RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12802
(1637 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 69.3 bits (170), Expect = 2e-12
Identities = 59/287 (20%), Positives = 114/287 (39%), Gaps = 42/287 (14%)
Query: 28 SEGNVAGIWAWRGQNGRKSYV-----VKGLAFSPDSTKLAVAQSDNIIFIYKLGDDWGDK 82
S +W ++ V+ +A S D T LA SD I ++ D
Sbjct: 28 SGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTIRLW----DLETG 83
Query: 83 KVICNKFIQ-QCPVTTMVWLADGPIIYG-QSDGKIKAAHVKANK-TQTLYASNSFVVALC 139
+ + V+++ + DG I+ D IK V+ K TL +V ++
Sbjct: 84 ECV-RTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVA 142
Query: 140 LNVRGAGVLSGHADGSIVRYYVTEDASNFDQQQGRVVQ----HPVPPYALSW-PAGY-IL 193
+ G V S DG+I + +D + G+ V H ++++ P G +L
Sbjct: 143 FSPDGTFVASSSQDGTI---KL------WDLRTGKCVATLTGHTGEVNSVAFSPDGEKLL 193
Query: 194 AAGSDRIVTIYE-SDGRVHRIFDYTAPHYKEREFTVACSSPSGQAVVVGSYDN-IKLFAW 251
++ SD + +++ S G+ E SP G + GS D I+++
Sbjct: 194 SSSSDGTIKLWDLSTGKCLGTL-----RGHENGVNSVAFSPDGYLLASGSEDGTIRVW-- 246
Query: 252 SPSKSVWEEQPNKTIPNL-YTISALSWKRDGSRIACGGLCGSVELFE 297
+ + +T+ ++++L+W DG R+A G G++ +++
Sbjct: 247 ----DLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 45.4 bits (108), Expect = 2e-04
Identities = 36/177 (20%), Positives = 70/177 (39%), Gaps = 27/177 (15%)
Query: 125 TQTLYASNSFVVALCLNVRGAGVLSGHADGSIVRYYVTEDASNFDQQQGRVVQHPVPPYA 184
+TL V + + G + +G DG+I + + E +G H P
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTI-KVWDLETGELLRTLKG----HTGPVRD 56
Query: 185 LSWPA--GYILAAGSDRIVTIYE-SDGRVHRIFDYTAPHYKEREFTVACSSPSGQAVVVG 241
++ A Y+ + SD+ + +++ G R H +VA SP G+ +
Sbjct: 57 VAASADGTYLASGSSDKTIRLWDLETGECVRTL---TGH-TSYVSSVAF-SPDGRILSSS 111
Query: 242 SYDN-IKLFAWSPSKSVWEEQPNKTIPNLY----TISALSWKRDGSRIACGGLCGSV 293
S D IK VW+ + K + L ++++++ DG+ +A G++
Sbjct: 112 SRDKTIK---------VWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTI 159
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 49.3 bits (116), Expect = 1e-05
Identities = 61/258 (23%), Positives = 108/258 (41%), Gaps = 20/258 (7%)
Query: 46 SYVVKGLAFSPDSTKLAVA-QSDNIIFIYKLGDDWGDKKVICNKFIQQCPVTTMVWLADG 104
S V LAFSPD LA D I ++ L + + PV+++ + DG
Sbjct: 155 SESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHT----DPVSSLAFSPDG 210
Query: 105 P--IIYGQSDGKIKAAHVKANK-TQTLYASNSFVVALCLNVRGAGVLSGHADGSIVRYYV 161
I G SDG I+ + K ++ + +S V + G+ + SG +DG+I +
Sbjct: 211 GLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLW-- 268
Query: 162 TEDASNFDQQQGRVVQHPVPPYALSW-PAGYILAAGS-DRIVTIYESDGRVHRIFDYTAP 219
D + + H ++++ P G +LA+GS D V ++ D ++
Sbjct: 269 --DLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLW--DLETGKLLSSLTL 324
Query: 220 HYKEREFTVACSSPSGQAVVVGSYDNIKLFAWSPSKSVWEEQPNKTIPNLYTISALSWKR 279
E + SP G +V G D+ + W +P KT+ + ++S+
Sbjct: 325 KGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTG----KPLKTLEGHSNVLSVSFSP 380
Query: 280 DGSRIACGGLCGSVELFE 297
DG ++ G G+V L++
Sbjct: 381 DGRVVSSGSTDGTVRLWD 398
Score = 46.2 bits (108), Expect = 1e-04
Identities = 42/211 (19%), Positives = 78/211 (36%), Gaps = 15/211 (7%)
Query: 53 AFSPDSTKLAVAQSDNIIFIYKLGDDWGDKKVICNKFIQQCPVTTMVWLADGPIIY-GQS 111
+FSPD + LA SD I ++ L ++ V ++ + DG ++ G S
Sbjct: 248 SFSPDGSLLASGSSDGTIRLWDLRS---SSSLLRTLSGHSSSVLSVAFSPDGKLLASGSS 304
Query: 112 DGKIKAAHVKANKTQ---TLYASNSFVVALCLNVRGAGVLSGHADGSIVRYYVTEDASNF 168
DG ++ ++ K TL V +L + G+ ++SG +D +R + D
Sbjct: 305 DGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLW---DLRTG 361
Query: 169 DQQQGRVVQHPVPPYALSWPAGYILAAGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTV 228
+ V + S + + +D V +++ T
Sbjct: 362 KPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTS----RVTS 417
Query: 229 ACSSPSGQAVVVGSYDNIKLFAWSPSKSVWE 259
SP G+++ GS DN + W S+
Sbjct: 418 LDFSPDGKSLASGSSDNT-IRLWDLKTSLKS 447
Score = 45.1 bits (105), Expect = 2e-04
Identities = 53/262 (20%), Positives = 100/262 (38%), Gaps = 35/262 (13%)
Query: 49 VKGLAFSPDSTKLAVAQS-DNIIFIYKLGDDWGDKKVICNKFIQQCPVTTMVWLADGPII 107
V LAFSPD L + S D I ++ L K++ + + DG ++
Sbjct: 201 VSSLAFSPDGGLLIASGSSDGTIRLWDL----STGKLLRSTLSGHSDSVVSSFSPDGSLL 256
Query: 108 YGQS-DGKIKA--AHVKANKTQTLYASNSFVVALCLNVRGAGVLSGHADGSIVRYYVTED 164
S DG I+ ++ +TL +S V+++ + G + SG +DG++ + +
Sbjct: 257 ASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTV---RLWDL 313
Query: 165 ASNFDQQQGRVVQHPVPPYALSWPAGYILAAGSDRIVTIYESDGRVHRIFDY-----TAP 219
+ + H P +LS+ +V+ DG + R++D
Sbjct: 314 ETGKLLSSLTLKGHEGPVSSLSFS------PDGSLLVSGGSDDGTI-RLWDLRTGKPLKT 366
Query: 220 HYKEREFTVACSSPSGQAVVVGSYDNIKLFAWSPSKSVWEEQPNKTIPNLYT----ISAL 275
SP G+ V GS D + +W+ + NL +++L
Sbjct: 367 LEGHSNVLSVSFSPDGRVVSSGSTDG--------TVRLWDLSTGSLLRNLDGHTSRVTSL 418
Query: 276 SWKRDGSRIACGGLCGSVELFE 297
+ DG +A G ++ L++
Sbjct: 419 DFSPDGKSLASGSSDNTIRLWD 440
Score = 43.2 bits (100), Expect = 0.001
Identities = 37/172 (21%), Positives = 69/172 (40%), Gaps = 11/172 (6%)
Query: 46 SYVVKGLAFSPDSTKLAVAQSDNIIFIYKLGDDWGDKKVICNKFIQQCPVTTMVWLADGP 105
S V +AFSPD LA SD + ++ L + G + PV+++ + DG
Sbjct: 284 SSSVLSVAFSPDGKLLASGSSDGTVRLWDL--ETGKLLSSLTLKGHEGPVSSLSFSPDGS 341
Query: 106 IIY--GQSDGKIKAAHVKANKTQTLYASNSFVVALCLNVRGAGVLSGHADGSIVRYYV-- 161
++ G DG I+ ++ K +S V+++ + G V SG DG++ + +
Sbjct: 342 LLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLST 401
Query: 162 TEDASNFDQQQGRVVQHPVPPYALSWPAGYILAAGSDRIVTIYESDGRVHRI 213
N D RV P + + SD + +++ + +
Sbjct: 402 GSLLRNLDGHTSRVTSLDFSPD-----GKSLASGSSDNTIRLWDLKTSLKSV 448
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 34.3 bits (79), Expect = 0.096
Identities = 30/124 (24%), Positives = 43/124 (34%), Gaps = 36/124 (29%)
Query: 861 GELYEKEGDHQTALNYYLKANFTSKACNLVQNEPYLLENHDVVSQIVKGLIKNESYIKAG 920
G LY K GD+ AL YY KA L + D ++Y
Sbjct: 7 GNLYYKLGDYDEALEYYEKA---------------LELDPDN----------ADAYYNLA 41
Query: 921 QIYEFTNENEKALECYRKGKVYDKCIDLTRKINPKNVTALEEEWGDHLIENKQYNAAINH 980
Y + E+ALE Y K +++P N A G + +Y A+
Sbjct: 42 AAYYKLGKYEEALEDYEKAL----------ELDPDNAKAY-YNLGLAYYKLGKYEEALEA 90
Query: 981 YIEA 984
Y +A
Sbjct: 91 YEKA 94
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 33.1 bits (76), Expect = 0.15
Identities = 12/76 (15%), Positives = 31/76 (40%), Gaps = 10/76 (13%)
Query: 1097 RLYLIIGEPDLAISMFKNQRQYENMIKLVRNYHPDLLDTTLLHLAQECEESKNYKQAEKY 1156
+ +G+ D A+ + + + + + + HP+ L +LA+ +Y +A +Y
Sbjct: 13 LVLRRLGDYDEALELLEKALE---LARELGEDHPETA-RALNNLARLYLALGDYDEALEY 68
Query: 1157 YLDCNEWKLAIKMYRS 1172
A+ + +
Sbjct: 69 LEK------ALALREA 78
Score = 30.0 bits (68), Expect = 1.5
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 16/75 (21%)
Query: 806 IYLENNEIHKAIDMYLKLYKWEDALSLAETNNYEYNELKKKYIKWLTDTRQEDKAGELYE 865
+ + +A+++ K AL LA E E + + L + LY
Sbjct: 14 VLRRLGDYDEALELLEK------ALELAR----ELGEDHPETARALNN------LARLYL 57
Query: 866 KEGDHQTALNYYLKA 880
GD+ AL Y KA
Sbjct: 58 ALGDYDEALEYLEKA 72
Score = 30.0 bits (68), Expect = 1.9
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 18/78 (23%)
Query: 861 GELYEKEGDHQTALNYYLKANFTSKACNLVQNEPYLLENHDVVSQIVKGLIKNESYIKAG 920
+ + GD+ AL KA ++ L E+H + +
Sbjct: 12 ALVLRRLGDYDEALELLEKA---------LELARELGEDHPETA---------RALNNLA 53
Query: 921 QIYEFTNENEKALECYRK 938
++Y + ++ALE K
Sbjct: 54 RLYLALGDYDEALEYLEK 71
>gnl|CDD|216001 pfam00577, Usher, Type VII secretion system (T7SS), usher protein.
The chaperone-usher (CU) pathway or Type VII secretion
system (T7SS) in Gram-negative (diderm) bacteria is
responsible for the secretion and assembly of prepilins
for fimbriae biogenesis, the prototypical Type 1 pili.
Following the prepilins export to the periplasm by the
Sec translocon, the biogenesis of fimbriae requires a
two-component assembly and transport system which is
composed of a periplasmic chaperone and an outer
membrane protein, which has been termed a molecular
'usher'. The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed of
membrane-spanning beta-sheets, a structure reminiscent
of porins. Although the degree of sequence similarity of
these proteins is not very high they share a number of
characteristics. One of these is the presence of two
pairs of cysteines, the first one located in the
N-terminal part and the second at the C-terminal
extremity that are probably involved in disulphide
bonds. The best conserved region is located in the
central part of these proteins.
Length = 552
Score = 36.1 bits (84), Expect = 0.17
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 171 QQGRVV-QHPVP--PYALS--WPAGYILAAGSDRIVTIYESDGRVHR-IFDYTAPHYKER 224
Q G V+ Q VP P+ ++ +P+G G D VT+ ESDG V Y++ R
Sbjct: 105 QNGYVIYQTTVPPGPFEITDLYPSGS----GGDLDVTVTESDGSVQTFTVPYSSVPNLLR 160
Query: 225 E 225
Sbjct: 161 P 161
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only if
a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 34.7 bits (80), Expect = 0.56
Identities = 75/368 (20%), Positives = 120/368 (32%), Gaps = 73/368 (19%)
Query: 950 RKINPKNVTA-LEEEWGDHLIENKQYNAAINHYIEAGKNNKAL----------------- 991
R N + A LE+ + E + A +Y+ G+ KAL
Sbjct: 545 RTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEAW 604
Query: 992 ----DTSIKAKQWKKAVQILQVITNKQ-DIAQHVKTLAQHFKTVKDYKTAEKIYS----- 1041
+ A KAV + + Q D A + LA + +K+Y A
Sbjct: 605 LMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALEL 664
Query: 1042 HCDMHE-QIVDM--YHQTGQWEKAYAIAEQHLNVGEIKATFIQKCKQLEEENKFKEAERL 1098
D E QI + E A IA+ +QK F+ L
Sbjct: 665 KPDNTEAQIGLAQLLLAAKRTESAKKIAKS-----------LQKQHPKAAL-GFELEGDL 712
Query: 1099 YLIIGEPDLAISMFKNQRQYE----NMIKLVRNY-----HPDLLDTTLLHLAQECEESK- 1148
YL + AI ++ + N IKL R + + T L ++
Sbjct: 713 YLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVL 772
Query: 1149 NYKQAEKYYLDCNEWKLAIKMYRSLNLWEDAYRIALSNGGQEAVEPVVYLWAKSLGGDSA 1208
AE YL ++ AIK Y+++ + L+N + +L+ + L A
Sbjct: 773 RTALAE-LYLAQKDYDKAIKHYQTVVKKAPDNAVVLNN--------LAWLYLE-LKDPRA 822
Query: 1209 VRLLNRLSLLESCISNACDTY--------QFDFAFELAK--IGMKSKLEEVHYKYALVLE 1258
+ R L I DT + D A L + + + + + Y AL L
Sbjct: 823 LEYAERALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALALL 882
Query: 1259 DNGQFNEA 1266
G+ EA
Sbjct: 883 ATGRKAEA 890
Score = 30.8 bits (70), Expect = 8.3
Identities = 24/169 (14%), Positives = 49/169 (28%), Gaps = 23/169 (13%)
Query: 914 ESYIKAGQIYEFTNENEKALECYRKGKVYDKCIDLTRKINPKNVTALEEEWGDHLIENKQ 973
+ + Y KA+ ++ L K + T + L+ K+
Sbjct: 636 LALLLLADAYAVMKNYAKAITSLKRA--------LELK---PDNTEAQIGLAQLLLAAKR 684
Query: 974 YNAAIN--HYIEAGKNNKAL------DTSIKAKQWKKAVQILQVITNKQDIAQHVKTLAQ 1025
+A ++ AL D ++ K + A+Q + + +Q+ L +
Sbjct: 685 TESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHR 744
Query: 1026 HFKTVKDYKTAEKIYSHC--DMHEQIVDMYHQTGQW--EKAYAIAEQHL 1070
+ A K V + +K Y A +H
Sbjct: 745 ALLASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHY 793
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 32.6 bits (75), Expect = 0.71
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 1137 LLHLAQECEESKNYKQAEKYYLDCNEWKLAIKMYRSLNLWEDAYRIA 1183
L +A+ CE++ Y++A Y +K AI + + L L++DA A
Sbjct: 73 LEKVAKLCEKADLYEEAVILYKKNGNYKEAISLLKKLKLYKDAIEYA 119
Score = 29.9 bits (68), Expect = 4.9
Identities = 9/50 (18%), Positives = 19/50 (38%)
Query: 965 GDHLIENKQYNAAINHYIEAGKNNKALDTSIKAKQWKKAVQILQVITNKQ 1014
+ Y A+ Y + G +A+ K K +K A++ + +
Sbjct: 77 AKLCEKADLYEEAVILYKKNGNYKEAISLLKKLKLYKDAIEYAVKSNDPE 126
Score = 29.9 bits (68), Expect = 5.1
Identities = 16/101 (15%), Positives = 36/101 (35%), Gaps = 15/101 (14%)
Query: 1392 EQNGEFYNA-VECYLKIKNVDVNLMVKILNEVTQLTLKYLNHDQSYKILPSLVPKLMEFK 1450
+N A +E Y K ++ + L ++L + +Y + + +
Sbjct: 39 RENPALQTALLELYAKYEDPE-KLE------------EFLKKNNNYDL-EKVAKLCEKAD 84
Query: 1451 QYDLAVRVYLNIDMVKEAVDIFIYTQNWNKARKLCAELKPE 1491
Y+ AV +Y KEA+ + + + A + +
Sbjct: 85 LYEEAVILYKKNGNYKEAISLLKKLKLYKDAIEYAVKSNDP 125
Score = 29.1 bits (66), Expect = 9.6
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 1237 LAKIGMKSKLEEV-----HY---KYALVLEDNGQFNEAETQFIKANKPKEAISMYIHNQD 1288
AK KLEE +Y K A + E + EA + K KEAIS+ +
Sbjct: 52 YAKYEDPEKLEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKNGNYKEAISLLKKLKL 111
Query: 1289 WENAERIANEHDPTSIGDILLNQS 1312
+++A A + + + + LLN
Sbjct: 112 YKDAIEYAVKSNDPELWEKLLNAL 135
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 29.6 bits (67), Expect = 0.83
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 49 VKGLAFSPDSTKLAVAQSDNIIFIYK 74
V +AFSPD LA D I ++
Sbjct: 15 VTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 29.6 bits (67), Expect = 1.0
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 49 VKGLAFSPDSTKLAVAQSDNIIFIYK 74
V +AFSPD LA D + ++
Sbjct: 14 VTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|227610 COG5290, COG5290, IkappaB kinase complex, IKAP component
[Transcription].
Length = 1243
Score = 33.8 bits (77), Expect = 1.1
Identities = 33/164 (20%), Positives = 61/164 (37%), Gaps = 9/164 (5%)
Query: 1124 LVRNYHPDLLDTTLLHLAQECEESKNYKQAEKYYLDCNEWKLAIKMYRSLNLWEDAYRIA 1183
L+ Y +L + A ++ + A K Y ++ A Y S +W + I+
Sbjct: 912 LLYRYDGELQKFKINIFAGNLVDNLYHISAAKAYEVEGKYIEAHGAYDSALMWRECGSIS 971
Query: 1184 LSNGGQEAVEPVVYLWAKSL------GGDSAVRLLNRLSLLESCISNACDTYQFDFAFEL 1237
G E L L GD+ LL L L ++ C ++ AF
Sbjct: 972 TQEKGYE-FNLCAELLPSDLLVEFRKAGDAEKILLTYLENLYEAVAMDCKGSEYREAFCE 1030
Query: 1238 AKIGMKSKLEEVHYKYALVLEDNGQFNE-AETQFIKANKPKEAI 1280
A + + E+ HY+ + E+ G E A ++++ + +
Sbjct: 1031 AMVSRLVESEK-HYEAGQLGEEFGGKPELAADEYVQIKSQGDRL 1073
>gnl|CDD|238972 cd02014, TPP_POX, Thiamine pyrophosphate (TPP) family, Pyruvate
oxidase (POX) subfamily, TPP-binding module; composed of
proteins similar to Lactobacillus plantarum POX, which
plays a key role in controlling acetate production under
aerobic conditions. POX decarboxylates pyruvate,
producing hydrogen peroxide and the energy-storage
metabolite acetylphosphate. It requires FAD in addition
to TPP and a divalent cation as cofactors.
Length = 178
Score = 32.1 bits (74), Expect = 1.3
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 13/57 (22%)
Query: 688 NHQLGY----ELDESLIEFGTAVHDSDFGKAILYLESLGI------NKKEAEGMWQN 734
N LG+ + EFG + + DF K E++GI + E E
Sbjct: 105 NSDLGFIKWEQEVMGQPEFGVDLPNPDFAK---IAEAMGIKGIRVEDPDELEAALDE 158
>gnl|CDD|238843 cd01699, RNA_dep_RNAP, RNA_dep_RNAP: RNA-dependent RNA polymerase
(RdRp) is an essential protein encoded in the genomes of
all RNA containing viruses with no DNA stage. RdRp
catalyzes synthesis of the RNA strand complementary to a
given RNA template. RdRps of many viruses are products
of processing of polyproteins. Some RdRps consist of one
polypeptide chain, and others are complexes of several
subunits. The domain organization and the 3D structure
of the catalytic center of a wide range of RdRps,
including those with a low overall sequence homology,
are conserved. The catalytic center is formed by several
motifs containing a number of conserved amino acid
residues. This subfamily represents the RNA-dependent
RNA polymerases from all positive-strand RNA eukaryotic
viruses with no DNA stage.
Length = 278
Score = 32.6 bits (75), Expect = 1.3
Identities = 13/80 (16%), Positives = 22/80 (27%), Gaps = 10/80 (12%)
Query: 158 RYYVTEDASNFDQQQGRVVQHPVPPYALSWPAGYILAAGSDRIVTIYESDGRVHRIFDYT 217
+ D S FD + P L I A D + + + + + +
Sbjct: 96 PVAIALDYSRFDSS--------LSPQLLEA-EHSIYNALYDDDDELERRN-LLRSLTNNS 145
Query: 218 APHYKEREFTVACSSPSGQA 237
+ V PSG
Sbjct: 146 LHIGFNEVYKVRGGRPSGDP 165
>gnl|CDD|218251 pfam04762, IKI3, IKI3 family. Members of this family are
components of the elongator multi-subunit component of a
novel RNA polymerase II holoenzyme for transcriptional
elongation. This region contains WD40 like repeats.
Length = 903
Score = 33.0 bits (76), Expect = 1.5
Identities = 38/206 (18%), Positives = 66/206 (32%), Gaps = 44/206 (21%)
Query: 52 LAFSPDSTKLAVAQSDNIIFIYKLGDDWGDKKVICNKFIQQCPVTTMVWLADGPII--YG 109
+AFS ++ +AV SD I IY+L +K P T + D
Sbjct: 417 VAFSKSNSCVAVLTSDGDISIYEL--SLKKRKPG------SPPKLTSKFSLDKVENSDSE 468
Query: 110 QSDGKIKAAHVKANKTQTLYASNSFVVALCLNVRGAGVLSGHADGSIVRYYVTEDASNFD 169
+ G ++ Q + ++S ++ L +I + + D
Sbjct: 469 VALGSLR---------QLAFLNDSELLVLS------------DSDNITEIVLVDVD---D 504
Query: 170 QQQGRVVQHPVPPYALSWPAGYILAAGSDRIVTIYESDGRVHRI-----FDYTAPHYKER 224
+ V + IL++ + V I DG+V + R
Sbjct: 505 TENPLSVSVITEIEGIVL----ILSSNDYKHVYIETRDGKVLSLSAEGELSEIGFPQLCR 560
Query: 225 EFTVACSSPSGQAVVVGSYDNIKLFA 250
F V + + G DN KL+A
Sbjct: 561 WFRVVQIGNDER-LAFGLTDNGKLYA 585
>gnl|CDD|205362 pfam13181, TPR_8, Tetratricopeptide repeat.
Length = 34
Score = 28.6 bits (65), Expect = 1.7
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 914 ESYIKAGQIYEFTNENEKALECYRK 938
+Y GQIY + E+A E Y K
Sbjct: 2 RAYYLLGQIYLQLGDYEEAKEYYEK 26
>gnl|CDD|235020 PRK02264, PRK02264, N(5),N(10)-methenyltetrahydromethanopterin
cyclohydrolase; Provisional.
Length = 317
Score = 32.1 bits (74), Expect = 2.6
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 19/78 (24%)
Query: 690 QLGYELDESLI----EFGTAVHDSDFGKAILYLESLGINKKEAEGMWQNLAEVAIQLHNL 745
+L EL + L+ E VH+ + G ++ G+N A G E + L
Sbjct: 6 ELALELVDELLDDAEELRIEVHELENGATVI---DCGVN---APGSI----EAGLLL--- 52
Query: 746 HVAEICYAALGDISTTHF 763
AEIC L ++
Sbjct: 53 --AEICMGGLATVTIRPG 68
>gnl|CDD|225729 COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility
and secretion / Intracellular trafficking and
secretion].
Length = 835
Score = 32.3 bits (74), Expect = 2.9
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 171 QQGRVV-QHPVPPYALSWPAGYILAAGSDRIVTIYESDGRVHRIFDYTAPHY 221
Q G V+ Q VPP + D VT+ E+DG V ++ P
Sbjct: 296 QNGYVIYQTTVPPGPFEINDLPPTSGSGDLDVTVKEADGSVQT---FSVPFS 344
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 32.1 bits (73), Expect = 2.9
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 10/72 (13%)
Query: 795 ILNKQFKVAEGIYLENNEIHKAIDM--------YLKLYKWEDALSLAETNNYEYNELKKK 846
+L Q + + I L N ++ I+ YL L K+ L T+NYE+N K +
Sbjct: 303 VLQSQL-LEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQIL-KDNTDNYEFNIFKMQ 360
Query: 847 YIKWLTDTRQED 858
+ WLT+T D
Sbjct: 361 VLVWLTETETGD 372
>gnl|CDD|224459 COG1542, COG1542, Uncharacterized conserved protein [Function
unknown].
Length = 593
Score = 32.2 bits (73), Expect = 3.2
Identities = 43/173 (24%), Positives = 61/173 (35%), Gaps = 24/173 (13%)
Query: 801 KVAEGIYLENNEIHKAIDMYLKLYKWEDALSLAETNNYE-YNELKKKYIKWLTDTRQEDK 859
+ EG E E+ + LY WE L+ A + + Y E+ K Y K ED+
Sbjct: 232 ALEEGEQPETEEMLE-----RGLYAWEGKLTPAGEHLLDAYKEMGKVYPKTPPIYILEDE 286
Query: 860 A------GELYEK--EGDHQTALNYYLKANFTSKACNLVQNEPYLLENHDVVSQIVKGLI 911
+L +K + + +K +LV Y LE+ GLI
Sbjct: 287 IRLLKAIDKLKKKHETNPAPEIKPIEKEIKWETKIDDLVTAALYTLESF--------GLI 338
Query: 912 KNESYIKAGQIYEFTNENEKALECYRKGKVYD--KCIDLTRKINPKNVTALEE 962
K E Y T EK LE K D K I T + + N E+
Sbjct: 339 KREVVKNGDLTYVLTEFGEKVLEDLEKSVTADGVKAITYTEEFDAPNAEWYEQ 391
>gnl|CDD|182098 PRK09828, PRK09828, putative fimbrial outer membrane usher protein;
Provisional.
Length = 865
Score = 32.0 bits (73), Expect = 3.5
Identities = 23/58 (39%), Positives = 27/58 (46%), Gaps = 23/58 (39%)
Query: 180 VPPYA-----LSWPAGYILAAGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTVACSS 232
VPP A LS P+GY GSD IVTI E+DG +R F+ SS
Sbjct: 311 VPPGAFVIDDLS-PSGY----GSDLIVTIEEADG-------------SKRTFSQPFSS 350
>gnl|CDD|202685 pfam03564, DUF1759, Protein of unknown function (DUF1759). This is
a family of proteins of unknown function. Most of the
members are gag-polyproteins.
Length = 146
Score = 30.4 bits (69), Expect = 3.8
Identities = 24/117 (20%), Positives = 45/117 (38%), Gaps = 6/117 (5%)
Query: 876 YYLKANFTSKACNLVQNEPYLLENHDVVSQIVKGLIKNESYIKAGQIYEFTNE---NEKA 932
YLK+ +A LV + P N+DV + +K N I + + N +
Sbjct: 32 NYLKSALEGEAATLVTHLPITAANYDVAWEALKERYDNPRVIIRSLLNKLMKLPSTNNDS 91
Query: 933 LECYRKGKVYDKCIDLTRKINPKNVTALEEEWGDHLIENKQYNAAINHYIEAGKNNK 989
+ R ++YD+ ++ R++ A ++ HL+ K +I K
Sbjct: 92 VSQLR--RLYDEANEIIRQLEQLGENA-DDTILAHLLLQKLDEEIRRKWISFSKKLD 145
>gnl|CDD|226371 COG3853, TelA, Uncharacterized protein involved in tellurite
resistance [Inorganic ion transport and metabolism].
Length = 386
Score = 31.6 bits (72), Expect = 3.8
Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 9/87 (10%)
Query: 955 KNVTALEEEWGDHLIENKQYNAAINHYIEAGK-NNKALDTSIKAKQWKKAVQILQVITNK 1013
++ LE + N++Y + YI AG+ ++ L+T I + KA Q+ +
Sbjct: 162 RDNKMLELLYEK----NREYFEHLEKYIAAGELKDEELETEIIPELKTKAESGNQMDVQQ 217
Query: 1014 -QDIAQHVKTLAQHFKTVKDYKTAEKI 1039
++ + L Q V D A +
Sbjct: 218 VNELTLFINRLEQR---VYDLLLARMV 241
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 31.5 bits (72), Expect = 4.7
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 1063 YAIAEQHLNVG--EIKATFIQKCKQLEEENKFKEAERLY 1099
Y E+ L I+ ++ K EE+ K EA+RL
Sbjct: 246 YVTPEERLERAIKNIEKELEERLKYFEEQGKLLEAQRLK 284
>gnl|CDD|132580 TIGR03541, reg_near_HchA, LuxR family transcriptional regulatory,
chaperone HchA-associated. Members of this protein
family belong to the LuxR transcriptional regulator
family, and contain both autoinducer binding (pfam03472)
and transcriptional regulator (pfam00196) domains.
Members, however, occur only in a few members of the
Gammaproteobacteria that have the
chaperone/aminopeptidase HchA, and are always encoded by
the adjacent gene.
Length = 232
Score = 30.9 bits (70), Expect = 4.9
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 54 FSPDSTKLAVAQSDNIIFIYKLGDDWGDKKVI--CNKFIQQCPVTTMVWLADGPIIYGQS 111
FS S K + + I ++ DW D +++ CPVT + AD P + ++
Sbjct: 39 FSAHSAKDELI--ERIFWVE---GDWFDDGNAVDAQTYLRHCPVTRHILEADEPFFWSKT 93
Query: 112 DGK 114
+
Sbjct: 94 PNE 96
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 31.7 bits (72), Expect = 5.0
Identities = 31/169 (18%), Positives = 58/169 (34%), Gaps = 22/169 (13%)
Query: 888 NLVQNEPYLLENHDVVSQIVKGL-----IKNESYIKAGQIYEFTNENEKALECYR----- 937
+L +N+ L + + + ++ +N+ + E N+ L Y
Sbjct: 764 HLYENDKDLPDGKNTYEEFLQYKDTILNKENKISNDINILKENKKNNQDLLNSYNILIQK 823
Query: 938 ----KGKVYDKCIDLTRKINPKNVTALEEEWGDHLIENKQYNAAINHYIEAGKNN----K 989
K ++ L +K ++ +E EN Q I IE N K
Sbjct: 824 LEAHTEKNDEELKQLLQKFPTEDENLNLKELEKEFNENNQIVDNIIKDIENMNKNINIIK 883
Query: 990 ALDTSIKAKQWKKAVQILQVITNKQDIAQHVKTLAQHFKTVKDYKTAEK 1038
L+ +I K + + ++ NK D+ L QH K + +K
Sbjct: 884 TLNIAINRSNSNKQL-VEHLLNNKIDL---KNKLEQHMKIINTDNIIQK 928
>gnl|CDD|197478 smart00028, TPR, Tetratricopeptide repeats. Repeats present in 4
or more copies in proteins. Contain a minimum of 34
amino acids each and self-associate via a "knobs and
holes" mechanism.
Length = 34
Score = 27.0 bits (61), Expect = 7.2
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 861 GELYEKEGDHQTALNYYLKA 880
G Y K GD+ AL YY KA
Sbjct: 8 GNAYLKLGDYDEALEYYEKA 27
>gnl|CDD|116500 pfam07888, CALCOCO1, Calcium binding and coiled-coil domain
(CALCOCO1) like. Proteins found in this family are
similar to the coiled-coil transcriptional coactivator
protein coexpressed by Mus musculus (CoCoA/CALCOCO1).
This protein binds to a highly conserved N-terminal
domain of p160 coactivators, such as GRIP1, and thus
enhances transcriptional activation by a number of
nuclear receptors. CALCOCO1 has a central coiled-coil
region with three leucine zipper motifs, which is
required for its interaction with GRIP1 and may regulate
the autonomous transcriptional activation activity of the
C-terminal region.
Length = 546
Score = 30.7 bits (69), Expect = 7.9
Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 7/98 (7%)
Query: 943 DKCIDLTRKINPKNVTALEEEWGDHLIE---NKQYNAAINHYIEAGKNNKALDTSIKAKQ 999
D+ L+ ++ EE +E + + E + L ++++ Q
Sbjct: 371 DRIQKLSAELLKLEEWLQEERSQREKLEVELGIEKDCNRVQLSENRRELSELRSALRVLQ 430
Query: 1000 WKKAVQILQVITNKQDIAQHVKTLAQHFKTVKDYKTAE 1037
+K Q+ KQ++ +++ L D K AE
Sbjct: 431 KEKE----QLQEEKQELLDYIRVLELRLDKEADEKWAE 464
>gnl|CDD|187774 cd09643, Csn1, CRISPR/Cas system-associated protein Cas9. 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; Very large protein
containing McrA/HNH-nuclease related domain and a
RuvC-like nuclease domain; signature gene for type II.
Length = 799
Score = 30.5 bits (69), Expect = 9.1
Identities = 60/337 (17%), Positives = 113/337 (33%), Gaps = 45/337 (13%)
Query: 806 IYLENNEIHKAIDMYLKLYKWEDALSLAETNNYEYNELKKKYIKWLTDTRQEDKAGELYE 865
+ + +++ ++ + + E + E + L KK R+ E
Sbjct: 285 LAEKFTVLNELNNLRIIEEQGETKILSKEEKQELLDLLFKKNKLTYKQKRKLLGLKEEEI 344
Query: 866 KEGDHQTALNYYLKANFTSKA----CNLVQNEPYLLE--NHDVVSQIVK--GLIKNESYI 917
+G L N + K + E N ++ +IVK L K+ I
Sbjct: 345 FKGLRYEGLKAEKNFNISLKTYHDLRKALGKEFLKDLELNEKILDEIVKILTLYKDREMI 404
Query: 918 KA-GQIYEFTNENEKALECYRKGKVYDKCIDLTRKINPKNVTALEEEWGDHLIENKQYNA 976
+ ++Y+ E+ + ++ + L+ K +E + K+Y+
Sbjct: 405 EKILELYKDLLNEEQLKKLLKRH--FTGWGRLSLKALRGIRPLME--------QGKRYDE 454
Query: 977 AINHYIEAGKNNKALDTSIKAKQWKKAVQILQVITN---KQDIAQHVKTLAQHFKTVKDY 1033
AI + N K +K K Q+ I N K+ + Q K + + VK Y
Sbjct: 455 AILE-LGGNHNQKINSDELKFLPIIKKAQVKDEILNPVVKRALLQARKVVNE---LVKKY 510
Query: 1034 KTAEKIYSHCDMHEQIVDMYHQTGQWEKAYA--IAEQHLNVGEIKATFIQKCKQLEEENK 1091
+KI +M + T + K + N+ E + QK K+L + K
Sbjct: 511 GPPDKI--VIEMAREN-----GTNKGTKNRKKRQKKNEDNIKEAASALEQKLKELPLDIK 563
Query: 1092 FKEAERLYLII---------GEPDLAISMFKNQRQYE 1119
K +L L G+ + I + YE
Sbjct: 564 SKNILKLRLYYQQNGKCMYTGKE-IDIDDLFDLSYYE 599
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 30.6 bits (70), Expect = 9.1
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 1063 YAIAEQHLN--VGEIKATFIQKCKQLEEENKFKEAERL 1098
Y + L + IK ++ K E+ NK EA+RL
Sbjct: 249 YVTPRERLEQAIESIKEELEERLKFFEKNNKLLEAQRL 286
>gnl|CDD|221837 pfam12895, Apc3, Anaphase-promoting complex, cyclosome, subunit 3.
Apc3, otherwise known as Cdc27, is one of the subunits of
the anaphase-promoting complex or cyclosome. The
anaphase-promoting complex is a multiprotein subunit E3
ubiquitin ligase complex that controls segregation of
chromosomes and exit from mitosis in eukaryotes. The
protein members of this family contain TPR repeats just
as those of Apc7 do, and it appears that these TPR units
bind the C-termini of the APC co-activators CDH1 and
CDC20.
Length = 80
Score = 28.0 bits (63), Expect = 9.8
Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 5/70 (7%)
Query: 1095 AERLYLIIGEPD----LAISMFKNQRQYENMIKLVRNYHPDLLDTTLLHLAQECEESKNY 1150
AE+L + + LA F Q QY+ +L+R D LAQ + Y
Sbjct: 12 AEKLLALTPSNEDAYLLAQCYF-LQGQYKRAYELLRKLKLDNSSGCRYLLAQCLLKLGKY 70
Query: 1151 KQAEKYYLDC 1160
+A
Sbjct: 71 DEAIAVLEKA 80
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 0.400
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 82,669,241
Number of extensions: 8228290
Number of successful extensions: 7373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7327
Number of HSP's successfully gapped: 84
Length of query: 1637
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1527
Effective length of database: 6,058,662
Effective search space: 9251576874
Effective search space used: 9251576874
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: 66 (29.2 bits)