RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13010
(573 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 = 307 bits (788), Expect = e-101
Identities = 142/310 (45%), Positives = 193/310 (62%), Gaps = 16/310 (5%)
Query: 44 YQLKGMNWLANLYDQGINGILADEMGLGKTVQSIAFL-CHIAETYDVWGPFLIISPASTL 102
YQL+G+NWL +L G+ GILADEMGLGKT+Q+IA L ++ E D GP L++ P STL
Sbjct: 1 YQLEGVNWLISLESNGLGGILADEMGLGKTLQTIALLATYLKEGKDRRGPTLVVCPLSTL 60
Query: 103 HNWQQEMERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFK 162
HNW E E++ P +VV Y G +ER LRQ K L T D VVIT+Y+++ D K
Sbjct: 61 HNWLNEFEKWAPALRVVVYHGDGRERSKLRQS-MAKRLDTYD----VVITTYEVLRKDKK 115
Query: 163 Y---FNRIKWQYLILDEAQAIKSSSSMRWKLLLGFSCRNRLLLSGTPIQNSMAELWALLH 219
N+++W ++LDEA +K+S S +K L RNRLLL+GTPIQN++ ELWALL+
Sbjct: 116 LLSLLNKVEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQNNLEELWALLN 175
Query: 220 FIMPSMFDSHDEFNEWFSKDIESHAENKTSIDERH---LSRLHMILKPFMLRRIKKDVEN 276
F+ P F S F EWF+ I + A+NK E+ ++RLH +LKPF+LRR K DVE
Sbjct: 176 FLRPGPFGSFKVFEEWFNIPIANTADNKNKNLEKGKEGINRLHKLLKPFLLRRTKDDVEK 235
Query: 277 ELSDKIEIMVYCPLTSRQKLLYSALKKKIKIEDLIHSSSGGSIQLSNNIASNLMNLVMQF 336
L K E ++YC L+ Q+ LY KK+ + + S N ++L+NL+MQ
Sbjct: 236 SLPPKTEHVLYCNLSDEQRKLY----KKLLTKRRLALSFAVEGGEKNVGIASLLNLIMQL 291
Query: 337 RKVCNHPELF 346
RK+CNHP LF
Sbjct: 292 RKICNHPYLF 301
Score = 43.1 bits (102), Expect = 3e-04
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 392 LPQQPTYLPVCFFESTQNMVSPALKKKIKIEDLIHSSSGGSIQLSNNIASNLMNLVMQFR 451
LP + ++ C Q L KK+ + + S N ++L+NL+MQ R
Sbjct: 237 LPPKTEHVLYCNLSDEQR----KLYKKLLTKRRLALSFAVEGGEKNVGIASLLNLIMQLR 292
Query: 452 KVCNHPELF 460
K+CNHP LF
Sbjct: 293 KICNHPYLF 301
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 273 bits (700), Expect = 6e-81
Identities = 126/315 (40%), Positives = 190/315 (60%), Gaps = 24/315 (7%)
Query: 33 QPGLFRGNLKHYQLKGMNWLANLYDQGINGILADEMGLGKTVQSIAFLCHIAETYDVWGP 92
QP +G ++ YQL G+NWL LY+ GINGILADEMGLGKT+Q+I+ L ++ E + GP
Sbjct: 162 QPSCIKGKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGP 221
Query: 93 FLIISPASTLHNWQQEMERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVIT 152
++++P STL NW E+ RF P + V + G+P+ER R+ + F V +T
Sbjct: 222 HMVVAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELLVAG------KFDVCVT 275
Query: 153 SYQLVVSDFKYFNRIKWQYLILDEAQAIKSSSSMRWKLLLGFSCRNRLLLSGTPIQNSMA 212
S+++ + + R W+Y+I+DEA IK+ +S+ K + FS RLL++GTP+QN++
Sbjct: 276 SFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPLQNNLH 335
Query: 213 ELWALLHFIMPSMFDSHDEFNEWFSKDIESHAENKTSIDERHLSRLHMILKPFMLRRIKK 272
ELWALL+F++P +F S + F+EWF I + + + +LH +L+PF+LRR+K
Sbjct: 336 ELWALLNFLLPEIFSSAETFDEWFQ--ISGENDQQEVV-----QQLHKVLRPFLLRRLKS 388
Query: 273 DVENELSDKIEIMVYCPLTSRQKLLYSALKKKIKIEDLIHSSSGGSIQLSNNIASNLMNL 332
DVE L K E ++ ++ QK Y AL +K DL ++GG L+N+
Sbjct: 389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQK----DLDVVNAGGE-------RKRLLNI 437
Query: 333 VMQFRKVCNHPELFE 347
MQ RK CNHP LF+
Sbjct: 438 AMQLRKCCNHPYLFQ 452
Score = 97.6 bits (243), Expect = 5e-21
Identities = 45/125 (36%), Positives = 71/125 (56%), Gaps = 22/125 (17%)
Query: 441 SNLMNLVMQFRKVCNHPELFERRDAKAPLAMSCEDYVIPKLVFEEALLCHKLTLVYDAGK 500
L+N+ MQ RK CNHP LF+ + P Y + H LV ++GK
Sbjct: 432 KRLLNIAMQLRKCCNHPYLFQGAEPGPP-------YTTGE---------H---LVENSGK 472
Query: 501 LSVLDDLLKRLKASGHRVLVYSQMTKMIDLLEEFMVYRKYRFMRLDGSSKISERRDM--- 557
+ +LD LL +LK RVL++SQMT+++D+LE++++YR Y++ R+DG++ +R
Sbjct: 473 MVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDA 532
Query: 558 FAVPG 562
F PG
Sbjct: 533 FNKPG 537
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 244 bits (624), Expect = 3e-71
Identities = 128/369 (34%), Positives = 191/369 (51%), Gaps = 19/369 (5%)
Query: 23 PSFSTEVERPQPGLFRGNLKHYQLKGMNWLAN-LYDQGINGILADEMGLGKTVQSIAFLC 81
+ P+P L+ YQL+G+NWL+ L + GILAD+MGLGKTVQ+IA L
Sbjct: 321 RLSEDLLNAPEPVDLSAELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLL 380
Query: 82 HIAETYDVW-GPFLIISPASTLHNWQQEMERFVPDFK-VVPYWGSPQERKILRQFW-DMK 138
+ E+ V+ GP LI+ PAS L NW++E E+F PD + V+ Y G E R+ D+
Sbjct: 381 SLLESIKVYLGPALIVVPASLLSNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRDLL 440
Query: 139 NLHTKDASFHVVITSYQLVVS---DFKYFNRIKWQYLILDEAQAIKSSSSMRWKLLLGFS 195
LH F VVIT+Y+L+ D +I+W ++LDEA IK+ S K L
Sbjct: 441 KLH-LVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQFLK 499
Query: 196 CRNRLLLSGTPIQNSMAELWALL-HFIMPSMFD-SHDEFNEWFSKDIESHAE-NKTSIDE 252
NRL L+GTP++N + ELW+LL F+ P + S F F K I++ + E
Sbjct: 500 ALNRLDLTGTPLENRLGELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARE 559
Query: 253 RHLSRLHMILKPFMLRRIKKDVE--NELSDKIEIMVYCPLTSRQKLLYSA-LKKKIKIED 309
+ L +L PF+LRR K+DVE EL KIE ++ C L+ Q+ LY A L+ K +
Sbjct: 560 LGIELLRKLLSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQ 619
Query: 310 LIHSS--SGGSIQLSNNIASNLMNLVMQFRKVCNHPELFERRD---AKAPLAMSCEDYHR 364
L+ + + N++ L+ + R++CNHP L + + + ED
Sbjct: 620 LLEDLEKADSDENRIGDSELNILALLTRLRQICNHPALVDEGLEATFDRIVLLLREDKDF 679
Query: 365 LYRGRQMER 373
Y + + +
Sbjct: 680 DYLKKPLIQ 688
Score = 71.3 bits (174), Expect = 7e-13
Identities = 35/122 (28%), Positives = 64/122 (52%), Gaps = 8/122 (6%)
Query: 442 NLMNLVMQFRKVCNHPELFERRDAKAPLAMSCEDYVIPKLVFEEALLCHKLTLVYDAGKL 501
N++ L+ + R++CNHP L + + V+ ++ K + GKL
Sbjct: 640 NILALLTRLRQICNHPALVDEGLEATF-----DRIVLLLREDKDFDYLKKPLIQLSKGKL 694
Query: 502 SVLDDLLK-RLKASGH--RVLVYSQMTKMIDLLEEFMVYRKYRFMRLDGSSKISERRDMF 558
LD+LL +L GH +VL++SQ T ++DLLE+++ +++RLDGS+ R+++
Sbjct: 695 QALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELI 754
Query: 559 AV 560
Sbjct: 755 DR 756
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 102 bits (256), Expect = 4e-25
Identities = 43/202 (21%), Positives = 76/202 (37%), Gaps = 23/202 (11%)
Query: 34 PGLFRGNLKHYQLKGMNWLANLYDQGINGILADEMGLGKTVQSIAFLCHIAETYDVWGPF 93
L+ YQ + + L + + ILA G GKT+ ++ + G
Sbjct: 2 EKFGFEPLRPYQKEAIEALLSGLR---DVILAAPTGSGKTLAALLPALEALKRGK-GGRV 57
Query: 94 LIISPASTL-HNWQQEMERFVPDF--KVVPYWGSPQERKILRQFWDMKNLHTKDASFHVV 150
L++ P L W +E+++ P KVV +G +R+ LR+ + ++
Sbjct: 58 LVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKL--------ESGKTDIL 109
Query: 151 ITSYQLVVSDFK--YFNRIKWQYLILDEAQAIKS---SSSMRWKLLLGFSCRNRLLLSGT 205
+T+ ++ + + +ILDEA + + L L LLLS T
Sbjct: 110 VTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSAT 169
Query: 206 P---IQNSMAELWALLHFIMPS 224
P I+N + FI
Sbjct: 170 PPEEIENLLELFLNDPVFIDVG 191
>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 = 89.3 bits (222), Expect = 4e-21
Identities = 31/152 (20%), Positives = 57/152 (37%), Gaps = 15/152 (9%)
Query: 61 NGILADEMGLGKTVQSIAFLCHIAETYDVWGPFLIISPASTLHNWQQE-MERFVPDFKVV 119
+ +LA G GKT+ ++ + + ++ G L+++P L N E ++ + V
Sbjct: 2 DVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGEGIKV 60
Query: 120 PYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFK--YFNRIKWQYLILDEA 177
Y + +V+ + ++ + + + K LILDEA
Sbjct: 61 GYLI--------GGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEA 112
Query: 178 QAIKSSSS---MRWKLLLGFSCRNRLLLSGTP 206
+ + LL R LLLS TP
Sbjct: 113 HRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>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 = 45.3 bits (108), Expect = 6e-06
Identities = 19/61 (31%), Positives = 27/61 (44%)
Query: 494 LVYDAGKLSVLDDLLKRLKASGHRVLVYSQMTKMIDLLEEFMVYRKYRFMRLDGSSKISE 553
L + KL L +LLK G +VL++ KM+D L E + + L G E
Sbjct: 7 LPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEE 66
Query: 554 R 554
R
Sbjct: 67 R 67
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 36.3 bits (84), Expect = 0.040
Identities = 37/176 (21%), Positives = 65/176 (36%), Gaps = 25/176 (14%)
Query: 37 FRGNLKHYQLKGMNWLANLYDQGINGILADEMGLGKTVQSIAFLCHIAETYDVWGPFLII 96
F L+ YQ + ++ L G++ G GKTV + IAE L++
Sbjct: 33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEA---IAELKR---STLVL 86
Query: 97 SPASTL-HNWQQEMERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQ 155
P L W + +++F+ + +G + K L V + + Q
Sbjct: 87 VPTKELLDQWAEALKKFLLLNDEIGIYGGGE-----------KELE----PAKVTVATVQ 131
Query: 156 LVVSD--FKYFNRIKWQYLILDEAQAIKSSSSMRWKLLLGFSCRNRLLLSGTPIQN 209
+ F ++ +I DE + + S R LL + RL L+ TP +
Sbjct: 132 TLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLS-AAYPRLGLTATPERE 186
>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 = 33.5 bits (77), Expect = 0.32
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 501 LSVLDDLLKRLKASGHRVLVY-------SQMTKMIDLLEEFMVYRKYRFMRLDGSSKISE 553
L +LD LL+ A +L+Y Q ++ +L+ + K F R G + E
Sbjct: 104 LPILDHLLRDPSARA--LLLYPTNALANDQAERLRELISDL--PGKVTFGRYTGDTPPEE 159
Query: 554 RRDMFAVPG--ILT 565
RR + P +LT
Sbjct: 160 RRAIIRNPPDILLT 173
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 33.2 bits (76), Expect = 0.39
Identities = 48/322 (14%), Positives = 92/322 (28%), Gaps = 37/322 (11%)
Query: 15 SQQFGSTTPSFSTEVERPQPGLFRGNLK-----HYQLKGMNWLANLYDQGINGILADEMG 69
++Q + + Q K + + L + + +L G
Sbjct: 165 AKQEARLLKPLLLLLSAIARINKFKSFIEHEGYELQEKALELILRLEKRSLLVVLEAPTG 224
Query: 70 LGKTVQSIAFLCHIAETYDVWGP-FLIISPASTLHNWQQEMERFVPDFKVV--------- 119
GKT S+ + + + + P T+ + + V
Sbjct: 225 YGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIGKSLHSSS 284
Query: 120 --PYWGSPQERKILRQFWDMKNLHTKDASFHV-VITSYQLVVSDFKYFN-----RIKWQY 171
P P + N K + V+T Q+++ K F +
Sbjct: 285 KEPLLLEPDQDI---LLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSL 341
Query: 172 LILDEAQAIKSSSSMRWKLLLGFSCRNRLLLSGTPIQNSMAELWALLHFIMPSMFDSHDE 231
+ILDE + + LL G P+ A L L + E
Sbjct: 342 VILDEVHLYADETMLA--ALLALLEALAEA--GVPVLLMSATLPPFLKEKLKKALGKGRE 397
Query: 232 FNEWFSKDIESHAENKTSIDERHLSRLHMILKPFMLRRIKKDVENELSDKIEIMVYCPLT 291
E E++ + + + + ++ I ++V+ ++V
Sbjct: 398 VVE---NAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKK----VLVIVNTV 450
Query: 292 SRQKLLYSALKKKIKIEDLIHS 313
R LY LK+K L+HS
Sbjct: 451 DRAIELYEKLKEKGPKVLLLHS 472
>gnl|CDD|212875 cd11942, SH3_JIP2, Src homology 3 domain of JNK-interacting protein
2. JNK-interacting protein 2 (JIP2) is also called
Mitogen-activated protein kinase 8-interacting protein 2
(MAPK8IP2) or Islet-brain-2 (IB2). It is widely
expressed in the brain, where it forms complexes with
fibroblast growth factor homologous factors (FHFs),
which facilitates activation of the p38delta MAPK. JIP2
is enriched in postsynaptic densities and may play a
role in motor and cognitive function. In addition to a
JNK binding domain, JIP2 also contains SH3 and
Phosphotyrosine-binding (PTB) domains. The SH3 domain of
the related protein JIP1 homodimerizes at the interface
usually involved in proline-rich ligand recognition,
despite the lack of this motif in the domain itself. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 29.5 bits (66), Expect = 0.51
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 336 FRKVCNHPELFERRDAKAPLAMSCEDYHRLYRGRQMEREEGTILPEF 382
FR + H + E D PL + E+ YRG M E I P F
Sbjct: 6 FRFIPRHEDELEL-DVDDPLLVEAEEDDYWYRGYNMRTGERGIFPAF 51
>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 = 31.9 bits (73), Expect = 0.77
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 494 LVYDAGKLSVLDDLLKRLKASGH--RVLVYSQMTKMIDLLEEFMVYRKYRFMRLDGSSKI 551
L +GK VL+DL+ L S VL+ S+ K +DL+E ++ + + RL G S
Sbjct: 90 LAETSGKFLVLNDLINLLIRSERDLHVLIISRSVKTLDLVEALLLGKGLNYKRLSGESLY 149
Query: 552 SERRDM 557
E +
Sbjct: 150 EENHKV 155
>gnl|CDD|165523 PHA03265, PHA03265, envelope glycoprotein D; Provisional.
Length = 402
Score = 31.2 bits (70), Expect = 1.5
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 16/67 (23%)
Query: 358 SCEDYHRLYRGRQMEREEGTILPEFPHVPRDPVILPQQPTYLPVCFFESTQNMVSPALKK 417
+CE R RGRQ EFP P + Y + + +T + SP +
Sbjct: 29 TCEKAKRAVRGRQDRP------KEFP---------PPRYNYTILTRYNAT-ALASPFIND 72
Query: 418 KIKIEDL 424
++K DL
Sbjct: 73 QVKNVDL 79
>gnl|CDD|233171 TIGR00890, 2A0111, oxalate/formate antiporter family transporter.
This subfamily belongs to the major facilitator family.
Members include the oxalate/formate antiporter of
Oxalobacter formigenes, where one substrate is
decarboxylated in the cytosol into the other to consume
a proton and drive an ion gradient [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 377
Score = 30.1 bits (68), Expect = 2.9
Identities = 9/41 (21%), Positives = 17/41 (41%)
Query: 58 QGINGILADEMGLGKTVQSIAFLCHIAETYDVWGPFLIISP 98
GI+ + M + + FL +A + WG + + P
Sbjct: 277 FGISAVGMAAMLFIPMLNDVLFLATVALVFFTWGGTISLFP 317
>gnl|CDD|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated.
Length = 956
Score = 30.2 bits (69), Expect = 3.4
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 17/56 (30%)
Query: 64 LADEMGLGKTV--------QSIAFLCHIAETYDVWGPFLIISPASTLHNWQQEMER 111
LADE+GLGKT+ Q + LI+ P + H W EM R
Sbjct: 174 LADEVGLGKTIEAGMIIHQQLLTGRAERV---------LILVPETLQHQWLVEMLR 220
>gnl|CDD|188234 TIGR02591, cas_Csh1, CRISPR-associated protein Cas8b/Csh1, subtype
I-B/HMARI. This domain is found in the C-terminal 2/3
of a family of CRISPR associated proteins of the Hmari
subtype. Except for the two sequences from halophilic
archaea this domain contains a pair of CXXC motifs
[Mobile and extrachromosomal element functions, Other].
Length = 393
Score = 29.3 bits (66), Expect = 5.5
Identities = 16/90 (17%), Positives = 27/90 (30%), Gaps = 7/90 (7%)
Query: 214 LWALLHFIMPSMFDSHDEFNEWFSKDIESHAENKTSIDERHLSRLHMILKPFMLRRIKKD 273
+ F++ + F DEF +K ++ L ++ D
Sbjct: 178 FGQVYAFLLDNDFFEDDEFLNLLDAIFRGGPLDKDTLFTEFLKKIKD-------EFFGGD 230
Query: 274 VENELSDKIEIMVYCPLTSRQKLLYSALKK 303
N L + M L LL +L K
Sbjct: 231 SINNLIVASQNMRLLLLAREALLLLLSLDK 260
>gnl|CDD|173961 cd08551, Fe-ADH, iron-containing alcohol dehydrogenases
(Fe-ADH)-like. Large metal-containing alcohol
dehydrogenases (ADH), known as iron-containing alcohol
dehydrogenases. They contain a dehydroquinate
synthase-like protein structural fold and mostly contain
iron. They are distinct from other alcohol
dehydrogenases which contains different protein domains.
There are several distinct families of alcohol
dehydrogenases: Zinc-containing long-chain alcohol
dehydrogenases; insect-type, or short-chain alcohol
dehydrogenases; iron-containing alcohol dehydrogenases,
and others. The iron-containing family has a Rossmann
fold-like topology that resembles the fold of the
zinc-dependent alcohol dehydrogenases, but lacks
sequence homology, and differs in strand arrangement.
ADH catalyzes the reversible oxidation of alcohol to
acetaldehyde with the simultaneous reduction of NAD(P)+
to NAD(P)H.
Length = 370
Score = 29.2 bits (66), Expect = 6.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 491 KLTLVYDAG--KLSVLDDLLKRLKASGHRVLVYSQ 523
K +V D G K VLD ++ LK +G V+++
Sbjct: 25 KALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDG 59
>gnl|CDD|187803 cd09672, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as TM1802 family.
Length = 545
Score = 29.0 bits (65), Expect = 7.2
Identities = 23/121 (19%), Positives = 40/121 (33%), Gaps = 20/121 (16%)
Query: 195 SCRNRLLLSGTPIQNSMAELW--ALLHFIMPSMFDSHDEFNEWFSKDIESHAENKTSIDE 252
C ++ IQ +++ + L I F+ + W E E
Sbjct: 209 DCYKDVIYGRKFIQENLSTRFGGNDLWIIPGLFFNGKELKESWIRISREFKKSTFNLKFE 268
Query: 253 RHLSRLHMILKPFMLRRIKKDVENELSDKIEIMVYCPLTSRQKLLYSALKKKIKIEDLIH 312
RI++++ N L K V ++K SA K K+ I+D+
Sbjct: 269 E---------------RIERNIINYLEFKDGGTVDFLFYEKEK---SAEKIKLYIKDVHP 310
Query: 313 S 313
S
Sbjct: 311 S 311
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 28.5 bits (64), Expect = 8.0
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 264 PFMLRRIKKDVENELSDKIEIMVYCPLTSRQK 295
PF R K+ ++ +E + PL R K
Sbjct: 158 PFFGRGGKRGLDAGRETVVEFELLLPLPGRAK 189
>gnl|CDD|188535 TIGR04020, seco_metab_LLM, natural product biosynthesis
luciferase-like monooxygenase domain. This model
describes a subfamily within the bacterial
luciferase-like monooxygenase (LLM) family that
regularly occurs within large non-ribosomal protein
synthases/polyketide synthases, but also as small
proteins. The LLM family includes members that bind
either FMN or F420, and FMN is more likely in this case
because many members are from species that lack F420
biosynthesis capability. An example member is the MupA
protein of mupirocin biosynthesis in Pseudomonas
fluorescens NCIMB 10586.
Length = 341
Score = 28.8 bits (65), Expect = 8.8
Identities = 17/66 (25%), Positives = 23/66 (34%), Gaps = 21/66 (31%)
Query: 343 PELFERRDAKAPLAMSCEDYHRLYRGRQMEREEGT-------ILPEFPHVPRDPVILPQQ 395
PE +E R + + + RL+RG + G LP P Q
Sbjct: 116 PENYEDR--REVMFEGIDTVRRLWRGETVTFPGGGGREVEVKTLPR-----------PVQ 162
Query: 396 PTYLPV 401
P LPV
Sbjct: 163 PE-LPV 167
>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 = 28.0 bits (63), Expect = 9.3
Identities = 29/156 (18%), Positives = 48/156 (30%), Gaps = 29/156 (18%)
Query: 69 GLGKT-VQSIAFLCHIAETYDVWGPFLIISPASTLHNWQQEMERFV-----PDFKVVPYW 122
G GKT + L + L+++P L Q E +V
Sbjct: 24 GSGKTLAFLLPILQALLPKKGG-PQALVLAPTREL-AEQI-YEELKKLFKILGLRVALLT 80
Query: 123 GSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVS-----DFKYFNRIKWQYLILDEA 177
G ++ + L A +++ + ++ K +K L+LDEA
Sbjct: 81 GGTSLKE------QARKLKKGKA--DILVGTPGRLLDLLRRGKLKLLKNLK--LLVLDEA 130
Query: 178 QAIKSSSSMRWKLLLGFSCRN----RLLLSGTPIQN 209
+ L S LLLS T +N
Sbjct: 131 HRL-LDMGFGDDLEEILSRLPPDRQILLLSATLPRN 165
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 27.2 bits (61), Expect = 9.8
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 168 KWQYLILDEAQAIKSSSSMRWKLLLGFSCRNRLL-LSGTPI 207
+ +I+DEA SS+ +++ +L LL L+ TP
Sbjct: 61 QALVIIIDEAH--HSSAKTKYRKILEKFKPAFLLGLTATPE 99
>gnl|CDD|172552 PRK14061, PRK14061, unknown domain/lipoate-protein ligase A fusion
protein; Provisional.
Length = 562
Score = 28.5 bits (63), Expect = 10.0
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 264 PFMLRRIKKDVENELSDKIEIMVYCPLTSRQKLLYSALK 302
PF+L K E E S+K E CP+T+R++++ S L+
Sbjct: 195 PFLLTASKPVPEEEESEKKE----CPITTRKEIVMSTLR 229
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
0.322 0.136 0.408
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: 29,568,369
Number of extensions: 2914177
Number of successful extensions: 2631
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2606
Number of HSP's successfully gapped: 40
Length of query: 573
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 471
Effective length of database: 6,413,494
Effective search space: 3020755674
Effective search space used: 3020755674
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 (21.9 bits)
S2: 62 (27.8 bits)