RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8893
(820 letters)
>gnl|CDD|216231 pfam00995, Sec1, Sec1 family.
Length = 554
Score = 288 bits (739), Expect = 1e-87
Identities = 121/532 (22%), Positives = 224/532 (42%), Gaps = 39/532 (7%)
Query: 33 KKAIIWDDALAGPVGLVANVQLLNERDVKRNIHLKPGSLPPMENIANVIFITRPIVKHMD 92
K ++ D + V V L E V +++ P+ ++ I+ RP +++D
Sbjct: 1 WKVLVLDKETTKILSSVLTVSDLLEHGVTLVENIEN-KREPLPDL-PAIYFIRPTEENVD 58
Query: 93 IIADNIKRKEKEKRSDTRRIDYHLFFVPRKSLLCEQRLQENGVLGNFNIIEAFTCNLFPF 152
I D++K + YH+FF S +RL E V ++ + P
Sbjct: 59 RIIDDLKNP--------KYKSYHIFFTNSLSRSLLERLAEADVAELVKQVKEIYLDFIPL 110
Query: 153 DNDLVSMEMELAYREYHL-EKDPTCLYEVAQAIITLQNLYGIIPRVSGKGP-CVQQVWDL 210
++DL S+E+ ++R+ + + D + L +A+ + +L G IP + +G +++ +
Sbjct: 111 ESDLFSLELPNSFRDLYSPDGDESDLERIAEGLFSLLLTLGEIPIIRYQGNSAAERLAEK 170
Query: 211 TKRL----SLEPKNKNVNQCKTSQISQLILIDRNVDVLTPLATQLTYEGLIDEIFGIHNT 266
+L N + + L+++DR++D++TPL Q TY+ ++ ++ GI N
Sbjct: 171 LAQLLQENLDLFDADNPSTPPSKPRPVLLILDRSIDLITPLLHQWTYQAMVHDLLGIKNN 230
Query: 267 TAKFPGAKFSQSEEDSNFEKIVSDKKSIILNSGDELFAALRDKIFTGVGPYLSKRAKFIS 326
KK ++L+ D + R F V + K K
Sbjct: 231 RVTLDTPGNGGES-----------KKEVVLDENDPFWVENRHLHFPDVAEKIKKELKEYK 279
Query: 327 AQFDTQNYHEKSVSEMKTLVQQLPHMINTKKLLANHTNIAELIKDVTDTAEFLDALHAEQ 386
+ N +KS+S++K V++LP K L+ H N+AE + + EQ
Sbjct: 280 EENKNSNKKKKSISDLKEFVEKLPEFQKEKGKLSLHLNLAEELMKQIKERKLDKVSELEQ 339
Query: 387 EIFLGVDTDKALPYIENAI-AHKKPLMKVLKLICMQSFTSSGLKPKVLEYYKREIIQT-Y 444
++ G D DK I + K PL L+L+ + S G K K LE ++ ++
Sbjct: 340 DLATGSDADKQKKDILELLNNPKVPLEDKLRLLLLYSLR-DGGKGKDLEDLRKLLLHAGI 398
Query: 445 GFQHILTLSNLEQAGLLKNSQNSGTRQYTLLRKMMRLTVEDSSELAPADINFVHSIYAPL 504
G + + + NLEQ G L + ++ LR ++L V++ S+ P + V S Y PL
Sbjct: 399 GPEALNLVKNLEQLGGL--LSRTSGSNFSDLRDKLKLLVKEVSKSLPKGVKNVLSRYKPL 456
Query: 505 SIRLVQRLTRE-------PSIIPQDLLALLPGAVLEETQTTTSSRRNRNTQE 549
R+++ L + P P+ A P L + T + + + Q
Sbjct: 457 LKRILEDLIKGKLDTDSYPYFDPKLANASGPQGSLRSKRPTAAGQGRQPPQR 508
>gnl|CDD|110234 pfam01217, Clat_adaptor_s, Clathrin adaptor complex small chain.
Length = 142
Score = 119 bits (301), Expect = 1e-31
Identities = 43/141 (30%), Positives = 70/141 (49%), Gaps = 5/141 (3%)
Query: 562 TIKGIAILDNDGHRLLAKYYDPNILSTVKDQKAFEKNLFNKTHRA--NAEIIMLEGLTCV 619
IK I I + G LAK+Y P S + QK E+ + R + I L +
Sbjct: 1 MIKAILIFNRQGKPRLAKWYTP--YSDPEQQKLIEQIYALISARKPKMSNFIEFNDLKVI 58
Query: 620 YKSNVDLFFYVMGSSHENELILMSVLNCLYDAISQILRKNVEKRNVLDNLDIVMLALDEI 679
YK L+F V+ +NELI++ +++ +++ + NV + +++ N + V L LDE+
Sbjct: 59 YKRYATLYFVVIVDDQDNELIILELIHRFVESLDRYFG-NVCELDLIFNFEKVYLILDEM 117
Query: 680 CDGGIIQEADSSAVVQRVALR 700
GG I E + V+ RVAL
Sbjct: 118 VMGGEILETSKNEVLHRVALL 138
>gnl|CDD|227487 COG5158, SEC1, Proteins involved in synaptic transmission and
general secretion, Sec1 family [Intracellular
trafficking and secretion].
Length = 582
Score = 128 bits (324), Expect = 6e-31
Identities = 112/579 (19%), Positives = 214/579 (36%), Gaps = 72/579 (12%)
Query: 15 VQDFARTQFLELLEKCSGK---KAIIWDDALAGPVGLVANVQLLNERDVKRNIHLKPGSL 71
+ + + + L+ + K ++ D + + L E + ++
Sbjct: 4 LLELQKNKILDEIFLVQPANIWKVLLLDKDTTSILSSLITTSELLEHGITLVDLIEN--- 60
Query: 72 PPMENIANV--IFITRPIVKHMDIIADNIKRKEKEKRSDTRRIDYHLFFVPRKSLLCEQR 129
E I+++ I+ RP +++D+I E ++ D ++YH+ F+ + +
Sbjct: 61 -KREPISDLPAIYFVRPTKENIDLIL------EDLEQWDPFYLNYHISFLNTVTESLLEL 113
Query: 130 LQENGVLGNFNIIEAFTCNLFPFDNDLVSMEMELAYREYHLEKDPTCLYEVAQAIITLQN 189
L E+GV + + F ++DL S+ + ++ E L L ++ + +L
Sbjct: 114 LAESGVFEKILSVYEIYLDFFVLESDLFSLNLPESFLESSLPSTTEALIKIVNGLFSLCV 173
Query: 190 LYGIIP--RVSGKGPCVQQVWDLTKRLSLEPKNKNVNQCKTSQI-SQLILIDRNVDVLTP 246
G IP R SG L+ + E + + LI++DR++D +TP
Sbjct: 174 SLGRIPIIRYSGGKNAEHMAKKLSDEIRNELSINFDGVVSKNPLRPILIILDRSLDPITP 233
Query: 247 LATQLTYEGLIDEIFGIHNTTAKFPGAKFSQSEEDSNFEKIVSDKKSIILNSGDELFAAL 306
L Q TY+ ++ ++ GI+N P + +KK + + D +
Sbjct: 234 LLHQWTYQAMLHDLLGINNNIVTIP-----------SSSVNGPEKKFSLSDKDDPFWNDN 282
Query: 307 RDKIFTGVGPYLSKRAKFISAQFDTQNYHE-KSVSEMKTLVQQLPHMINTKKLLANHTNI 365
+ F VG L K AK + + ++ KSV+++K V +LP + + L H +
Sbjct: 283 KFLNFGEVGEKLKKLAKELKTKAQLRHKENAKSVNDIKEFVDKLPELQKRSRSLNKHLTL 342
Query: 366 AELIKDVTDTAEFLDALHAEQ---------EIFLGVDTDKALPYIENAIAHKKPLMKVLK 416
A + V + D EQ + E+ L+
Sbjct: 343 ASELLKVVEERYLDDFSEIEQNLSTGNDVKSDISDLIELLESGVEED---------DKLR 393
Query: 417 LICMQSFTSSGLKPKVLEYYKREIIQTYGFQHILTLSNLEQAGLLKNSQNSGTRQYTLLR 476
L+ + S T GL K ++ + IQ YG + + L++ G L + L R
Sbjct: 394 LLILYSLTKDGLI-KDIDELRLLRIQGYGIEALNFFQRLKELGFLTLKDSKTIS---LKR 449
Query: 477 KMMRLTVEDSSELA-------PADINFVHSIYAPLSIRLVQRLTREPSIIPQDLL--ALL 527
+ + + D+ V+S PL IP DLL L
Sbjct: 450 GDKDSLFQWFNTYSLSREHQGVPDLENVYSGLIPLKKD-----------IPIDLLVRRLF 498
Query: 528 PGAVLEETQTTTSSRRNRNTQENKMLTFQEASLYTIKGI 566
+ Q+ SR ++ NK + Q ++ I G+
Sbjct: 499 EPLKSSQQQSLRLSRPKGRSRSNKKIPQQRILVFVIGGV 537
>gnl|CDD|227828 COG5541, RET3, Vesicle coat complex COPI, zeta subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 187
Score = 108 bits (271), Expect = 5e-27
Identities = 49/147 (33%), Positives = 76/147 (51%), Gaps = 8/147 (5%)
Query: 559 SLYTIKGIAILDNDGHRLLAKYYDP--------NILSTVKDQKAFEKNLFNKTHRANAEI 610
SLY ++ + ILD+ G R+ KYY P + ++VK +K FEK L KT + I
Sbjct: 4 SLYDVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKDRESI 63
Query: 611 IMLEGLTCVYKSNVDLFFYVMGSSHENELILMSVLNCLYDAISQILRKNVEKRNVLDNLD 670
+M + K D+ Y++ ENE L V + + A+ I++ +KRNV +N D
Sbjct: 64 LMFYDRLVMCKRLDDVLLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYD 123
Query: 671 IVMLALDEICDGGIIQEADSSAVVQRV 697
++L +DE D G+I E S + RV
Sbjct: 124 QIVLLVDETIDEGVILETKSDEIADRV 150
>gnl|CDD|227363 COG5030, APS2, Clathrin adaptor complex, small subunit
[Intracellular trafficking and secretion].
Length = 152
Score = 38.5 bits (90), Expect = 0.004
Identities = 34/146 (23%), Positives = 62/146 (42%), Gaps = 23/146 (15%)
Query: 563 IKGIAILDNDGHRLLAKYYDP-----------NILSTVKDQKAFEKNLFNKTHRANAEII 611
IK + I + G L K+Y P +I + +K E N I
Sbjct: 2 IKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESN-----------FI 50
Query: 612 MLEGLTCVYKSNVDLFFYVMGSSHENELILMSVLNCLYDAISQILRKNVEKRNVLDNLDI 671
+ VY+ L+F + +NELI++ +++ + + + NV + +++ N
Sbjct: 51 EGKNEKIVYRRYATLYFVFGVDNDDNELIILELIHNFVEILDRFF-GNVCELDLIFNFQK 109
Query: 672 VMLALDEICDGGIIQEADSSAVVQRV 697
V LDE+ GG I E+ + V++ V
Sbjct: 110 VYAILDEMILGGEIIESSKNEVLEHV 135
>gnl|CDD|236405 PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.
Length = 565
Score = 32.4 bits (75), Expect = 1.2
Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 15/73 (20%)
Query: 49 VANVQLLNERDVKRNIHLKPGSLPPMENIANVIFITRPIVKHMD--IIADNIKRKEKEKR 106
A ++L E +++ + PG L P+ +V I V M ++ N
Sbjct: 309 AAPLELATEEEIRAALGAVPGFLGPVGLPKDVPIIADRSVADMSNFVVGANED------- 361
Query: 107 SDTRRIDYHLFFV 119
DYH V
Sbjct: 362 ------DYHYVGV 368
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 31.5 bits (72), Expect = 2.1
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 33 KKAIIWDDALAGPVGLVANVQLLNERDVKRNIHLKPGSLPPMENIANVIFITRPIVKH 90
K +W D + ++ V+ L++ VK I LK P +E IA + I + KH
Sbjct: 91 KHPYVWVD---IELSIIERVEALDDYTVK--ITLKRPYAPFLEKIATTVPI---LPKH 140
>gnl|CDD|237269 PRK13014, PRK13014, methionine sulfoxide reductase A; Provisional.
Length = 186
Score = 30.8 bits (70), Expect = 2.2
Identities = 28/124 (22%), Positives = 46/124 (37%), Gaps = 22/124 (17%)
Query: 249 TQLTYEGLIDEIFGIHNTTAK---FP-------GAKFSQSEEDSNFEKIVSDKKSIILNS 298
Q++YE L+ F H+ T P A F EE +K+ + + +
Sbjct: 69 KQVSYENLLQIFFSTHDPTQLNRQGPDRGEQYRSAIFYHDEEQ---KKVAEAYIAQLDEA 125
Query: 299 GDELFAALRDKIFTGVGPYLSKRAKFISAQFDTQNYHEKSVSEMKTLVQQLPHMINTKKL 358
G +F I T + PY F A+ Q+Y +K+ + + LP K
Sbjct: 126 G--IFKK---PIVTPIKPY----KNFYPAEDYHQDYLKKNPTHPYIVYNDLPKGSGLKAF 176
Query: 359 LANH 362
+H
Sbjct: 177 FESH 180
>gnl|CDD|237267 PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1;
Provisional.
Length = 896
Score = 31.4 bits (72), Expect = 2.3
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 349 LPHMINTKKLLANHTNIAELIKDVTDTAEFL-DALHAEQEIFLGVDTDKALPYIENAIA 406
L ++ +LLA+ + + VT E D L AE+ LG + +PY+ +A
Sbjct: 744 LREVLAAARLLADDWGVDADVWSVTSFTELRRDGLAAERANLLGPAEEARVPYVTQCLA 802
>gnl|CDD|130764 TIGR01703, hybrid_clust, hydroxylamine reductase. This model
represents a family of proteins containing an unusual
4Fe-2S-2O hydrid cluster. Earlier reports had proposed a
6Fe-6S prismane cluster. This subfamily is heterogeneous
with respect to the presence or absence of a region of
about 100 amino acids not far from the N-terminus of the
protein. Members have been described as monomeric. The
general function is unknown, although members from E.
coli and several other species have hydroxylamine
reductase activity. Members are found in various
bacteria, in Archaea, and in several parasitic
eukaryotes: Giardia intestinalis, Trichomonas vaginalis,
and Entamoeba histolytica [Cellular processes,
Detoxification, Energy metabolism, Amino acids and
amines].
Length = 522
Score = 30.6 bits (69), Expect = 4.4
Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 6/83 (7%)
Query: 505 SIRLVQRLTREPSIIPQDLLALLPGAVLEETQTTTSSRRNRNTQENK-MLTFQEASLYTI 563
R+V+ + + + + L A + + + N + + ++ LY I
Sbjct: 76 EDRIVEYI-EDAIKLREKLKKKCRLADSNSLLIQSFALNGDKSHVNDDVNSLRDLLLYGI 134
Query: 564 KGI-AILDNDGHRLLAKYYDPNI 585
KGI A L H Y D I
Sbjct: 135 KGIAAYLY---HARELGYDDEEI 154
>gnl|CDD|238609 cd01278, aprataxin_related, aprataxin related: Aprataxin, a HINT
family hydrolase is mutated in ataxia oculomotor apraxia
syndrome. All the members of this subgroup have the
conserved HxHxHxx (where x is a hydrophobic residue)
signature motif. Members of this subgroup are
predominantly eukaryotic in origin.
Length = 104
Score = 28.5 bits (64), Expect = 4.4
Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 73 PMENIANVIFITR---PIVKHMDIIADNIKRKEKEKRSDTRRIDYHL 116
P E+IA++ +T+ P+++HM+ + + R +H
Sbjct: 43 PKEHIASLKALTKEDVPLLEHMETVGREKLLRSDNTDPSEFRFGFHA 89
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 30.4 bits (68), Expect = 4.6
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 601 NKTHRANAEIIMLEGLTCVYKSNVDLFFYVM---GSSHENELILMSVLNCLYDAISQILR 657
N H N I+++ L + LF Y + S+H +LIL L L S +L+
Sbjct: 1318 NILHNDNYSKIIIDNLAAI------LFSYRINCASSAHSGQLILPDTLKLLPLFTSSLLK 1371
Query: 658 KNVEKRNVLDNLDIVML 674
NV K+ +L +L + L
Sbjct: 1372 HNVTKKEILHDLKVYSL 1388
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 30.2 bits (68), Expect = 5.2
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 3 THLSGGKVNISLVQDFARTQFLELLEKCSGKKAIIWDDAL----AGPVGLVANVQLLNER 58
G + +Q + TQ + L G++ I WD+ L ANV +++
Sbjct: 452 LMEKLGNKDTFELQSYFITQVGKTLAS-KGRRLIGWDEGAHGGDVNGTALTANVTVMSWY 510
Query: 59 DVKRNIHLKP 68
+ I L
Sbjct: 511 GKDKAIELAK 520
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 29.8 bits (68), Expect = 6.5
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 20/89 (22%)
Query: 500 IYAPLSIRLVQRLTREPSIIPQDLLALLPGAVLEETQTTTSSRRNRNTQENKMLTFQEAS 559
+ APL R V+RL + + L E R+ + +QE
Sbjct: 242 VEAPLEER-VERLLEDYVLRMHAAGFQAYPEYLAEA--LQRIRKRLGGE-----RYQELL 293
Query: 560 LYTIKGIAILDNDGHR-----LLAKYYDP 583
A+LD GH LL +YYDP
Sbjct: 294 -------ALLDAGGHLAWIEELLLEYYDP 315
>gnl|CDD|217727 pfam03786, UxuA, D-mannonate dehydratase (UxuA). UxuA (this
family) and UxuB are required for hexuronate
degradation.
Length = 350
Score = 29.3 bits (66), Expect = 7.8
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 161 MELAYREYHLEKDPTCLYEVAQAIITLQNLYGIIPRVSGKGPCVQQVWDLTKRLSL 216
MEL +R Y DP L+ + Q I + + G + + V +VW + ++L
Sbjct: 1 MELTWRWYGPGNDPVTLWRIRQ-IPGVTGVVGALHDIP-----VGEVWPKEEIMAL 50
>gnl|CDD|221125 pfam11500, Cut12, Spindle-body formation-associated protein. This
is the central coiled-coil region of cut12 also found in
other fungi, barring S. cerevisiae. The full protein has
two predicted coiled-coil regions, and one consensus
phosphorylation site for p34cdc2 and two for MAP kinase.
During fission yeast mitosis, the duplicated spindle
pole bodies (SPBs) nucleate microtubule arrays that
interdigitate to form the mitotic spindle. Cut12 is
localised to the SPB throughout the cell cycle,
predominantly around the inner face of the interphase
SPB, adjacent to the nucleus. Cut12 associates with Fin1
and is important in this context for the activity of
Plo1.
Length = 149
Score = 28.1 bits (63), Expect = 9.8
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 319 SKRAKFISAQFDTQNYHEKSVSEMKTLVQ 347
S+ K+ A+FD +YH + EMK L+Q
Sbjct: 63 SQSGKYWKAEFD--SYHSDTELEMKKLIQ 89
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 0.135 0.378
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,741,166
Number of extensions: 4040769
Number of successful extensions: 3253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3234
Number of HSP's successfully gapped: 20
Length of query: 820
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 715
Effective length of database: 6,280,432
Effective search space: 4490508880
Effective search space used: 4490508880
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 (21.8 bits)
S2: 63 (28.1 bits)