSDLLEA--LRDEPDELREAALVDDEEEAAEELALALERLLDGALGGL-FDG 181
Query: 240 GSKAEID--NKLNSF-MQTYGRRPVNPILV----ISYETFRSHASVLHKNEVGLVLCDEG 292
+ ++D +L F + ++ L+ ++ A + L++ DE
Sbjct: 182 PTTVDLDLDARLVVFDLSGLKGPELDKALMAAVLLALWAAARRAFEAPRGLRKLIVIDEA 241
Query: 293 HRLKN 297
RL +
Sbjct: 242 WRLLS 246
>gnl|CDD|226115 COG3587, COG3587, Restriction endonuclease [Defense mechanisms].
Length = 985
Score = 30.1 bits (68), Expect = 5.3
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 17/100 (17%)
Query: 119 QLSAHDLLKIDKDKIQVHVVVDPVLSNILRPHQREGVKFMYECVTGVRIEDAYGCIMADE 178
Q SA+ +I DK D +L NI + G+ VRI+D + E
Sbjct: 35 QRSANPQFEIGADK-------DLLLENINNIQSKNGIT-----QGSVRIDDKLNIDILME 82
Query: 179 MGLGKTLQCITLMWTLLRQGPLAKPLIDKAIIVAPSSLVK 218
G GKT + M+ L ++ L K IIV PS +K
Sbjct: 83 TGTGKTYTYLRTMFELHKKYGLF-----KFIIVVPSLAIK 117
>gnl|CDD|183242 PRK11627, PRK11627, hypothetical protein; Provisional.
Length = 192
Score = 29.3 bits (66), Expect = 5.5
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 601 DQAMARVWRDGQK---KPCFVYRFLSTGSIEEKMMQR 634
DQA+A+V RDGQ P RFL +E++M R
Sbjct: 55 DQALAKVNRDGQLVTLTPSRDLRFLLQEVLEKQMTAR 91
>gnl|CDD|227377 COG5044, MRS6, RAB proteins geranylgeranyltransferase component A
(RAB escort protein) [Posttranslational modification,
protein turnover, chaperones].
Length = 434
Score = 29.8 bits (67), Expect = 6.4
Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 11/85 (12%)
Query: 530 FERLSKLRGYKYVRLDGSMTIKKRAKVVETFNK----------TSNEFIFMLSSKAGGCG 579
F R S + G Y+ L+ ++ K VET +K S+ F SK+ G
Sbjct: 235 FARSSAVYGGTYM-LNQAIDEINETKDVETVDKGSLTQKAGKIISSPTYFREDSKSVGQF 293
Query: 580 LNLIGANRLVMFDPDWNPANDDQAM 604
+I A +++ P D
Sbjct: 294 YRIIRAICILLVHPVPFTTGLDSLQ 318
>gnl|CDD|224733 COG1820, NagA, N-acetylglucosamine-6-phosphate deacetylase
[Carbohydrate transport and metabolism].
Length = 380
Score = 29.2 bits (66), Expect = 8.2
Identities = 46/225 (20%), Positives = 77/225 (34%), Gaps = 58/225 (25%)
Query: 425 DAVRRTMKGGENTKLGMTALSSITSLKKLCNHPDLVMDKIQTGADGFE---NAMNILPTG 481
+ +R G +G + + + + GA NAM +G
Sbjct: 177 ELIRLLANAGIVVSIGHSNATY-----------EQARAAFEAGATFVTHLFNAM----SG 221
Query: 482 Y--------AASYKSGKLLIELSAKLMVLD--TMLAVIKMTTDDKIVLVSNYTQTLDLFE 531
A+ + + E+ A + + + +K DKIVLV++ L +
Sbjct: 222 LHHREPGVVGAALDNPDVYAEIIADGVHVHPAAIRLALKAKGGDKIVLVTDAMAAAGLPD 281
Query: 532 RLSKLRGYK-YVR----------LDGS-MTIKKRAK-VVETFNKTSNEFIFMLSS---KA 575
L G V L GS +T+ + + +VE + E + M S KA
Sbjct: 282 GEYILGGQTVTVADGARRLEDGTLAGSTLTMDEAVRNLVEWGGISLAEAVRMASLNPAKA 341
Query: 576 GG----CGLNLIG--ANRLVMFDPDWNPANDDQAMARVWRDGQKK 614
G G G A+ LV+ D D N + W +G+K
Sbjct: 342 LGLDDRLGSIKPGKDAD-LVVLDDDLN-------VKATWINGEKV 378
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
0.318 0.134 0.394
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 37,798,970
Number of extensions: 3700964
Number of successful extensions: 3149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3113
Number of HSP's successfully gapped: 28
Length of query: 755
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 651
Effective length of database: 6,324,786
Effective search space: 4117435686
Effective search space used: 4117435686
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 (21.7 bits)
S2: 63 (28.0 bits)