RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17363
(790 letters)
>gnl|CDD|217892 pfam04100, Vps53_N, Vps53-like, N-terminal. Vps53 complexes with
Vps52 and Vps54 to form a multi- subunit complex
involved in regulating membrane trafficking events.
Length = 375
Score = 408 bits (1051), Expect = e-136
Identities = 175/372 (47%), Positives = 265/372 (71%), Gaps = 3/372 (0%)
Query: 36 DFDSVQYINSLFPTEQSLSNIDDVIMKMESNIKEMDEEIETVVRSQSGVGQDGKKALEDS 95
DF +++YIN LFPTEQSL+NID +I K++ I+ +D I+TVVR Q+ VG+ GK+AL+++
Sbjct: 3 DFSALEYINQLFPTEQSLTNIDSLIQKIQEEIRRLDANIKTVVRGQANVGEKGKEALDEA 62
Query: 96 QKVIMQLFSQVRDIKSKAEKSEEMVREITRDIKLLDTAKRNLTTAITCLNHLHMLVTGVH 155
QK I +LF ++++IKSKAE +EEMV+EITRDIK LD AK+NLTT+IT L+ LHMLVTGV
Sbjct: 63 QKAIEELFQKIKEIKSKAESTEEMVKEITRDIKQLDFAKKNLTTSITTLHRLHMLVTGVE 122
Query: 156 SLRTLIEQRQYGEIVMPLQGVIEVMKHFQDSTDIPQILELRSQVAQIQNTLSEQITQDLK 215
SL LI++R YGE PLQ +++++ HF + +I L +++++ +L QI QD K
Sbjct: 123 SLNALIQKRSYGEAASPLQAILQLLNHFIKYKSVDEIANLSESISKLKGSLLSQIFQDFK 182
Query: 216 NAFQNPSSGS-FVPSKQIAEALRVVSILDPKVKKNILEWFISLQLSEYLVLFDESEDSAW 274
+AF + + +++++A V LDP V++ +++WF S QL EY +F E+E++AW
Sbjct: 183 SAFGSQGEHRTGLLLQKLSDACLVADALDPSVREELIKWFCSQQLEEYEQIFRENEEAAW 242
Query: 275 LDKIDKRYAWFKKQLLHVEDKFGTLFPPHWQLSEKITLEFCERTRSELGKIMSKRKFEID 334
LDKID+RYAWFK+ L E+K+G +FP W ++E++T+EFC TR +L KI+ +R E+D
Sbjct: 243 LDKIDRRYAWFKRLLRDFEEKYGPIFPADWHVAERLTVEFCHVTRKQLAKILVRRDKELD 302
Query: 335 VKLLLYAIQKTSNFEQLLEKRFADDETEGENKTK--FDGIIGSCFQNYLYIYIESLDRNL 392
VKLLL+A+Q T FE+ L+KRF++ + + F G I SCF+ +L +YIES ++ L
Sbjct: 303 VKLLLFALQSTLEFEKFLDKRFSNTSKKTPEPKELAFHGAISSCFEPHLTLYIESQEKEL 362
Query: 393 SDLIDRFAEDSK 404
S+L+++F + K
Sbjct: 363 SELLEKFVSEEK 374
>gnl|CDD|222469 pfam13949, ALIX_LYPXL_bnd, ALIX V-shaped domain binding to HIV.
The binding of the LYPxL motif of late HIV p6Gag and
EIAV p9Gag to this domain is necessary for viral
budding.This domain is generally central between an
N-terminal Bro1 domain, pfam03097 and a C-terminal
proline-rich domain. The retroviruses thus used this
domain to hijack the ESCRT system of the cell.
Length = 292
Score = 33.8 bits (78), Expect = 0.30
Identities = 31/174 (17%), Positives = 73/174 (41%), Gaps = 18/174 (10%)
Query: 50 EQSLSNIDDVIMKMESNIKE----MDEEIETVVRSQSGVGQDGKKALEDSQKVIMQLFSQ 105
E+SL ++ ++ + E + E +DEE + ++ G+ + S ++ +L +
Sbjct: 28 ERSLDDLPELSQRNEEILDEIKELLDEEESEDEQLRAKYGE--RWTRPPSSELTAELREE 85
Query: 106 VRDIKS---KAEKSEEMVR----EITRDIKLLDTAKRNLTTAITCLNHLHMLVTG--VHS 156
+R + +A +S+ +R E +++LL + L + + +
Sbjct: 86 LRKYRGYLEQASESDAQLRSKLEEHEENLELLSGPEEELEALLPSSSPSKTPEVSEQISR 145
Query: 157 LRTLIEQRQYGEIVMPLQGVIEVMKHFQDSTDIPQIL-ELRSQVAQIQNTLSEQ 209
LR L+ + E+ + ++E +K DI ++L L + + L E+
Sbjct: 146 LRELLNKLN--ELKAEREKLLEELKEKAQDDDISKLLIALNKLGSSNEEQLFEE 197
>gnl|CDD|181518 PRK08643, PRK08643, acetoin reductase; Validated.
Length = 256
Score = 31.2 bits (71), Expect = 2.0
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 518 AEYCLETTQQLEQKLKEKVDPNLANKIDLSNEQDVFHNV 556
+Y ET Q KL + +A K D+S+ VF V
Sbjct: 32 VDYNEETAQAAADKLSKDGGKAIAVKADVSDRDQVFAAV 70
>gnl|CDD|238441 cd00869, PI3Ka_II, Phosphoinositide 3-kinase (PI3K) class II,
accessory domain (PIK domain); PIK domain is conserved
in all PI3 and PI4-kinases. Its role is unclear but it
has been suggested to be involved in substrate
presentation. In general, class II PI3-kinases
phosphorylate phosphoinositol (PtdIns),
PtdIns(4)-phosphate, but not PtdIns(4,5)-bisphosphate.
They are larger, having a C2 domain at the C-terminus.
Length = 169
Score = 30.5 bits (69), Expect = 2.1
Identities = 8/33 (24%), Positives = 13/33 (39%)
Query: 261 EYLVLFDESEDSAWLDKIDKRYAWFKKQLLHVE 293
E L+ + + + L DK W K+ E
Sbjct: 5 EKLLDLIQKQSTYTLSTEDKDLLWEKRLYCTNE 37
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 31.1 bits (71), Expect = 2.7
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 66 NIKEMDEEIETVVRSQ-SGVGQDGKKALED-SQKVIMQLFSQVRDIKSKAEKSEEMVREI 123
++ E+ E +E VV++ S + Q+G E+ KV Q S V D+K+ + ++ +
Sbjct: 318 DVTEILENLEEVVKADFSSIVQEGNSTFEEIPSKVKNQTSSVVPDVKAALDSLGTDIKSV 377
Query: 124 TRDI 127
D+
Sbjct: 378 AEDL 381
>gnl|CDD|218871 pfam06046, Sec6, Exocyst complex component Sec6. Sec6 is a
component of the multiprotein exocyst complex. Sec6
interacts with Sec8, Sec10 and Exo70.These exocyst
proteins localise to regions of active exocytosis-at the
growing ends of interphase cells and in the medial
region of cells undergoing cytokinesis-in an
F-actin-dependent and exocytosis- independent manner.
Length = 557
Score = 30.8 bits (70), Expect = 3.5
Identities = 27/161 (16%), Positives = 55/161 (34%), Gaps = 17/161 (10%)
Query: 521 CLETTQQLEQKLKEKVDPNLANKIDLSNEQ--DVFHNVISSCIQLLVQDLELACEPALTA 578
C + L QK KV +I E+ D F ++ CI LL++ + +PAL+
Sbjct: 320 CADYASSLLQKYLPKVSSKYEERITEEFEELLDGFVDLSKECISLLLELIFNDLQPALSK 379
Query: 579 MVKTNWSSVESVGDQSGYVTAITSHLKQSVPLIRTNLSSSRKYFTQFCVKFANSFIPKLV 638
+ W + E + I ++ + + L F + + + + + +
Sbjct: 380 LFTKKWYTGEL-------MEQIVETIEDYLNDYQEYLHPP--LFQELLEELLDELVVEYL 430
Query: 639 QHVF--KCKPLSTV----GAEQLLLDIHMLKTVLLDLPSIG 673
+ + + AE++ D L L
Sbjct: 431 RALRNKRLVFKGAEERKQFAEKMKRDAEQLYDFFQKLGDAA 471
>gnl|CDD|218088 pfam04437, RINT1_TIP1, RINT-1 / TIP-1 family. This family includes
RINT-1, a Rad50 interacting protein which participates
in radiation induced checkpoint control, as well as the
TIP-1 protein from yeast that seems to be involved in a
complex with Sec20p that is required for golgi
transport.
Length = 483
Score = 30.4 bits (69), Expect = 3.7
Identities = 33/180 (18%), Positives = 62/180 (34%), Gaps = 25/180 (13%)
Query: 506 QEQAKICCVLTTAEYCLETTQQLEQK---LKEKVDPNLANKIDLSNEQDVFHNVISSCIQ 562
E + C L A Y + L+E ++AN+ S+ +F I+S +
Sbjct: 242 AELERTCRKLNAANYLESKLKDWSDDVFFLQEASLGDIANRTS-SSYGALFDETINSLER 300
Query: 563 L-----------LVQDLELACEPALTAMVKTNWSSVESVGDQSGYVTAITSHLKQSVPLI 611
L LV+ + A + WSS+ S + ++ L +++ +
Sbjct: 301 LRLDSEGSIVHRLVKGFKAALRNY---FKISTWSSLSSTSALE--SLSPSAELVEALRYL 355
Query: 612 RTNLSSSRKY-----FTQFCVKFANSFIPKLVQHVFKCKPLSTVGAEQLLLDIHMLKTVL 666
R +S + F + + S ++ + S GA Q D+ L V
Sbjct: 356 RRRISKLERLLPLAIFLRIWRQLLLSLDTYIISSILMLNKFSEGGAAQFHFDMRNLFEVF 415
>gnl|CDD|226385 COG3867, COG3867, Arabinogalactan endo-1,4-beta-galactosidase
[Carbohydrate transport and metabolism].
Length = 403
Score = 30.2 bits (68), Expect = 3.9
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 364 ENKTKFDGIIGSCFQNYLYIYIESLDRNLSDLIDRFAEDSKQVLNNINETCETSAAPVLP 423
+ FD +IGS + Y + + +L NL+D+ R+ K V+ ET+ L
Sbjct: 240 KRNVDFD-VIGSSYYPYWHGTLNNLTTNLNDIASRY---HKDVM-----VVETAYTYTLE 290
Query: 424 SC 425
Sbjct: 291 DG 292
>gnl|CDD|145900 pfam02994, Transposase_22, L1 transposable element.
Length = 370
Score = 30.4 bits (68), Expect = 4.1
Identities = 14/82 (17%), Positives = 38/82 (46%)
Query: 60 IMKMESNIKEMDEEIETVVRSQSGVGQDGKKALEDSQKVIMQLFSQVRDIKSKAEKSEEM 119
+M+++ +E+ EE ++ + D + + V +++++++ + +E+
Sbjct: 100 LMELKKKARELKEECRSIKKEHMETTLDIENQKKRQGVVDTSFTNRIQEMEERISGAEDS 159
Query: 120 VREITRDIKLLDTAKRNLTTAI 141
+ EI R K + K+ L I
Sbjct: 160 IEEIKRTGKFNEKRKKRLEQNI 181
>gnl|CDD|237400 PRK13498, PRK13498, chemoreceptor glutamine deamidase CheD;
Provisional.
Length = 167
Score = 29.4 bits (66), Expect = 5.0
Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 13/85 (15%)
Query: 79 RSQSGVGQDGKKALEDSQKVIMQLF--------SQVRDIKSKAEKSEEMVREITRDIKLL 130
R + DG+ A E M+L + D + K M E+ +D+ L
Sbjct: 56 RIRKHQPLDGRYADE-----AMELLIRHALANGTPPEDYQVKLFGGGNMFPELQQDLHTL 110
Query: 131 DTAKRNLTTAITCLNHLHMLVTGVH 155
+ A +N+ A+ + +
Sbjct: 111 NVADKNIHAALALAEQNGLHLKAQD 135
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 29.9 bits (68), Expect = 5.3
Identities = 12/73 (16%), Positives = 42/73 (57%)
Query: 58 DVIMKMESNIKEMDEEIETVVRSQSGVGQDGKKALEDSQKVIMQLFSQVRDIKSKAEKSE 117
D +++++ +++ E+E + ++ + ++ +AL+ + +L ++V+++K K ++ E
Sbjct: 29 DKLLELDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKELE 88
Query: 118 EMVREITRDIKLL 130
+ E+ ++ L
Sbjct: 89 AALDELEAELDTL 101
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 29.9 bits (68), Expect = 5.7
Identities = 26/108 (24%), Positives = 56/108 (51%), Gaps = 20/108 (18%)
Query: 43 INSLFPTEQSLSNIDDVIMKMESNIKEMDEEIETVVRSQ-------SGVGQDGKKALEDS 95
+ SL E++L + + E N+ E +EE+E ++ Q SG+ Q E++
Sbjct: 96 MESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISGLTQ------EEA 149
Query: 96 QKVIMQLFSQVRDIKSKAEKSEEMVREITRDIKLL--DTAKRNLTTAI 141
++++++ +V + +++ E + ++++EI + K AK L TAI
Sbjct: 150 KEILLE---EVEE-EARHEAA-KLIKEIEEEAKEEADKKAKEILATAI 192
>gnl|CDD|185272 PRK15374, PRK15374, pathogenicity island 1 effector protein SipB;
Provisional.
Length = 593
Score = 29.9 bits (67), Expect = 6.8
Identities = 22/111 (19%), Positives = 48/111 (43%), Gaps = 10/111 (9%)
Query: 12 LNYPKSVQDALKEIMPSTDVLDDHDFDSVQYINSLFPTEQSLSNIDDVIMKMESNIKEMD 71
+ K Q AL E +TD+ + I + + + + ++ ++ +D
Sbjct: 123 IQVSKEFQTALGEAQEATDLYEAS-------IKKTDTAKSVYDAAEKKLTQAQNKLQSLD 175
Query: 72 EEIETVVRSQSGVGQDGKKALEDSQKVIMQLFSQVR---DIKSKAEKSEEM 119
++++ V Q GK+A E + + + V+ D K+KAEK++ +
Sbjct: 176 PADPGYAQAEAAVEQAGKEATEAKEALDKATDATVKAGTDAKAKAEKADNI 226
>gnl|CDD|219176 pfam06785, UPF0242, Uncharacterized protein family (UPF0242).
Length = 401
Score = 29.5 bits (66), Expect = 7.6
Identities = 17/59 (28%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 60 IMKMESNIKEMDEEIETVVRSQSGVGQD-GKKALEDSQKVIMQLFSQVRDIKSKAEKSE 117
I K+E+ ++++ EI +++ +SG+ ++ K + S+ V+ QL S+++ I K E E
Sbjct: 203 IGKLEAKVQDLMCEIRNLLQLESGIKENLPGKPVAASRDVVAQLVSELKKIAFKVENIE 261
>gnl|CDD|177848 PLN02197, PLN02197, pectinesterase.
Length = 588
Score = 29.6 bits (66), Expect = 7.7
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 521 CLETTQQLEQKLKEKVDPNLAN-KIDLSNEQDVFHNVISSCIQL 563
CL+ + E L++ + +AN KI SN D+FH+V+S+ +L
Sbjct: 156 CLDDIE--EDDLRKTIGEGIANSKILTSNAIDIFHSVVSAMAKL 197
>gnl|CDD|232833 TIGR00118, acolac_lg, acetolactate synthase, large subunit,
biosynthetic type. Two groups of proteins form
acetolactate from two molecules of pyruvate. The type of
acetolactate synthase described in this model also
catalyzes the formation of acetohydroxybutyrate from
pyruvate and 2-oxobutyrate, an early step in the
branched chain amino acid biosynthesis; it is therefore
also termed acetohydroxyacid synthase. In bacteria, this
catalytic chain is associated with a smaller regulatory
chain in an alpha2/beta2 heterotetramer. Acetolactate
synthase is a thiamine pyrophosphate enzyme. In this
type, FAD and Mg++ are also found. Several isozymes of
this enzyme are found in E. coli K12, one of which
contains a frameshift in the large subunit gene and is
not expressed [Amino acid biosynthesis, Pyruvate
family].
Length = 558
Score = 29.7 bits (67), Expect = 8.0
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 248 KNILEWFISLQLSEYLVLFDESEDSAWLDKIDKRYAWFKKQLLHVEDKFGTLFP 301
+N+LE + +L E E ++SAWL++I+K W K+ L ++ + P
Sbjct: 320 RNVLEELLK-KLFEL----KERKESAWLEQINK---WKKEYPLKMDYTEEGIKP 365
>gnl|CDD|214599 smart00283, MA, Methyl-accepting chemotaxis-like domains
(chemotaxis sensory transducer). Thought to undergo
reversible methylation in response to attractants or
repellants during bacterial chemotaxis.
Length = 262
Score = 29.2 bits (66), Expect = 8.0
Identities = 13/87 (14%), Positives = 35/87 (40%), Gaps = 3/87 (3%)
Query: 49 TEQSLSNIDDVIMKMESNIKEMDEEIETV---VRSQSGVGQDGKKALEDSQKVIMQLFSQ 105
+ +S I+ +I +++ E +E V + ++ ALE+ + ++
Sbjct: 142 SAESAKEIESLIKEIQEETNEAVAAMEESSSEVEEGVELVEETGDALEEIVDSVEEIADL 201
Query: 106 VRDIKSKAEKSEEMVREITRDIKLLDT 132
V++I + ++ E+ I +
Sbjct: 202 VQEIAAATDEQAAGSEEVNAAIDEIAQ 228
>gnl|CDD|238677 cd01381, MYSc_type_VII, Myosin motor domain, type VII myosins.
Myosins in this group have been associated with
functions in sensory systems such as vision and hearing.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 671
Score = 29.7 bits (67), Expect = 8.2
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 622 FTQFCVKFANSFIPK-LVQHVFK 643
F Q C+ FAN + + VQH+FK
Sbjct: 380 FEQLCINFANENLQQFFVQHIFK 402
>gnl|CDD|232989 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit.
Every known example of the phenylalanyl-tRNA synthetase,
except the monomeric form of mitochondrial, is an alpha
2 beta 2 heterotetramer. The beta subunits break into
two subfamilies that are considerably different in
sequence, length, and pattern of gaps. This model
represents the subfamily that includes the beta subunit
from eukaryotic cytosol, the Archaea, and spirochetes
[Protein synthesis, tRNA aminoacylation].
Length = 551
Score = 29.3 bits (66), Expect = 9.0
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 39 SVQYINSLFPTEQSLSNIDDVIMKMESNIKEMDEEIETVV 78
SV+YINSL S I + KM + + DE+++ V+
Sbjct: 283 SVEYINSLLGLNLSADEIAHSLKKMRLDAVQSDEKLKVVI 322
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.7 bits (67), Expect = 9.1
Identities = 33/163 (20%), Positives = 78/163 (47%), Gaps = 16/163 (9%)
Query: 50 EQSLSNIDDVIMKMESNIKEMDEEIETVVRSQSGVGQDGKKALEDSQKVIMQLFSQVRDI 109
++ L + I +++S ++E+ EE+E + + K+ +E+ + I L ++ ++
Sbjct: 259 QEELEEAEKEIEELKSELEELREELEELQEELLEL----KEEIEELEGEISLLRERLEEL 314
Query: 110 KSKAEKSEEMVREITRDIKLLDTAKRNLTTAITCLNHLHMLVTGVHSLRTLIEQRQYGEI 169
+++ E+ EE + E+ I+ L K L T L L L+ + + +E++
Sbjct: 315 ENELEELEERLEELKEKIEAL---KEELEERETLLEELEQLLAELEEAKEELEEKLSAL- 370
Query: 170 VMPLQGVIEVMKHFQDSTDIPQILELRSQVAQIQNTLSEQITQ 212
L+ + E+ + ++ EL +++A+I+N L E +
Sbjct: 371 ---LEELEELFEALREELA-----ELEAELAEIRNELEELKRE 405
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
0.316 0.131 0.363
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,037,370
Number of extensions: 3678359
Number of successful extensions: 4207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4192
Number of HSP's successfully gapped: 77
Length of query: 790
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 685
Effective length of database: 6,280,432
Effective search space: 4302095920
Effective search space used: 4302095920
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 (28.1 bits)