RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8503
(421 letters)
>gnl|CDD|227565 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 232 bits (593), Expect = 2e-68
Identities = 119/352 (33%), Positives = 176/352 (50%), Gaps = 57/352 (16%)
Query: 1 MISDSNRSIATLAITTLLKTGSESSVDRLMKQIATFVSEISDEFKIVVVEAIRALCLKFP 60
+ISD NR+I+T AITTLLKTG+E ++DRL+ I +FV ++SD FKI+ ++A+R+L L FP
Sbjct: 348 LISDENRTISTYAITTLLKTGTEETIDRLVNLIPSFVHDMSDGFKIIAIDALRSLSLLFP 407
Query: 61 RKHAVLMNFLSAMLRDEGVFRGGIDVLVRSKLAVSADTGVTMQLTVRSTSGLEYKASIAD 120
K ++FL + L EG GLE+K + D
Sbjct: 408 SKKLSYLDFLGSSLLQEG--------------------------------GLEFKKYMVD 435
Query: 121 TIITIIEENPEAKETGLAHLCEFIEDCEHTSLAVRILHLLGKEGPRAKQPSKYIRFIYNR 180
I +E +P++KE L LC FIEDCE+ + VRIL +LG+EGPRAK P KY+R IYNR
Sbjct: 436 AISDAMENDPDSKERALEVLCTFIEDCEYHQITVRILGILGREGPRAKTPGKYVRHIYNR 495
Query: 181 VILENATVRAAAVTAMAQFG----------------ALCQMDGDDEVRDRATYYHSILAS 224
+ILEN VR+AAV A+++F C D DDEVRDRA++ +
Sbjct: 496 LILENNIVRSAAVQALSKFALNISDVVSPQSVENALKRCLNDQDDEVRDRASF--LLRNM 553
Query: 225 QNKQLIQDYIIEPLMVSIPSLERALHAY-NLHPSPTPFDMSSIPLSTITTSDPTEMADR- 282
+ + + IPSLE L Y + T FD++ + T + +
Sbjct: 554 RLSDACEPLFSSDELGDIPSLELELIGYISEDSFATAFDVNQVRKFTEDEMKAINLKRKK 613
Query: 283 ----LRTPSGGVASEPTAQATARVESYYEKLSAALPEIANLPGTLFKSAAPV 330
L T + ++A +++ Y ++ +I G L S+ +
Sbjct: 614 SETTLDTTESVPKEDANSKADPNIKTKYADELLSIEQI-KPFGQLVNSSREI 664
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha, beta
and gamma subunits of the AP-1, AP-2 and AP-3 adaptor
protein complexes. The adaptor protein (AP) complexes
are involved in the formation of clathrin-coated pits
and vesicles. The N-terminal region of the various
adaptor proteins (APs) is constant by comparison to the
C-terminal which is variable within members of the AP-2
family; and it has been proposed that this constant
region interacts with another uniform component of the
coated vesicles.
Length = 522
Score = 162 bits (411), Expect = 1e-44
Identities = 68/242 (28%), Positives = 99/242 (40%), Gaps = 53/242 (21%)
Query: 1 MISDSNRSIATLAITTLLKTGSESSVDRLMKQIATFVSEISD-EFKIVVVEAIRALCLKF 59
+ +D + SI A+ L K ES+V ++K++ +VSEI+D EFKI +V+AI L KF
Sbjct: 310 LKTDDDISIRLRALDLLYKLVDESNVKEIVKELLKYVSEIADPEFKIKLVKAIGRLAEKF 369
Query: 60 PRKHAVLMNFLSAMLRDEGVFRGGIDVLVRSKLAVSADTGVTMQLTVRSTSGLEYKASIA 119
P ++ L +L G + I
Sbjct: 370 PTDAEWCIDVLLELLSLAGSY---------------------------------VVDEIV 396
Query: 120 DTIITIIEENPEAKETGLAHLCEFIEDCEHTSLAVRILHLLGKEGPR-AKQPSKYIRFIY 178
+ I II + PE +E L HLCE +ED E L +LG+ G PS +R I
Sbjct: 397 EVIRDIIRKYPELREYILEHLCELLEDIESPEARAAALWILGEYGELIPNSPSDLLRSIL 456
Query: 179 NRVILENATVRAAAVTAMAQFGALC------------------QMDGDDEVRDRATYYHS 220
+LE+ VR A +TA+ + Q D E+RDRA Y
Sbjct: 457 EVFVLESLKVRLALLTALVKLSLTFPDEEVQNLIVQVVLSLATQDSSDLELRDRAVEYLR 516
Query: 221 IL 222
+L
Sbjct: 517 LL 518
>gnl|CDD|220003 pfam08752, Gamma-COP, Coatomer gamma subunit appendage domain.
COPI-coated vesicles function in retrograde transport
from the Golgi to the ER, and in intra-Golgi transport.
This domain corresponds to the coatomer gamma subunit
appendage domain. It contains a protein-protein
interaction site and a second proposed binding site that
interacts with the alpha, beta,epsilon COPI subcomplex.
Length = 269
Score = 57.7 bits (140), Expect = 2e-09
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 359 LEDLEISLSDQMAKVNKPNFLALWEEAETDESMNEMEDTFCLSKMESIQEAVASIL 414
+EDLE+++SD + + NF A W+E + E +TF LS ++S+QEAV ++
Sbjct: 146 IEDLELNVSDFIQPLRVGNFKAAWDELPNEH---EAVETFSLSNVKSLQEAVNKLV 198
Score = 49.6 bits (119), Expect = 1e-06
Identities = 19/33 (57%), Positives = 25/33 (75%)
Query: 78 GVFRGGIDVLVRSKLAVSADTGVTMQLTVRSTS 110
G F GG VLVR++LA+S GVT+++TVRS S
Sbjct: 225 GKFLGGGKVLVRARLALSKQKGVTLKVTVRSES 257
>gnl|CDD|225795 COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion
transport and metabolism].
Length = 717
Score = 31.7 bits (72), Expect = 0.85
Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 3/79 (3%)
Query: 262 DMSSIPLSTITTSDPTEMADRLRTPSGGVA--SEPTAQATARVESYYEKLSAALPEIANL 319
++ + T E + P G S+ A+A +V YY L P + +
Sbjct: 99 KADALSPEELKTRVKDEYRNNSYDPEDGSVVVSDERAKAIEQVLDYYHALFGDDPALQTM 158
Query: 320 PGTLFKSAAPVRRDLRSVF 338
R L + F
Sbjct: 159 KNNTLPDQED-REKLFAFF 176
>gnl|CDD|177847 PLN02196, PLN02196, abscisic acid 8'-hydroxylase.
Length = 463
Score = 31.1 bits (70), Expect = 1.2
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 305 YY--EKLSAALPEIANLPGTLFKSAAPVRRDLRSVFHSYAVSMRRQ--LDVHSASGVGLE 360
YY EK ++P NLPGTLF + R++L + + +S RRQ + G +
Sbjct: 199 YYILEKGYNSMP--INLPGTLFHKSMKARKELAQIL-AKILSKRRQNGSSHNDLLGSFMG 255
Query: 361 DLEISLSDQMA 371
D E +Q+A
Sbjct: 256 DKEGLTDEQIA 266
>gnl|CDD|224603 COG1689, COG1689, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 274
Score = 29.5 bits (66), Expect = 3.1
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 150 TSLAVRILHLLGKEGPRAKQPSKYIRFIYNRVILENATVRAAAVTAMAQFGA 201
T A++I LLG E PR + K I F+Y+++ V A A+ + GA
Sbjct: 38 TYYAIKIYSLLGHEVPRKE---KTIEFLYDQMQTAGVGV-AMAIEFLRILGA 85
>gnl|CDD|215171 PLN02302, PLN02302, ent-kaurenoic acid oxidase.
Length = 490
Score = 29.3 bits (66), Expect = 3.8
Identities = 26/94 (27%), Positives = 37/94 (39%), Gaps = 22/94 (23%)
Query: 289 GVASEPTAQATARVESYYEKLSAALPEIA-NLPGTLFKSAAPVRRDLRSVFHSYAVSMRR 347
SE +A +E Y L+ + +A NLPG + A R+ L ++F S V RR
Sbjct: 199 SSESELVMEA---LEREYTTLNYGVRAMAINLPGFAYHRALKARKKLVALFQS-IVDERR 254
Query: 348 Q-----------------LDVHSASGVGLEDLEI 364
LD +G L+D EI
Sbjct: 255 NSRKQNISPRKKDMLDLLLDAEDENGRKLDDEEI 288
>gnl|CDD|187817 cd09686, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
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;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to have
a Rossmann-like fold; loosely associated with CRISPR/Cas
systems; also known as NE0113 family.
Length = 209
Score = 29.0 bits (65), Expect = 4.0
Identities = 21/68 (30%), Positives = 26/68 (38%), Gaps = 4/68 (5%)
Query: 219 HSILASQNKQLIQDYIIEPLMVSIPSLERALHAYNLHPSPTPFDMSSIPLSTITTSDPTE 278
H I S K+ IQ ++ P L + H Y P P PFD I L P
Sbjct: 33 HVITTSDGKRDIQQQLLTPDEAGQGVLAKLRHDYFQGPRP-PFDELRIYLIPTGQRKP-- 89
Query: 279 MADRLRTP 286
+RTP
Sbjct: 90 -LADIRTP 96
>gnl|CDD|131633 TIGR02584, cas_NE0113, CRISPR-associated protein, NE0113 family.
Members of this minor CRISPR-associated (Cas) protein
family are found in cas gene clusters in Vibrio
vulnificus YJ016, Nitrosomonas europaea ATCC 19718,
Mannheimia succiniciproducens MBEL55E, and
Verrucomicrobium spinosum [Mobile and extrachromosomal
element functions, Other].
Length = 209
Score = 29.0 bits (65), Expect = 4.3
Identities = 21/68 (30%), Positives = 26/68 (38%), Gaps = 4/68 (5%)
Query: 219 HSILASQNKQLIQDYIIEPLMVSIPSLERALHAYNLHPSPTPFDMSSIPLSTITTSDPTE 278
H I S K+ IQ ++ P L + H Y P P PFD I L P
Sbjct: 33 HVITTSDGKRDIQQQLLTPDEAWQGVLAKLRHDYFQGPRP-PFDELRIYLIPTGQRKP-- 89
Query: 279 MADRLRTP 286
+RTP
Sbjct: 90 -LADIRTP 96
>gnl|CDD|176522 cd08580, GDPD_Rv2277c_like, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial protein Rv2277c and
similar proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in uncharacterized bacterial protein Rv2277c and
similar proteins. Members in this subfamily are
bacterial homologous of mammalian GDE4, a transmembrane
protein whose cellular function has not yet been
elucidated.
Length = 263
Score = 28.8 bits (65), Expect = 4.3
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 240 VSIPSLERALHAYNLHPSPTPF--DMSSIPLSTITT 273
V IP+LE+ L A+ TPF DM S+P
Sbjct: 92 VGIPTLEQVLRAF----PDTPFILDMKSLPADPQAK 123
>gnl|CDD|233988 TIGR02734, crtI_fam, phytoene desaturase. Phytoene is converted to
lycopene by desaturation at four (two symmetrical pairs
of) sites. This is achieved by two enzymes (crtP and
crtQ) in cyanobacteria (Gloeobacter being an exception)
and plants, but by a single enzyme in most other
bacteria and in fungi. This single enzyme is called the
bacterial-type phytoene desaturase, or CrtI. Most
members of this family, part of the larger Pfam family
pfam01593, which also contains amino oxidases, are CrtI
itself; it is likely that all members act on either
phytoene or on related compounds such as
dehydrosqualene, for carotenoid biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 502
Score = 28.8 bits (65), Expect = 5.7
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 70 LSAMLRDEGVF--RGGIDVLVRSKLAVSADTGVTMQLTVRSTS 110
+SA+ R+ GV+ RGG LV + ++ D G ++L
Sbjct: 202 ISALEREWGVWFPRGGTGALVAAMAKLAEDLGGELRLNAEVIR 244
>gnl|CDD|240415 PTZ00429, PTZ00429, beta-adaptin; Provisional.
Length = 746
Score = 28.7 bits (64), Expect = 6.5
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 17 LLKTGSESSVDRLMKQIATFVSEISDEFKIVVVEAIRALCLK 58
LLK + S ++K++A + S + F + VV AI +L +K
Sbjct: 357 LLKLVTPSVAPEILKELAEYASGVDMVFVVEVVRAIASLAIK 398
>gnl|CDD|239206 cd02812, PcrB_like, PcrB_like proteins. One member of this family,
a protein from Archaeoglobus fulgidus, has been
characterized as a (S)-3-O-geranylgeranylglyceryl
phosphate synthase (AfGGGPS). AfGGGPS catalyzes the
formation of an ether linkage between
sn-glycerol-1-phosphate (G1P) and geranylgeranyl
diphosphate (GGPP), the committed step in archaeal lipid
biosynthesis. Therefore, it has been proposed that
PcrB-like proteins are either prenyltransferases or are
involved in lipoteichoic acid biosynthesis although the
exact function is still unknown.
Length = 219
Score = 28.0 bits (63), Expect = 8.2
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 113 EYKASIADTII--TIIEENPEA 132
E + ADTI+ I+EE+P A
Sbjct: 192 EMAEAGADTIVVGNIVEEDPNA 213
>gnl|CDD|223374 COG0297, GlgA, Glycogen synthase [Carbohydrate transport and
metabolism].
Length = 487
Score = 28.4 bits (64), Expect = 8.7
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 6/32 (18%)
Query: 106 VRSTSGLEYKASIADTIITIIEENPEAKETGL 137
VR T GL ADT++ E + TG
Sbjct: 397 VRETGGL------ADTVVDRNEWLIQGVGTGF 422
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 27.7 bits (62), Expect = 8.8
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 45 KIVVVEAIRALCLKFPRKHAVLMNFLSAM 73
++V+ A+R L LK R + VL + + +
Sbjct: 116 RVVIPSALRVLRLKPERPYTVLGDLSAHV 144
>gnl|CDD|221624 pfam12532, DUF3732, Protein of unknown function (DUF3732). This
domain family is found in bacteria and eukaryotes, and
is typically between 180 and 198 amino acids in length.
There is a conserved DQP sequence motif.
Length = 190
Score = 27.7 bits (62), Expect = 9.0
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 25 SVDRLMKQIATFVSEISDEFKIVVVE 50
+V + +A FV EI +F+I+V+E
Sbjct: 136 AVRKAFSLLADFVKEIKGKFQIIVLE 161
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 28.3 bits (64), Expect = 9.4
Identities = 22/80 (27%), Positives = 31/80 (38%), Gaps = 17/80 (21%)
Query: 298 ATARVESYYEKLSAALPEI------ANLPGTLFKSAAPVRRDLRS--VFHSYAVSMRRQL 349
A A VES +K E+ + L G ++ R+ V V+ L
Sbjct: 267 AKALVESVAKKAGVEDYEVLETFKGSELEGLRYEHPFYDFVYDRAFPVILGDHVT----L 322
Query: 350 D-----VHSASGVGLEDLEI 364
D VH+A G G ED E+
Sbjct: 323 DDGTGLVHTAPGHGEEDYEV 342
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 0.131 0.363
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,999,501
Number of extensions: 2044870
Number of successful extensions: 1900
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1891
Number of HSP's successfully gapped: 37
Length of query: 421
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 322
Effective length of database: 6,546,556
Effective search space: 2107991032
Effective search space used: 2107991032
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: 60 (26.9 bits)