RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9769
(1026 letters)
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 169 bits (431), Expect = 1e-44
Identities = 98/409 (23%), Positives = 174/409 (42%), Gaps = 39/409 (9%)
Query: 66 CDVKLI--ADGVEVAAHKMVLAACSPYFHAMFISFEESKQERIVLKGVDPNALKLLIDYV 123
CD +I G + HK++L++ S YF K+ I L D ++ +I Y+
Sbjct: 10 CDESIIIVNGGGIIKVHKIILSSSSEYF-KKMFK-NNFKENEINLNI-DYDSFNEVIKYI 66
Query: 124 YSCEIYVTEENVQMLLPAANLLQLTDVRDACCDFLQCQLHPTNCLGIRAFADLHSCLDLL 183
Y+ +I +T NV+ +L AN L + + + C +++ + NC+ I F+ + C L
Sbjct: 67 YTGKINITSNNVKDILSIANYLIIDFLINLCINYIIKIIDDNNCIDIYRFSFFYGCKKLY 126
Query: 184 STAENYIELHFAEIVECEEFLSLSHEQVLGLISSDKLMVSNEEKVFECVIAWVNYDLESR 243
S A NYI + I +F+ LS +++ ++S DKL VS+E+ V E +I W+ ++
Sbjct: 127 SAAYNYIRNNIELIYNDPDFIYLSKNELIKILSDDKLNVSSEDVVLEIIIKWLTSKKNNK 186
Query: 244 QKHVAELMEYVRLPLLSEDYLI-------QRVEEETVFKNDIRCKDYLIEALKYHILVKK 296
K + +++ +R+ LSE+ + + +++ VF I KK
Sbjct: 187 YKDICLILKVLRITFLSEEGIKKLKRWKLRIKKKKIVFNKRCIK----------IIYSKK 236
Query: 297 GEVNKLTLVRTPRTKPRQPLRVPKVMLVVGGQAPKAIRSVECYDFKTERWQSVAEMPTRR 356
+NK+ + + + + ++ ++
Sbjct: 237 YNLNKILPRSSTFGSI----------IYIHITMSIFTYNYITNYSPLSEINTIIDIHYVY 286
Query: 357 CRAGLVFLHEKVYAVGGFNGSLRV------YDPSTNEWSSAPPMEARRSTLGVAVLNSLI 410
C G V L+ +Y +GG N + YD T W+ P + R GV V N+ I
Sbjct: 287 C-FGSVVLNNVIYFIGGMNKNNLSVNSVVSYDTKTKSWNKVPELIYPRKNPGVTVFNNRI 345
Query: 411 YAVGGFDGSSGLNSAEVYDPSTEKWNMIAPMSTRRSSVGVGVLNGCLYA 459
Y +GG S LN+ E + P KW P+ R + V +N +Y
Sbjct: 346 YVIGGIYNSISLNTVESWKPGESKWREEPPLIFPRYNPCVVNVNNLIYV 394
Score = 72.9 bits (179), Expect = 4e-13
Identities = 29/113 (25%), Positives = 51/113 (45%), Gaps = 8/113 (7%)
Query: 333 IRSVECYDFKTERWQSVAEMPTRRCRAGLVFLHEKVYAVGGFNGSLRV--------YDPS 384
+++VEC+ T +W + +P ++ K+Y +GG + + Y+P
Sbjct: 405 LKTVECFSLNTNKWSKGSPLPISHYGGCAIYHDGKIYVIGGISYIDNIKVYNIVESYNPV 464
Query: 385 TNEWSSAPPMEARRSTLGVAVLNSLIYAVGGFDGSSGLNSAEVYDPSTEKWNM 437
TN+W+ + R + + N+ IY VGG +N EVYD T W +
Sbjct: 465 TNKWTELSSLNFPRINASLCIFNNKIYVVGGDKYEYYINEIEVYDDKTNTWTL 517
Score = 68.6 bits (168), Expect = 9e-12
Identities = 28/136 (20%), Positives = 57/136 (41%), Gaps = 9/136 (6%)
Query: 333 IRSVECYDFKTERWQSVAEMPTRRCRAGLVFLHEKVYAVGGFN------GSLRVYDPSTN 386
+ +VE + +W+ + R +V ++ +Y +GG + ++ + +TN
Sbjct: 357 LNTVESWKPGESKWREEPPLIFPRYNPCVVNVNNLIYVIGGISKNDELLKTVECFSLNTN 416
Query: 387 EWSSAPPMEARRSTLGVAVLNSLIYAVGGF---DGSSGLNSAEVYDPSTEKWNMIAPMST 443
+WS P+ + IY +GG D N E Y+P T KW ++ ++
Sbjct: 417 KWSKGSPLPISHYGGCAIYHDGKIYVIGGISYIDNIKVYNIVESYNPVTNKWTELSSLNF 476
Query: 444 RRSSVGVGVLNGCLYA 459
R + + + N +Y
Sbjct: 477 PRINASLCIFNNKIYV 492
Score = 54.8 bits (132), Expect = 2e-07
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 775 IGVGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGG-HDGPL 833
IG G Y+ IS L++VE + P + W +++ R V ++N++Y +GG
Sbjct: 348 IG-GIYNSIS---LNTVESWKPGESKWREEPPLIFPRYNPCVVNVNNLIYVIGGISKNDE 403
Query: 834 VRKSVEAYDPETQTWS 849
+ K+VE + T WS
Sbjct: 404 LLKTVECFSLNTNKWS 419
Score = 54.0 bits (130), Expect = 3e-07
Identities = 32/135 (23%), Positives = 47/135 (34%), Gaps = 12/135 (8%)
Query: 774 TIGVGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGH---D 830
I V G + + L +VE +S N W + G D +Y +GG D
Sbjct: 391 LIYVIGGISKNDELLKTVECFSLNTNKWSKGSPLPISHYGGCAIYHDGKIYVIGGISYID 450
Query: 831 GPLVRKSVEAYDPETQTWSGVPDMALCRRNAVLESVASTAEVNLGDEVSCVVKGISVRGV 890
V VE+Y+P T W+ + + R NA L + VV G
Sbjct: 451 NIKVYNIVESYNPVTNKWTELSSLNFPRINASLCIF---------NNKIYVVGGDKYEYY 501
Query: 891 IAQVGYYKLKATCEN 905
I ++ Y K
Sbjct: 502 INEIEVYDDKTNTWT 516
Score = 51.3 bits (123), Expect = 2e-06
Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 777 VGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDGPLVRK 836
+GG + + ++SV Y + +W V +++Y R GV V +N +Y +GG +
Sbjct: 300 IGGMNK-NNLSVNSVVSYDTKTKSWNKVPELIYPRKNPGVTVFNNRIYVIGGIYNSISLN 358
Query: 837 SVEAYDPETQTWSGVPDMALCRRNAVLESV 866
+VE++ P W P + R N + +V
Sbjct: 359 TVESWKPGESKWREEPPLIFPRYNPCVVNV 388
Score = 47.8 bits (114), Expect = 3e-05
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 777 VGGYDGISR-QCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDGPLVR 835
+GG I + + VE Y+P N W + + + R A + + +N +Y VGG
Sbjct: 443 IGGISYIDNIKVYNIVESYNPVTNKWTELSSLNFPRINASLCIFNNKIYVVGGDKYEYYI 502
Query: 836 KSVEAYDPETQTWSGVPD 853
+E YD +T TW+
Sbjct: 503 NEIEVYDDKTNTWTLFCK 520
Score = 41.7 bits (98), Expect = 0.002
Identities = 26/129 (20%), Positives = 48/129 (37%), Gaps = 11/129 (8%)
Query: 735 IVKKTI-FEDSSVSGTEAVNQNCSRPSFKREKSSRNAELSTIGVGGYDGISRQCLSSVEM 793
I KK I F + + N ++ + +
Sbjct: 217 IKKKKIVFNKRCIKIIYSKKYNLNKILPRSSTFGSIIYIHITMSIFTYNYIT-------- 268
Query: 794 YSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDG-PLVRKSVEAYDPETQTWSGVP 852
+ + D+ Y V VL+N++Y +GG + L SV +YD +T++W+ VP
Sbjct: 269 NYSPLSEINTIIDIHYVYCFGSV-VLNNVIYFIGGMNKNNLSVNSVVSYDTKTKSWNKVP 327
Query: 853 DMALCRRNA 861
++ R+N
Sbjct: 328 ELIYPRKNP 336
>gnl|CDD|149006 pfam07707, BACK, BTB And C-terminal Kelch. This domain is found
associated with pfam00651 and pfam01344. The BACK domain
is found juxtaposed to the BTB domain; they are
separated by as little as two residues. This family
appears to be closely related to the BTB domain (Finn
RD, personal observation).
Length = 101
Score = 143 bits (363), Expect = 3e-40
Identities = 53/101 (52%), Positives = 72/101 (71%)
Query: 167 CLGIRAFADLHSCLDLLSTAENYIELHFAEIVECEEFLSLSHEQVLGLISSDKLMVSNEE 226
CLGI FAD + C +L A +I +F E+ + EEFL LS EQ+L L+SSD+L V +EE
Sbjct: 1 CLGIYRFADTYGCEELAEVALRFILKNFLEVSKSEEFLELSKEQLLELLSSDELNVPSEE 60
Query: 227 KVFECVIAWVNYDLESRQKHVAELMEYVRLPLLSEDYLIQR 267
+VFE VI WV +D+E+R+KH+ EL+ VRLPLLS +YL+
Sbjct: 61 EVFEAVIKWVKHDVENRKKHLPELLSAVRLPLLSPEYLLDV 101
>gnl|CDD|197943 smart00875, BACK, BTB And C-terminal Kelch. The BACK domain is
found juxtaposed to the BTB domain; they are separated
by as little as two residues.
Length = 101
Score = 130 bits (329), Expect = 8e-36
Identities = 54/101 (53%), Positives = 72/101 (71%)
Query: 167 CLGIRAFADLHSCLDLLSTAENYIELHFAEIVECEEFLSLSHEQVLGLISSDKLMVSNEE 226
CLGIR FAD H +L A +I +F+E+ EEFL L EQ+L L+SSD L VS+EE
Sbjct: 1 CLGIRRFADAHGLEELAEKALRFILQNFSEVSSSEEFLELPLEQLLELLSSDDLNVSSEE 60
Query: 227 KVFECVIAWVNYDLESRQKHVAELMEYVRLPLLSEDYLIQR 267
+VFE V+ WV +D E R++H+ EL+E+VRLPLLS DYL++
Sbjct: 61 EVFEAVLRWVKHDPEKRREHLPELLEHVRLPLLSPDYLLEV 101
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab) or
POZ (for Pox virus and Zinc finger) domain is present
near the N-terminus of a fraction of zinc finger
(pfam00096) proteins and in proteins that contain the
pfam01344 motif such as Kelch and a family of pox virus
proteins. The BTB/POZ domain mediates homomeric
dimerisation and in some instances heteromeric
dimerisation. The structure of the dimerised PLZF
BTB/POZ domain has been solved and consists of a tightly
intertwined homodimer. The central scaffolding of the
protein is made up of a cluster of alpha-helices flanked
by short beta-sheets at both the top and bottom of the
molecule. POZ domains from several zinc finger proteins
have been shown to mediate transcriptional repression
and to interact with components of histone deacetylase
co-repressor complexes including N-CoR and SMRT. The POZ
or BTB domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 115 bits (291), Expect = 1e-30
Identities = 43/104 (41%), Positives = 63/104 (60%), Gaps = 3/104 (2%)
Query: 56 MNIMRKQNLLCDVKLIADGVEVAAHKMVLAACSPYFHAMFISFEESKQERIVLKGVDPNA 115
+N +R+ LCDV L+ E AHK VLAACSPYF A+F +E I L+ V P
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFKALFTGNKEV---EITLEDVSPED 57
Query: 116 LKLLIDYVYSCEIYVTEENVQMLLPAANLLQLTDVRDACCDFLQ 159
+ L++++Y+ ++ +TEENV LL A+ LQ+ + D C +FL
Sbjct: 58 FEALLEFIYTGKLEITEENVDDLLALADKLQIPALIDKCEEFLI 101
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 101 bits (255), Expect = 8e-26
Identities = 40/97 (41%), Positives = 60/97 (61%), Gaps = 1/97 (1%)
Query: 67 DVKLIADGVEVAAHKMVLAACSPYFHAMFIS-FEESKQERIVLKGVDPNALKLLIDYVYS 125
DV L+ G + AHK VLAA SPYF A+F S F+ES + I L V P + L++++Y+
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPEDFRALLNFLYT 60
Query: 126 CEIYVTEENVQMLLPAANLLQLTDVRDACCDFLQCQL 162
++ + EENV+ LL A+ LQ+ + + C +FL L
Sbjct: 61 GKLDLPEENVEELLELADYLQIPGLVELCEEFLLKLL 97
>gnl|CDD|240198 cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs1_sc1: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 1 (hs1) and S.
cerevisiae S1 repeat 1 (sc1). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 100
Score = 88.4 bits (220), Expect = 4e-21
Identities = 41/94 (43%), Positives = 57/94 (60%), Gaps = 5/94 (5%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSN-----GTIEEIPELSNL 520
+LG VKEIT L+I LPN L+ V IT ISD Y++ LE+ EE+P+L +L
Sbjct: 7 VLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDL 66
Query: 521 FSIGDLVVAKILECVTNNLGQKQIKASLNPHHVN 554
FS+G LV K++ + G+K+I+ SL P VN
Sbjct: 67 FSVGQLVRCKVVSLDKSKSGKKRIELSLEPELVN 100
>gnl|CDD|128874 smart00612, Kelch, Kelch domain.
Length = 47
Score = 74.5 bits (184), Expect = 9e-17
Identities = 27/47 (57%), Positives = 29/47 (61%)
Query: 409 LIYAVGGFDGSSGLNSAEVYDPSTEKWNMIAPMSTRRSSVGVGVLNG 455
IY VGGFDG L S EVYDP T KW + M T RS GV V+NG
Sbjct: 1 KIYVVGGFDGGQRLKSVEVYDPETNKWTPLPSMPTPRSGHGVAVING 47
Score = 63.0 bits (154), Expect = 1e-12
Identities = 23/45 (51%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 777 VGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDN 821
VGG+DG Q L SVE+Y PE N W P+ M RSG GV V++
Sbjct: 5 VGGFDG--GQRLKSVEVYDPETNKWTPLPSMPTPRSGHGVAVING 47
Score = 59.1 bits (144), Expect = 2e-11
Identities = 24/46 (52%), Positives = 30/46 (65%), Gaps = 5/46 (10%)
Query: 367 KVYAVGGFNG-----SLRVYDPSTNEWSSAPPMEARRSTLGVAVLN 407
K+Y VGGF+G S+ VYDP TN+W+ P M RS GVAV+N
Sbjct: 1 KIYVVGGFDGGQRLKSVEVYDPETNKWTPLPSMPTPRSGHGVAVIN 46
Score = 53.3 bits (129), Expect = 3e-09
Identities = 19/39 (48%), Positives = 22/39 (56%)
Query: 823 LYAVGGHDGPLVRKSVEAYDPETQTWSGVPDMALCRRNA 861
+Y VGG DG KSVE YDPET W+ +P M R
Sbjct: 2 IYVVGGFDGGQRLKSVEVYDPETNKWTPLPSMPTPRSGH 40
Score = 50.2 bits (121), Expect = 3e-08
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 324 VVGGQAPK-AIRSVECYDFKTERWQSVAEMPTRRCRAGLVFLHE 366
VVGG ++SVE YD +T +W + MPT R G+ ++
Sbjct: 4 VVGGFDGGQRLKSVEVYDPETNKWTPLPSMPTPRSGHGVAVING 47
>gnl|CDD|201739 pfam01344, Kelch_1, Kelch motif. The kelch motif was initially
discovered in Kelch. In this protein there are six
copies of the motif. It has been shown that the
Drosophila ring canal kelch protein is related to
Galactose Oxidase, for which a structure has been
solved. The kelch motif forms a beta sheet. Several of
these sheets associate to form a beta propeller
structure as found in pfam00064, pfam00400 and
pfam00415.
Length = 46
Score = 63.4 bits (155), Expect = 7e-13
Identities = 22/46 (47%), Positives = 27/46 (58%)
Query: 397 RRSTLGVAVLNSLIYAVGGFDGSSGLNSAEVYDPSTEKWNMIAPMS 442
RS GV VL IY +GG+DG L+S EVYDP T W+ + M
Sbjct: 1 PRSGAGVVVLGGKIYVIGGYDGGQSLSSVEVYDPETNTWSKLPSMP 46
Score = 63.1 bits (154), Expect = 1e-12
Identities = 26/45 (57%), Positives = 30/45 (66%)
Query: 810 KRSGAGVGVLDNILYAVGGHDGPLVRKSVEAYDPETQTWSGVPDM 854
RSGAGV VL +Y +GG+DG SVE YDPET TWS +P M
Sbjct: 1 PRSGAGVVVLGGKIYVIGGYDGGQSLSSVEVYDPETNTWSKLPSM 45
Score = 53.0 bits (128), Expect = 3e-09
Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 5/45 (11%)
Query: 355 RRCRAGLVFLHEKVYAVGGFNG-----SLRVYDPSTNEWSSAPPM 394
R AG+V L K+Y +GG++G S+ VYDP TN WS P M
Sbjct: 1 PRSGAGVVVLGGKIYVIGGYDGGQSLSSVEVYDPETNTWSKLPSM 45
Score = 43.4 bits (103), Expect = 7e-06
Identities = 18/31 (58%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 777 VGGYDGISRQCLSSVEMYSPERNTWEPVKDM 807
+GGYDG Q LSSVE+Y PE NTW + M
Sbjct: 17 IGGYDGG--QSLSSVEVYDPETNTWSKLPSM 45
Score = 39.6 bits (93), Expect = 2e-04
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 321 VMLVVGGQAP-KAIRSVECYDFKTERWQSVAEMP 353
+ V+GG +++ SVE YD +T W + MP
Sbjct: 13 KIYVIGGYDGGQSLSSVEVYDPETNTWSKLPSMP 46
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 72.0 bits (176), Expect = 8e-13
Identities = 86/419 (20%), Positives = 174/419 (41%), Gaps = 65/419 (15%)
Query: 45 NVHHTSKAFETMNIMRKQNLLCDVKL-IADGVEVAAHKMVLAACSPYFHAMFIS--FEES 101
++ H + ++ + ++LCDV + I DG E+ AHK +LAA S YF +F +
Sbjct: 5 DIKHNRRVVSNISNLLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRD 64
Query: 102 KQERIVLKGVDPNALKLLIDYVYSCEIYVTEENVQMLLPAANLLQLTDVRDACCDFLQCQ 161
R+ L+ D +A+K ++ Y+Y+ +++ NV +L A+ L + D+ C +++
Sbjct: 65 LVTRVNLQMFDKDAVKNIVQYLYN--RHISSMNVIDVLKCADYLLIDDLVTDCESYIKDY 122
Query: 162 LHPTNCLGI--RAFADLHSCLDLLSTAENYIELHFAEIVECEEFLSLSHEQVLGLISS-D 218
+ C+ + R + H + ++ + + + ++ + F E + +IS+ D
Sbjct: 123 TNHDTCIYMYHRLYEMSH--IPIVKYIKRMLMSNIPTLITTDAFKKTVFEILFDIISTND 180
Query: 219 KLMVSNEEKVFECVIAWVNYDLESRQK--------HVAELMEYVRLPLLSE--------- 261
+ + E ++ W+ Y+ + ++ + L + RL L S
Sbjct: 181 NVYLYREGYKVTILLKWLEYNYITEEQLLCILSCIDIQNLDKKSRLLLYSNKTINMYPSC 240
Query: 262 -DYLIQRVEEETVFKND--IRCKD------------YLIEALKYHIL--VKKGEVNKLTL 304
+L+ + + + C D Y I ++Y ++ + +N +
Sbjct: 241 IQFLLDNKQNRNIIPRQLCLVCHDTKYNVCNPCILVYNINTMEYSVISTIPNHIINYASA 300
Query: 305 VRTPRTKPRQPLRVPKVMLVVGGQAPKAIRSVECYDFKTERWQSVAEMP---TRRCRAGL 361
+ V +++ GG + Y E V E+P RCR L
Sbjct: 301 I------------VDNEIIIAGGYNFNNPSLNKVYKINIENKIHV-ELPPMIKNRCRFSL 347
Query: 362 VFLHEKVYAVGGFNG-----SLRVYDPSTNEWSSAPPMEARRSTLGVAVLNSLIYAVGG 415
+ + +YA+GG NG ++ Y ++W P M S+ G+ VL+ IY +GG
Sbjct: 348 AVIDDTIYAIGGQNGTNVERTIECYTMGDDKWKMLPDMPIALSSYGMCVLDQYIYIIGG 406
Score = 49.6 bits (118), Expect = 8e-06
Identities = 33/130 (25%), Positives = 58/130 (44%), Gaps = 14/130 (10%)
Query: 339 YDFKTERWQSVAEMPTRRCRAGLVFLHEKVYAVGGFNGSLRVYDPSTNE----------W 388
Y+ T + ++ +P + ++ GG+N + +PS N+
Sbjct: 277 YNINTMEYSVISTIPNHIINYASAIVDNEIIIAGGYNFN----NPSLNKVYKINIENKIH 332
Query: 389 SSAPPMEARRSTLGVAVLNSLIYAVGGFDGSSGLNSAEVYDPSTEKWNMIAPMSTRRSSV 448
PPM R +AV++ IYA+GG +G++ + E Y +KW M+ M SS
Sbjct: 333 VELPPMIKNRCRFSLAVIDDTIYAIGGQNGTNVERTIECYTMGDDKWKMLPDMPIALSSY 392
Query: 449 GVGVLNGCLY 458
G+ VL+ +Y
Sbjct: 393 GMCVLDQYIY 402
Score = 45.4 bits (107), Expect = 1e-04
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 775 IGVGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDGPLV 834
I GGY+ + L+ V + E + M+ R + V+D+ +YA+GG +G V
Sbjct: 307 IIAGGYN-FNNPSLNKVYKINIENKIHVELPPMIKNRCRFSLAVIDDTIYAIGGQNGTNV 365
Query: 835 RKSVEAYDPETQTWSGVPDM 854
+++E Y W +PDM
Sbjct: 366 ERTIECYTMGDDKWKMLPDM 385
Score = 32.3 bits (73), Expect = 1.5
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 776 GVGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGG 828
+GG +G + + ++E Y+ + W+ + DM S G+ VLD +Y +GG
Sbjct: 356 AIGGQNGTNVE--RTIECYTMGDDKWKMLPDMPIALSSYGMCVLDQYIYIIGG 406
>gnl|CDD|240199 cd05694, S1_Rrp5_repeat_hs2_sc2, S1_Rrp5_repeat_hs2_sc2: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 2 (hs2) and S.
cerevisiae S1 repeat 2 (sc2). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 74
Score = 63.8 bits (156), Expect = 1e-12
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 562 LETGLVLPACVHSKEDHGYLLDVGVKNTRAFI------KYDSVILGQIVTCMISKIKVAA 615
L G+VL CV S EDHGY+LD+G+ T F+ + + +GQ++ C++ K+K
Sbjct: 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDG 61
Query: 616 SMSIL 620
+ L
Sbjct: 62 RVVSL 66
>gnl|CDD|165153 PHA02790, PHA02790, Kelch-like protein; Provisional.
Length = 480
Score = 64.7 bits (157), Expect = 1e-10
Identities = 80/386 (20%), Positives = 161/386 (41%), Gaps = 43/386 (11%)
Query: 72 ADGVEVAAHKMVLAACSPYFHAMFISFEESKQERI--VLKGVDPNALKLLIDYVYSCEIY 129
A G + + +L SPYF ++ + V +D ++L ++ Y Y+ ++Y
Sbjct: 28 AIGGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYTGKVY 87
Query: 130 VTEENVQMLLPAANLLQLTDVRDACCDFLQCQLHPTNCLGIRAFADLHSCLDLLSTAENY 189
+ NV LL A+ L + + C +F+ C+ + +LL +++
Sbjct: 88 IDSHNVVNLLRASILTSVEFIIYTCINFILRDFRKEYCVECYMMGIEYGLSNLLCHTKDF 147
Query: 190 IELHFAE----IVECEEFLSLSHEQVLGLISSDKLMVSNEEKVFECVIAWVNYDLESRQK 245
I HF E I++ ++LS+ ++ SD+L V +E+ V + VI W R+
Sbjct: 148 IAKHFLELEDDIIDNFDYLSMKL-----ILESDELNVPDEDYVVDFVIKW----YMKRRN 198
Query: 246 HVAELMEYVRLPLLSEDYLIQR--------VEEETVFKNDIRCKDYLIEALKYHILVKKG 297
+ L+ ++ ++ +YL R ++ +F D + + ++ KY +
Sbjct: 199 RLGNLLLLIK-NVIRSNYLSPRGINNVKWILDCTKIFHCDKQPR----KSYKYPFIEYPM 253
Query: 298 EVNKLTLVRTPRTKPRQPLRVPKVMLVVGGQAPKAIR----SVECYDFKTERWQSVAEMP 353
++++ + T V +V+ ++GG I +V + W + M
Sbjct: 254 NMDQIIDIFHMCTST----HVGEVVYLIGGWMNNEIHNNAIAVNYI---SNNWIPIPPMN 306
Query: 354 TRRCRAGLVFLHEKVYAVGGFNG--SLRVYDPSTNEWSSAPPMEARRSTLGVAVLNSLIY 411
+ R A V + K+Y VGG S+ + W + P + R VA +N++IY
Sbjct: 307 SPRLYASGVPANNKLYVVGGLPNPTSVERWFHGDAAWVNMPSLLKPRCNPAVASINNVIY 366
Query: 412 AVGGFDGSSGLNSAEVYDPSTEKWNM 437
+GG + + E P+ ++W
Sbjct: 367 VIGGHSETD--TTTEYLLPNHDQWQF 390
Score = 36.6 bits (84), Expect = 0.075
Identities = 17/60 (28%), Positives = 29/60 (48%)
Query: 790 SVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDGPLVRKSVEAYDPETQTWS 849
+ E Y NTW + D +Y R + ++DN L +GG ++E Y+ T +W+
Sbjct: 416 NAEFYCESSNTWTLIDDPIYPRDNPELIIVDNKLLLIGGFYRGSYIDTIEVYNNRTYSWN 475
Score = 30.4 bits (68), Expect = 5.9
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 799 NTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDGPLVRKSVEAYDPETQTWSGVPDMALCR 858
N W P+ M R A +N LY VGG P SVE + W +P + R
Sbjct: 297 NNWIPIPPMNSPRLYASGVPANNKLYVVGGLPNP---TSVERWFHGDAAWVNMPSLLKPR 353
Query: 859 RNAVLESV 866
N + S+
Sbjct: 354 CNPAVASI 361
Score = 30.0 bits (67), Expect = 6.7
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 789 SSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNILYAVGGHDGPLVRKSVEAYDPETQTW 848
+SVE + W + +L R V ++N++Y +GGH + E P W
Sbjct: 331 TSVERWFHGDAAWVNMPSLLKPRCNPAVASINNVIYVIGGHSE--TDTTTEYLLPNHDQW 388
Query: 849 SGVP 852
P
Sbjct: 389 QFGP 392
>gnl|CDD|206134 pfam13964, Kelch_6, Kelch motif.
Length = 50
Score = 43.6 bits (103), Expect = 8e-06
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 403 VAVLNSLIYAVGGF-DGSSGLNSAEVYDPSTEKWNMIAPMSTRR 445
+ IY GG+ +GS N VYDP T W + P+ T R
Sbjct: 7 AVSVGGKIYVFGGYSNGSKASNKVLVYDPETGSWEKLPPLPTPR 50
Score = 40.5 bits (95), Expect = 9e-05
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 356 RCRAGLVFLHEKVYAVGGFNGSLR------VYDPSTNEWSSAPPMEARR 398
R V + K+Y GG++ + VYDP T W PP+ R
Sbjct: 2 RTGHSAVSVGGKIYVFGGYSNGSKASNKVLVYDPETGSWEKLPPLPTPR 50
Score = 35.5 bits (82), Expect = 0.007
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 811 RSGAGVGVLDNILYAVGGHDGPLVRKS-VEAYDPETQTWSGVPDM 854
R+G + +Y GG+ + V YDPET +W +P +
Sbjct: 2 RTGHSAVSVGGKIYVFGGYSNGSKASNKVLVYDPETGSWEKLPPL 46
Score = 34.3 bits (79), Expect = 0.014
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 324 VVGG--QAPKAIRSVECYDFKTERWQSVAEMPTRR 356
V GG KA V YD +T W+ + +PT R
Sbjct: 16 VFGGYSNGSKASNKVLVYDPETGSWEKLPPLPTPR 50
Score = 30.5 bits (69), Expect = 0.40
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 778 GGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKR 811
GGY S+ + V +Y PE +WE + + R
Sbjct: 18 GGYSNGSKA-SNKVLVYDPETGSWEKLPPLPTPR 50
>gnl|CDD|177844 PLN02193, PLN02193, nitrile-specifier protein.
Length = 470
Score = 48.4 bits (115), Expect = 1e-05
Identities = 33/111 (29%), Positives = 51/111 (45%), Gaps = 14/111 (12%)
Query: 345 RWQSV---AEMPTRRCRAGLVFLHEKVYAVGG-------FNGSLRVYDPSTNEWSSAPPM 394
+W V E P RC G+ + K+Y+ GG + L V+D T WS +P
Sbjct: 152 KWIKVEQKGEGPGLRCSHGIAQVGNKIYSFGGEFTPNQPIDKHLYVFDLETRTWSISPAT 211
Query: 395 E--ARRSTLGVAVLN--SLIYAVGGFDGSSGLNSAEVYDPSTEKWNMIAPM 441
S LGV +++ S +Y GG D S N +D +T +W ++ P+
Sbjct: 212 GDVPHLSCLGVRMVSIGSTLYVFGGRDASRQYNGFYSFDTTTNEWKLLTPV 262
Score = 41.5 bits (97), Expect = 0.002
Identities = 36/145 (24%), Positives = 60/145 (41%), Gaps = 13/145 (8%)
Query: 318 VPKVMLVVGGQ-APKAIRSVECYDFKTERWQ---SVAEMPTRRCRAGLVFLHEKVYAVGG 373
+ + V GG+ A + +D T W+ V E PT R + E VY GG
Sbjct: 227 IGSTLYVFGGRDASRQYNGFYSFDTTTNEWKLLTPVEEGPTPRSFHSMAADEENVYVFGG 286
Query: 374 FNGSLRV-----YDPSTNEW-SSAPPMEA--RRSTLGVAVLNSLIYAVGGFDGSSGLNSA 425
+ + R+ Y+ +W + P ++ R G+ V+ ++ V GF+G ++
Sbjct: 287 VSATARLKTLDSYNIVDKKWFHCSTPGDSFSIRGGAGLEVVQGKVWVVYGFNGCE-VDDV 345
Query: 426 EVYDPSTEKWNMIAPMSTRRSSVGV 450
YDP +KW + R S V
Sbjct: 346 HYYDPVQDKWTQVETFGVRPSERSV 370
Score = 39.6 bits (92), Expect = 0.007
Identities = 30/119 (25%), Positives = 50/119 (42%), Gaps = 10/119 (8%)
Query: 307 TPRTKPRQPLRVPKVMLVVGGQAPKAIRSVECYDFKTERW---QSVAEMPTRRCRAGLVF 363
TPR+ V + G A +++++ Y+ ++W + + + R AGL
Sbjct: 267 TPRSFHSMAADEENVYVFGGVSATARLKTLDSYNIVDKKWFHCSTPGDSFSIRGGAGLEV 326
Query: 364 LHEKVYAVGGFNG----SLRVYDPSTNEWSSAPPMEAR---RSTLGVAVLNSLIYAVGG 415
+ KV+ V GFNG + YDP ++W+ R RS A + I GG
Sbjct: 327 VQGKVWVVYGFNGCEVDDVHYYDPVQDKWTQVETFGVRPSERSVFASAAVGKHIVIFGG 385
Score = 38.0 bits (88), Expect = 0.028
Identities = 27/109 (24%), Positives = 48/109 (44%), Gaps = 12/109 (11%)
Query: 339 YDFKTERWQ---SVAEMPTRRCRA-GLVFLHEKVYAVGGFNGSLRV-----YDPSTNEWS 389
+D +T W + ++P C +V + +Y GG + S + +D +TNEW
Sbjct: 198 FDLETRTWSISPATGDVPHLSCLGVRMVSIGSTLYVFGGRDASRQYNGFYSFDTTTNEWK 257
Query: 390 SAPPME---ARRSTLGVAVLNSLIYAVGGFDGSSGLNSAEVYDPSTEKW 435
P+E RS +A +Y GG ++ L + + Y+ +KW
Sbjct: 258 LLTPVEEGPTPRSFHSMAADEENVYVFGGVSATARLKTLDSYNIVDKKW 306
>gnl|CDD|177814 PLN02153, PLN02153, epithiospecifier protein.
Length = 341
Score = 47.7 bits (113), Expect = 2e-05
Identities = 28/100 (28%), Positives = 44/100 (44%), Gaps = 11/100 (11%)
Query: 353 PTRRCRAGLVFLHEKVYAVGG-------FNGSLRVYDPSTNEWSSAPPM--EARRSTLGV 403
P RC G+ + +K+Y+ GG + L V+D +T+ WS AP R S LGV
Sbjct: 20 PGPRCSHGIAVVGDKLYSFGGELKPNEHIDKDLYVFDFNTHTWSIAPANGDVPRISCLGV 79
Query: 404 --AVLNSLIYAVGGFDGSSGLNSAEVYDPSTEKWNMIAPM 441
+ + +Y GG D + YD +W + +
Sbjct: 80 RMVAVGTKLYIFGGRDEKREFSDFYSYDTVKNEWTFLTKL 119
Score = 35.0 bits (80), Expect = 0.19
Identities = 32/158 (20%), Positives = 56/158 (35%), Gaps = 27/158 (17%)
Query: 320 KVMLVVGGQAPKAIRSVECYDFKTERWQSVAEM-----PTRRCRAGLVFLHEKVYAVGGF 374
K+ + G + YD W + ++ P R + VY GG
Sbjct: 87 KLYIFGGRDEKREFSDFYSYDTVKNEWTFLTKLDEEGGPEARTFHSMASDENHVYVFGGV 146
Query: 375 NG-----------SLRVYDPSTNEWSSAP-PME--ARRSTLGVAVLNSLIYAVGGFDGSS 420
+ ++ Y+ + +W P P E +R G AV+ I+ V GF S
Sbjct: 147 SKGGLMKTPERFRTIEAYNIADGKWVQLPDPGENFEKRGGAGFAVVQGKIWVVYGFATSI 206
Query: 421 --------GLNSAEVYDPSTEKWNMIAPMSTRRSSVGV 450
N+ + +DP++ KW + + S+ V
Sbjct: 207 LPGGKSDYESNAVQFFDPASGKWTEVETTGAKPSARSV 244
>gnl|CDD|211835 TIGR03548, mutarot_permut, cyclically-permuted mutarotase family
protein. Members of this protein family show
essentially full-length homology, cyclically permuted,
to YjhT from Escherichia coli. YjhT was shown to act as
a mutarotase for sialic acid, and by this ability to be
able to act as a virulence factor. Members of the YjhT
family (TIGR03547) and this cyclically-permuted family
have multiple repeats of the beta-propeller-forming
Kelch repeat.
Length = 323
Score = 47.5 bits (113), Expect = 2e-05
Identities = 30/126 (23%), Positives = 52/126 (41%), Gaps = 13/126 (10%)
Query: 320 KVMLVVGGQAPKAIRSVECYDFKTERWQSVAEMPTR-RCRAGLVFLHEKVYAVGGFNGSL 378
K+ + G K C++ +T+ W+ + + P R + V L ++Y GG +
Sbjct: 125 KLYVGGGNANGKPSNKFYCFNLETQEWEELPDFPGAPRVQPVCVKLQNELYVFGGGDNIA 184
Query: 379 RV----YDPSTNEWS--SAPPMEARRSTL----GVAVLNSLIYAVGGFDGSSGLNSAEVY 428
Y P T W + P + +L +A+ SL+ +GGF+ N A V
Sbjct: 185 YTDGYKYSPKTGTWEKVADPLSDGEPISLLGAASIAINESLLLCIGGFN-YDVFNDA-VI 242
Query: 429 DPSTEK 434
+T K
Sbjct: 243 RLATMK 248
Score = 29.7 bits (67), Expect = 8.0
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 334 RSVECYDFKTERWQSVAEMP-TRRCRAGLVFLHEKVYAVGG 373
V YD ++ +W+S+ P RC A L+ ++ + G
Sbjct: 271 DKVLIYDVRSGKWKSIGNSPFVARCGAALLLTGNNLFVING 311
Score = 29.3 bits (66), Expect = 9.2
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 794 YSPERNTWEPVKDMLYKR------SGAGVGVLDNILYAVGGHDGPLVRKSVEAYDPET 845
YSP+ TWE V D L A + + +++L +GG + + +V T
Sbjct: 191 YSPKTGTWEKVADPLSDGEPISLLGAASIAINESLLLCIGGFNYDVFNDAV--IRLAT 246
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 42.2 bits (100), Expect = 4e-05
Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 17/84 (20%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
+ G V EIT G ++L N + + I+E+SD + + + +G
Sbjct: 5 VVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKR--------------VKDPEEVLKVG 50
Query: 525 DLVVAKILECVTNNLGQKQIKASL 548
D V K+L + + +I SL
Sbjct: 51 DEVKVKVLSV---DEEKGRIILSL 71
Score = 37.6 bits (88), Expect = 0.002
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 948 KPGRLVWGVLKEKMPGGVRVEFDGDISGVFPTSAMSQATRTLVYTRFVIDTVIVCQILKY 1007
+ G +V G + E PGG V+ + G+ P S +S + + ++L
Sbjct: 1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 1008 --EDGELLLT 1015
E G ++L+
Sbjct: 61 DEEKGRIILS 70
>gnl|CDD|222113 pfam13415, Kelch_3, Galactose oxidase, central domain.
Length = 48
Score = 40.4 bits (95), Expect = 1e-04
Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 1/48 (2%)
Query: 407 NSLIYAVGGFDGSSG-LNSAEVYDPSTEKWNMIAPMSTRRSSVGVGVL 453
IY GG LN VYD T W + + R+ V+
Sbjct: 1 GGKIYVFGGLGDGGTRLNDLWVYDLDTNTWEKLGDLPGPRAGHAATVI 48
Score = 38.4 bits (90), Expect = 6e-04
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 777 VGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVL 819
GG L+ + +Y + NTWE + D+ R+G V+
Sbjct: 7 FGGLGD-GGTRLNDLWVYDLDTNTWEKLGDLPGPRAGHAATVI 48
Score = 31.9 bits (73), Expect = 0.12
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 322 MLVVGGQAPKAIRS--VECYDFKTERWQSVAEMPTRRC 357
+ V GG R + YD T W+ + ++P R
Sbjct: 4 IYVFGGLGDGGTRLNDLWVYDLDTNTWEKLGDLPGPRA 41
Score = 31.1 bits (71), Expect = 0.23
Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 6/47 (12%)
Query: 366 EKVYAVGGFNGSLR------VYDPSTNEWSSAPPMEARRSTLGVAVL 406
K+Y GG VYD TN W + R+ V+
Sbjct: 2 GKIYVFGGLGDGGTRLNDLWVYDLDTNTWEKLGDLPGPRAGHAATVI 48
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 45.5 bits (109), Expect = 1e-04
Identities = 42/202 (20%), Positives = 76/202 (37%), Gaps = 41/202 (20%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
+ G VK ITD+G + L + VH+++IS ++ E L+ G
Sbjct: 376 VVEGKVKNITDFGAFVGLEGGIDGLVHLSDIS-------------WDKKGEEAVELYKKG 422
Query: 525 DLVVAKILECVTNN----LGQKQIKASLNPHHVNEMYINTTLETGLVLPACVHSKEDHGY 580
D V A +L+ LG KQ L E + G ++ V +D G
Sbjct: 423 DEVEAVVLKVDVEKERISLGIKQ----LEEDPFEE--FAKKHKKGSIVTGTVTEVKDKGA 476
Query: 581 LLDVGVKNTRAFIK------------YDSVILGQIVTCMISKI-----KVAASMSILEVT 623
+++ I+ + + +G V + I +++ S+ L+
Sbjct: 477 FVELE-DGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 535
Query: 624 LDEELIRSANRLSPSQVSLLNL 645
++E I N S S+ +L +L
Sbjct: 536 EEKEAIAEYNSASDSKTTLGDL 557
Score = 31.7 bits (73), Expect = 2.5
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 19/90 (21%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
++ G V ITD+G +EL + VH++E+S ++ + S + S+G
Sbjct: 289 KVKGKVTNITDYGAFVELEEGIEGLVHVSEMS---------WTK----KNKHPSKVVSVG 335
Query: 525 DLVVAKILECVTNN----LGQKQIKASLNP 550
V +LE LG KQ K NP
Sbjct: 336 QEVEVMVLEIDEEKRRISLGLKQCKE--NP 363
>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
structure and biogenesis].
Length = 541
Score = 45.8 bits (109), Expect = 1e-04
Identities = 39/175 (22%), Positives = 67/175 (38%), Gaps = 33/175 (18%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
+ G VK ITD+G +EL + VH++++S + G
Sbjct: 366 VVEGKVKSITDFGAFVELEGGIDGLVHLSDLSW------------DRPGEEAE--KYKKG 411
Query: 525 DLVVAKILECVTNN----LGQKQIKASLNP-HHVNEMYINTTLETGLVLPACVHSKEDHG 579
D V AK+L LG KQ++ +P +E Y + V+ V S +D G
Sbjct: 412 DEVEAKVLAVDKEKERISLGIKQLEE--SPWEEFSEKYKKGS-----VVKGKVKSVKDKG 464
Query: 580 YLLDVGVKNT----RAFIKYDSVILGQIVTCMISKI---KVAASMSILEVTLDEE 627
+++G + + D + +G V ++ I +SI + EE
Sbjct: 465 AFVELGGGVEGLIRLSELSRDVLKVGDEVEAVVVSIDKKNRKILLSIKALERKEE 519
Score = 44.2 bits (105), Expect = 3e-04
Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 20/94 (21%)
Query: 461 NLDGRILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNL 520
+ ++ G V +TD+G +E+ + VH++EIS S +
Sbjct: 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTK--------------KNVPSEV 321
Query: 521 FSIGDLVVAKILECVTNN----LGQKQIKASLNP 550
+G V K+L+ LG KQ+K NP
Sbjct: 322 VKVGQEVEVKVLDIDPERRRISLGLKQLKE--NP 353
Score = 37.3 bits (87), Expect = 0.049
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 15/68 (22%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGD 525
+ G VK ITD+G +++ +HI+EIS D + +GD
Sbjct: 196 VEGVVKNITDYGAFVDIGGV-DGLLHISEISWKRVDHPSEV--------------VKVGD 240
Query: 526 LVVAKILE 533
V K++
Sbjct: 241 EVKVKVIS 248
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal protein.
This superfamily also contains the Cold Shock Domain
(CSD), which is a homolog of the S1 domain. Both domains
are members of the Oligonucleotide/oligosaccharide
Binding (OB) fold.
Length = 65
Score = 39.7 bits (93), Expect = 3e-04
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 14/67 (20%)
Query: 468 GCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLV 527
G V IT +G+ +EL + + VHI+E+SD + + + S +F +GD V
Sbjct: 3 GKVVSITKFGVFVELEDGVEGLVHISELSDKF--------------VKDPSEVFKVGDEV 48
Query: 528 VAKILEC 534
K+LE
Sbjct: 49 EVKVLEV 55
Score = 34.3 bits (79), Expect = 0.022
Identities = 10/57 (17%), Positives = 22/57 (38%)
Query: 955 GVLKEKMPGGVRVEFDGDISGVFPTSAMSQATRTLVYTRFVIDTVIVCQILKYEDGE 1011
G + GV VE + + G+ S +S F + + ++L+ + +
Sbjct: 3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
>gnl|CDD|237617 PRK14131, PRK14131, N-acetylneuraminic acid mutarotase;
Provisional.
Length = 376
Score = 43.9 bits (104), Expect = 4e-04
Identities = 36/143 (25%), Positives = 48/143 (33%), Gaps = 56/143 (39%)
Query: 345 RWQSVAEMPT-RRCRAGLVFLHEKVYAVGGF-----NGSLRV------YDPSTNEWS--- 389
W +A P R +A F+ K+Y GG GS +V YDP TN W
Sbjct: 63 GWTKIAAFPGGPREQAVAAFIDGKLYVFGGIGKTNSEGSPQVFDDVYKYDPKTNSWQKLD 122
Query: 390 SAPPMEARRSTLG---VAVLNSLIYAVGG-----FDG------SSGLNSAE--------- 426
+ P G V++ N Y GG FDG ++G +
Sbjct: 123 TRSP----VGLAGHVAVSLHNGKAYITGGVNKNIFDGYFEDLAAAGKDKTPKDKINDAYF 178
Query: 427 --------------VYDPSTEKW 435
YDPST +W
Sbjct: 179 DKKPEDYFFNKEVLSYDPSTNQW 201
Score = 34.6 bits (80), Expect = 0.23
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 801 WEPVKDML-YKRSGAGVGVLDNILYAVGG-----HDGPL-VRKSVEAYDPETQTWSGVP 852
W + R A +D LY GG +G V V YDP+T +W +
Sbjct: 64 WTKIAAFPGGPREQAVAAFIDGKLYVFGGIGKTNSEGSPQVFDDVYKYDPKTNSWQKLD 122
Score = 30.4 bits (69), Expect = 4.9
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 404 AVLNSLIYAVGGF-----DGS-SGLNSAEVYDPSTEKWNMIAPMSTRRSSVGVGV-LNG 455
A ++ +Y GG +GS + YDP T W + S + V V L+
Sbjct: 81 AFIDGKLYVFGGIGKTNSEGSPQVFDDVYKYDPKTNSWQKLDTRSPVGLAGHVAVSLHN 139
>gnl|CDD|116261 pfam07646, Kelch_2, Kelch motif. The kelch motif was initially
discovered in Kelch. In this protein there are six
copies of the motif. It has been shown that Drosophila
ring canal kelch protein is related to Galactose Oxidase
for which a structure has been solved. The kelch motif
forms a beta sheet. Several of these sheets associate to
form a beta propeller structure as found in pfam00064,
pfam00400 and pfam00415.
Length = 48
Score = 38.5 bits (90), Expect = 5e-04
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 811 RSGAGVGVLDNILYAVGG--HDGPLVRKSVEAYDPETQTWSGVPDM 854
R V+ LY VGG G L + DPET W+ +P +
Sbjct: 2 RYPHASVVVGGKLYVVGGSTGLGDLSSSDLWVLDPETNVWTELPAL 47
Score = 35.0 bits (81), Expect = 0.009
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 355 RRCRAGLVFLHEKVYAVGGFNG-------SLRVYDPSTNEWSSAPPM 394
R V + K+Y VGG G L V DP TN W+ P +
Sbjct: 1 PRYPHASVVVGGKLYVVGGSTGLGDLSSSDLWVLDPETNVWTELPAL 47
Score = 31.2 bits (71), Expect = 0.17
Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 397 RRSTLGVAVLNSLIYAVGGFDGSSGL--NSAEVYDPSTEKW 435
R V+ +Y VGG G L + V DP T W
Sbjct: 1 PRYPHASVVVGGKLYVVGGSTGLGDLSSSDLWVLDPETNVW 41
Score = 28.5 bits (64), Expect = 1.8
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 777 VGGYDGISRQCLSSVEMYSPERNTWEPVKDM 807
VGG G+ S + + PE N W + +
Sbjct: 17 VGGSTGLGDLSSSDLWVLDPETNVWTELPAL 47
>gnl|CDD|205596 pfam13418, Kelch_4, Galactose oxidase, central domain.
Length = 49
Score = 38.0 bits (89), Expect = 6e-04
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 403 VAVLNSLIYAVGGFDGSSG-LNSAEVYDPSTEKWNMIAPM 441
++ + +Y GG + L+ V+D ST W + +
Sbjct: 8 TSIGDGRLYLFGGENEDGSVLSDVWVFDLSTNTWTRLPSL 47
Score = 33.4 bits (77), Expect = 0.032
Identities = 7/35 (20%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 322 MLVVGGQAPKAIRS--VECYDFKTERWQSVAEMPT 354
+ + GG+ V +D T W + +P+
Sbjct: 15 LYLFGGENEDGSVLSDVWVFDLSTNTWTRLPSLPS 49
Score = 33.4 bits (77), Expect = 0.036
Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 1/44 (2%)
Query: 812 SGAGVGVLDNILYAVGGHDGPLVR-KSVEAYDPETQTWSGVPDM 854
+ D LY GG + V +D T TW+ +P +
Sbjct: 4 YHTSTSIGDGRLYLFGGENEDGSVLSDVWVFDLSTNTWTRLPSL 47
Score = 33.0 bits (76), Expect = 0.045
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 356 RCRAGLVFLHE-KVYAVGGFNGS------LRVYDPSTNEWSSAPPM 394
R + + ++Y GG N + V+D STN W+ P +
Sbjct: 2 RAYHTSTSIGDGRLYLFGGENEDGSVLSDVWVFDLSTNTWTRLPSL 47
Score = 33.0 bits (76), Expect = 0.052
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 777 VGGYDGISRQCLSSVEMYSPERNTWEPVKDM 807
GG + LS V ++ NTW + +
Sbjct: 18 FGGENE-DGSVLSDVWVFDLSTNTWTRLPSL 47
>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5
is found in eukaryotes but not in prokaryotes or
archaea.
Length = 77
Score = 38.1 bits (89), Expect = 0.001
Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 466 ILGCVKEITDWGLIIELPNF-LSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
I G V+ + D+G+ I++ +S H +EISD + + S LF +G
Sbjct: 6 IDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISD--------------NRVADASKLFRVG 51
Query: 525 DLVVAKILECVTNNLGQKQIKASLNPHH 552
D V AK+L+ + +K+I L +
Sbjct: 52 DKVRAKVLKI---DAEKKRISLGLKASY 76
>gnl|CDD|240211 cd05706, S1_Rrp5_repeat_sc10, S1_Rrp5_repeat_sc10: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5
is found in eukaryotes but not in prokaryotes or
archaea.
Length = 73
Score = 36.1 bits (84), Expect = 0.006
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 17/86 (19%)
Query: 463 DGRILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFS 522
+ G V ++ D ++++L N ++ IT+ D YS+ L F
Sbjct: 4 GDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALP--------------YKFK 49
Query: 523 IGDLVVAKILECVTNNLGQKQIKASL 548
D+V A +L N K+I SL
Sbjct: 50 KNDIVRACVLSVDVPN---KKIALSL 72
>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional.
Length = 139
Score = 37.3 bits (87), Expect = 0.010
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 18/71 (25%)
Query: 462 LDGRILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLF 521
L G++ G IT++G +ELP + VHI+E++D Y +++I +
Sbjct: 9 LQGKVTG----ITNFGAFVELPEGKTGLVHISEVADNY-----------VKDIND---HL 50
Query: 522 SIGDLVVAKIL 532
+GD V K+L
Sbjct: 51 KVGDEVEVKVL 61
>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo
sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1
repeat 7 (sc7)-like domains. Rrp5 is a trans-acting
factor important for biogenesis of both the 40S and 60S
eukaryotic ribosomal subunits. Rrp5 has two distinct
regions, an N-terminal region containing tandemly
repeated S1 RNA-binding domains (12 S1 repeats in S.
cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and
a C-terminal region containing tetratricopeptide repeat
(TPR) motifs thought to be involved in protein-protein
interactions. Mutational studies have shown that each
region represents a specific functional domain. Deletions
within the S1-containing region inhibit pre-rRNA
processing at either site A3 or A2, whereas deletions
within the TPR region confer an inability to support
cleavage of A0-A2. This CD includes H. sapiens S1 repeat
8 and S. cerevisiae S1 repeat 7. Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 83
Score = 35.6 bits (83), Expect = 0.013
Identities = 18/59 (30%), Positives = 28/59 (47%)
Query: 948 KPGRLVWGVLKEKMPGGVRVEFDGDISGVFPTSAMSQATRTLVYTRFVIDTVIVCQILK 1006
KPG +V G ++ P GV VEF G ++G+ P S +S T F + ++
Sbjct: 13 KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTS 71
Score = 29.1 bits (66), Expect = 2.1
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 14/66 (21%)
Query: 468 GCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLV 527
G V+ IT +G+ +E L+ + ISD + + + S F G V
Sbjct: 20 GYVRNITPYGVFVEFLGGLTGLAPKSYISDEF--------------VTDPSFGFKKGQSV 65
Query: 528 VAKILE 533
AK+
Sbjct: 66 TAKVTS 71
>gnl|CDD|234253 TIGR03547, muta_rot_YjhT, mutatrotase, YjhT family. Members of
this protein family contain multiple copies of the
beta-propeller-forming Kelch repeat. All are full-length
homologs to YjhT of Escherichia coli, which has been
identified as a mutarotase for sialic acid. This protein
improves bacterial ability to obtain host sialic acid,
and thus serves as a virulence factor. Some bacteria
carry what appears to be a cyclically permuted homolog
of this protein.
Length = 346
Score = 38.5 bits (90), Expect = 0.015
Identities = 35/142 (24%), Positives = 48/142 (33%), Gaps = 56/142 (39%)
Query: 346 WQSVAEMPT-RRCRAGLVFLHEKVYAVGGF-----NGSLRV------YDPSTNEWS---S 390
WQ +A+ P R +A + K+Y GG GS +V YDP N W +
Sbjct: 43 WQKIADFPGGPRNQAVAAAIDGKLYVFGGIGKANSEGSPQVFDDVYRYDPKKNSWQKLDT 102
Query: 391 APPMEARRSTLG---VAVLNSLIYAVGG-----FDG------SSGLNSAE---------- 426
P LG ++ N Y GG FDG ++ +S
Sbjct: 103 RSP----VGLLGASGFSLHNGQAYFTGGVNKNIFDGYFADLSAADKDSEPKDKLIAAYFS 158
Query: 427 -------------VYDPSTEKW 435
YDPST +W
Sbjct: 159 QPPEDYFWNKNVLSYDPSTNQW 180
Score = 30.4 bits (69), Expect = 5.0
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 811 RSGAGVGVLDNILYAVGG-----HDGPL-VRKSVEAYDPETQTWSGVP 852
R+ A +D LY GG +G V V YDP+ +W +
Sbjct: 54 RNQAVAAAIDGKLYVFGGIGKANSEGSPQVFDDVYRYDPKKNSWQKLD 101
Score = 30.0 bits (68), Expect = 6.0
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 373 GFNGSLRVYDPSTNEWSSA 391
+N ++ YDPSTN+W +
Sbjct: 165 FWNKNVLSYDPSTNQWRNL 183
>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1. This model describes
ribosomal protein S1, RpsA. This protein is found in
most bacterial genomes in a single copy, but is not
present in the Mycoplasmas. It is heterogeneous with
respect to the number of repeats of the S1 RNA binding
domain described by PFAM model pfam00575: six repeats in
E. coli and most other bacteria, four in Bacillus
subtilis and some other species. rpsA is an essential
gene in E. coli but not in B. subtilis. It is associated
with the cytidylate kinase gene cmk in many species, and
fused to it in Treponema pallidum. RpsA is proposed
(Medline:97323001) to assist in mRNA degradation. This
model provides trusted hits to most long form (6 repeat)
examples of RpsA. Among homologs with only four repeats
are some to which other (perhaps secondary) functions
have been assigned [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 516
Score = 37.8 bits (88), Expect = 0.028
Identities = 25/90 (27%), Positives = 38/90 (42%), Gaps = 19/90 (21%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
+I G V +TD+G+ +E+ + VH++E+S + S + G
Sbjct: 275 KITGRVTNLTDYGVFVEIEEGIEGLVHVSEMS---------WVKKNSHP----SKVVKKG 321
Query: 525 DLVVAKILECVTNN----LGQKQIKASLNP 550
D V IL+ LG KQ KA NP
Sbjct: 322 DEVEVMILDIDPERRRLSLGLKQCKA--NP 349
Score = 30.1 bits (68), Expect = 7.3
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 16/84 (19%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
R+ G +K+ITD+G +EL + +H+++IS ++ E +L+ G
Sbjct: 362 RVTGKIKKITDFGAFVELEGGIDGLIHLSDIS-------------WDKDGREADHLYKKG 408
Query: 525 DLVVAKILECVTNNLGQKQIKASL 548
D + A +L + +K+I +
Sbjct: 409 DEIEAVVLAV---DKEKKRISLGV 429
>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal
protein S1 domain) [Translation, ribosomal structure and
biogenesis].
Length = 129
Score = 35.3 bits (82), Expect = 0.041
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 18/71 (25%)
Query: 462 LDGRILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLF 521
L G+I G IT +G +EL + VHI+EI+D + +++I +
Sbjct: 9 LKGKITG----ITPYGAFVELEGGKTGLVHISEIADGF-----------VKDIHD---HL 50
Query: 522 SIGDLVVAKIL 532
+G V K+L
Sbjct: 51 KVGQEVKVKVL 61
>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 69
Score = 33.4 bits (77), Expect = 0.050
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 468 GCVKEITDWGLIIELPNFLSASVHITEISDVY 499
G V + +G +EL +S VHI++I+
Sbjct: 6 GTVTRLKPFGAFVELGGGISGLVHISQIAHKR 37
>gnl|CDD|240209 cd05704, S1_Rrp5_repeat_hs13, S1_Rrp5_repeat_hs13: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is
found in eukaryotes but not in prokaryotes or archaea.
Length = 72
Score = 33.1 bits (76), Expect = 0.085
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 467 LGCV-KEITDWGLIIELPNFLSASVHITEISDVYSDL-LEKYSNGTI 511
LG V K I GL ++LP + V I +SD Y++ LE + G I
Sbjct: 8 LGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKI 54
>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 5 (ec5) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 69
Score = 32.5 bits (74), Expect = 0.11
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEIS 496
+ G +K ITD+G+ + L + VHI++IS
Sbjct: 3 VVSGKIKSITDFGIFVGLDGGIDGLVHISDIS 34
>gnl|CDD|240212 cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5
is found in eukaryotes but not in prokaryotes or
archaea.
Length = 68
Score = 32.3 bits (74), Expect = 0.13
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 17/80 (21%)
Query: 468 GCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLV 527
G VK I + G+ + L + A V ++E+SD Y + + F +G LV
Sbjct: 6 GFVKNIANNGVFVTLGRGVDARVRVSELSDSY--------------LKDWKKRFKVGQLV 51
Query: 528 VAKILECVTNNLGQKQIKAS 547
KI+ + +I+ +
Sbjct: 52 KGKIVSI---DPDNGRIEMT 68
>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a
wide range of RNA associated proteins. It is
structurally similar to cold shock protein which binds
nucleic acids. The S1 domain has an OB-fold structure.
Length = 74
Score = 31.8 bits (73), Expect = 0.19
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 14/70 (20%)
Query: 465 RILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIG 524
+ G V +T G ++L N + + I+EISD + + + +G
Sbjct: 7 VVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDR--------------VEDPDEVLKVG 52
Query: 525 DLVVAKILEC 534
D V K+L+
Sbjct: 53 DEVEVKVLKV 62
Score = 27.6 bits (62), Expect = 7.4
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 948 KPGRLVWGVLKEKMPGGVRVEFDGDISGVFPTSAMSQATRTLVYTRFVI-DTVIVCQILK 1006
+ G +V G + GG V+ + G P S +S + D V V ++LK
Sbjct: 3 EEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEV-KVLK 61
Query: 1007 YEDGE 1011
+
Sbjct: 62 VDKER 66
>gnl|CDD|225597 COG3055, COG3055, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 381
Score = 33.5 bits (77), Expect = 0.51
Identities = 32/116 (27%), Positives = 44/116 (37%), Gaps = 30/116 (25%)
Query: 346 WQSVAEMP-TRRCRAGLVFLHEKVYAVGGF----NGSLRV------YDPSTNEWSSAPPM 394
W +A+ P R +A + K+Y GG+ + S +V YDPSTN W
Sbjct: 72 WTKIADFPGGARNQAVAAVIGGKLYVFGGYGKSVSSSPQVFNDAYRYDPSTNSWH----K 127
Query: 395 EARRSTLG-----VAVLNSL-IYAVGG-----FDGS-SGLNSAEVYDPSTEKWNMI 438
RS G LN IY GG F+G + +A E + I
Sbjct: 128 LDTRSPTGLVGASTFSLNGTKIYFFGGVNQNIFNGYFEDVGAAGK---DKEAVDKI 180
Score = 32.3 bits (74), Expect = 1.2
Identities = 22/88 (25%), Positives = 30/88 (34%), Gaps = 24/88 (27%)
Query: 404 AVLNSLIYAVGGFDGSSG------LNSAEVYDPSTEKWNMIAPMSTR--RSSVG------ 449
AV+ +Y GG+ G S N A YDPST W+ + TR VG
Sbjct: 89 AVIGGKLYVFGGY-GKSVSSSPQVFNDAYRYDPSTNSWHK---LDTRSPTGLVGASTFSL 144
Query: 450 ----VGVLNGCLYAENLDGRILGCVKEI 473
+ G +N+ V
Sbjct: 145 NGTKIYFFGG--VNQNIFNGYFEDVGAA 170
Score = 30.8 bits (70), Expect = 3.8
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 330 PKAIRSVECYDFKTERWQSVAEMPTRRCRAGLVFLHEKVYAVGG 373
K+ S E Y F W+ V E+P + + KV +GG
Sbjct: 315 SKSWNS-EVYIFDNGSWKIVGELPQGLAYGVSLSYNNKVLLIGG 357
>gnl|CDD|240215 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like
RNA-binding domains are found in a wide variety of
RNA-associated proteins. Rrp4 protein is a subunit of
the exosome complex. The exosome plays a central role in
3' to 5' RNA processing and degradation in eukarytes and
archaea. Its functions include the removal of
incorrectly processed RNA and the maintenance of proper
levels of mRNA, rRNA and a number of small RNA species.
In Saccharomyces cerevisiae, the exosome includes nine
core components, six of which are homologous to
bacterial RNase PH. These form a hexameric ring
structure. The other three subunits (RrP4, Rrp40, and
Csl4) contain an S1 RNA binding domain and are part of
the "S1 pore structure".
Length = 86
Score = 29.8 bits (68), Expect = 1.6
Identities = 13/66 (19%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGD 525
++G V E+ +++ + A + ++E+ L + T E+ + + GD
Sbjct: 10 VIGRVTEVGFKRWKVDINSPYDAVLPLSEV------NLPR----TDEDELNMRSYLDEGD 59
Query: 526 LVVAKI 531
L+VA++
Sbjct: 60 LIVAEV 65
>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase
(PNPase), ), S1-like RNA-binding domain. PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA. It is a trimeric multidomain protein. The
C-terminus contains the S1 domain which binds ssRNA.
This family is classified based on the S1 domain. PNPase
nonspecifically removes the 3' nucleotides from mRNA,
but is stalled by double-stranded RNA structures such as
a stem-loop. Evidence shows that a minimum of 7-10
unpaired nucleotides at the 3' end, is required for
PNPase degradation. It is suggested that PNPase also
dephosphorylates the RNA 5' end. This additional
activity may regulate the 5'-dependent activity of
RNaseE in vivo.
Length = 68
Score = 29.0 bits (66), Expect = 1.6
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 15/71 (21%)
Query: 464 GRI-LGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFS 522
G+I G V +I D+G +E+ VHI+E+SD E + ++ ++
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSD--------------ERVEKVEDVLK 46
Query: 523 IGDLVVAKILE 533
+GD V K++E
Sbjct: 47 VGDEVKVKVIE 57
>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein
S1 (RPS1) domain. RPS1 is a component of the small
ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain. While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 6 (ec6) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog.
Length = 73
Score = 29.2 bits (66), Expect = 1.8
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 14/65 (21%)
Query: 468 GCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLV 527
G V E+ G ++L + + + E+S + + + + F +GD V
Sbjct: 6 GKVTEVDAKGATVKLGDGVEGFLRAAELS--------------RDRVEDATERFKVGDEV 51
Query: 528 VAKIL 532
AKI
Sbjct: 52 EAKIT 56
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 32.2 bits (74), Expect = 1.9
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 17/83 (20%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGD 525
+LG V I +G +EL + VHI++IS I + ++ S G+
Sbjct: 566 VLGKVVRIAPFGAFVELEPGVDGLVHISQISWK--------------RIDKPEDVLSEGE 611
Query: 526 LVVAKILECVTNNLGQKQIKASL 548
V AKILE K+I+ S+
Sbjct: 612 EVKAKILEVDPEE---KRIRLSI 631
>gnl|CDD|236547 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4;
Provisional.
Length = 189
Score = 31.1 bits (71), Expect = 2.1
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 14/52 (26%)
Query: 481 ELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLVVAKIL 532
EL A +HI+++SD Y + L++ F IGD+V AK++
Sbjct: 93 ELATSKLAYIHISQVSDGY--------------VESLTDAFKIGDIVRAKVI 130
>gnl|CDD|226984 COG4637, COG4637, Predicted ATPase [General function prediction
only].
Length = 373
Score = 31.7 bits (72), Expect = 2.2
Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 6/87 (6%)
Query: 78 AAHKMVLAACSPYFHAMFISFEESKQERIVLKGVDPNALKLLIDYVYSCEIYVTEENVQM 137
+++ A + + + + RI LK D L D +++ ++
Sbjct: 225 DIFQLIEAVMDAFPGIRLLEPKPGEDGRIELKWQDRGFLDPFRDR------ELSDGTLRF 278
Query: 138 LLPAANLLQLTDVRDACCDFLQCQLHP 164
L A LL D + LHP
Sbjct: 279 LALATLLLSPRPPPLLLLDEPETSLHP 305
>gnl|CDD|145924 pfam03034, PSS, Phosphatidyl serine synthase. Phosphatidyl serine
synthase is also known as serine exchange enzyme. This
family represents eukaryotic PSS I and II which are
membrane bound proteins which catalyzes the replacement
of the head group of a phospholipid (phosphotidylcholine
or phosphotidylethanolamine) by L-serine.
Length = 278
Score = 31.5 bits (72), Expect = 2.2
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 81 KMVLAACSPYFHAM-FISFEESKQERIVLKGVDPNALKLLI--DYVYSCEIYVTE 132
++VL Y A+ F+ F+ + R +LK +DP K L Y +C IY E
Sbjct: 7 RLVLGLSVLYLLALVFLLFQNYEDARQILKFIDPKLGKPLPERSYAENCRIYTPE 61
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 31.0 bits (71), Expect = 2.5
Identities = 15/66 (22%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGD 525
++G V ++T G +++ + A + + S++L + N E +L IGD
Sbjct: 67 VIGKVTDVTFSGWEVDINSPYKAYLPV-------SEVLGRPVNV---EGTDLRKYLDIGD 116
Query: 526 LVVAKI 531
++AK+
Sbjct: 117 YIIAKV 122
>gnl|CDD|240207 cd05702, S1_Rrp5_repeat_hs11_sc8, S1_Rrp5_repeat_hs11_sc8: Rrp5 is
a trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 11 (hs11) and S.
cerevisiae S1 repeat 8 (sc8). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 70
Score = 28.7 bits (65), Expect = 2.6
Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 12/63 (19%)
Query: 470 VKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLVVA 529
VK + L ++L + + +H++E+ D + D S F IG + A
Sbjct: 8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSK------------FKIGQKIKA 55
Query: 530 KIL 532
+++
Sbjct: 56 RVI 58
>gnl|CDD|111311 pfam02404, SCF, Stem cell factor. Stem cell factor (SCF) is a
homodimer involved in hematopoiesis. SCF binds to and
activates the SCF receptor (SCFR), a receptor tyrosine
kinase. The crystal structure of human SCF has been
resolved and a potential receptor-binding site
identified.
Length = 273
Score = 31.0 bits (70), Expect = 2.8
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 482 LPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGDLV--VAKILECVTNNL 539
LP+ + + E+S ++LL+K+SN I E LSN I L V ++ C+ +
Sbjct: 64 LPSHCWLHLMVPELSRSLTNLLDKFSN--ISEG--LSNYSIIDKLTRIVDDLVACLAED- 118
Query: 540 GQKQIKASL 548
K IK S
Sbjct: 119 KNKDIKESG 127
>gnl|CDD|178574 PLN02995, PLN02995, Probable pectinesterase/pectinesterase
inhibitor.
Length = 539
Score = 31.2 bits (70), Expect = 3.7
Identities = 14/34 (41%), Positives = 17/34 (50%)
Query: 327 GQAPKAIRSVECYDFKTERWQSVAEMPTRRCRAG 360
G +PKA + C DF + W S A T CR G
Sbjct: 124 GVSPKAGAAKRCTDFDAQTWLSTALTNTETCRRG 157
>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain.
RNase R is a processive 3' to 5' exoribonuclease, which
is a homolog of RNase II. RNase R degrades RNA with
secondary structure having a 3' overhang of at least 7
nucleotides. RNase R and PNPase play an important role
in the degradation of RNA with extensive secondary
structure, such as rRNA, tRNA, and certain mRNA which
contains repetitive extragenic palindromic sequences.
The C-terminal S1 domain binds ssRNA.
Length = 83
Score = 28.5 bits (65), Expect = 4.3
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 460 ENLDGRILGCVKEITDWGLIIELPN-FLSASVHITEISDVY 499
E DG I G +T +GL +EL N + VH++ + D Y
Sbjct: 3 EEFDGVISG----VTSFGLFVELDNLTVEGLVHVSTLGDDY 39
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 30.0 bits (68), Expect = 4.6
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNL-FSIG 524
+ G V E+ ++G + + L VH+++I D Y D EK EE + +G
Sbjct: 85 VEGEVVEVVEFGAFVRI-GPLDGLVHVSQIMDDYIDYDEKNKVLIGEE----TKRVLKVG 139
Query: 525 DLVVAKILECVTNNLGQKQIKASL 548
D V A+I+ + ++ K L
Sbjct: 140 DKVRARIVGVSLKSRRPRESKIGL 163
>gnl|CDD|165217 PHA02890, PHA02890, hypothetical protein; Provisional.
Length = 278
Score = 30.3 bits (68), Expect = 4.6
Identities = 34/158 (21%), Positives = 62/158 (39%), Gaps = 38/158 (24%)
Query: 489 SVHITEISDVYSDLL-----EKYS--NGTIEEIPELSNL-----FSIGDLVVAKILECVT 536
+++ + IS V DL+ E+ +G +E+I E + FSI ++ +L
Sbjct: 4 TINTSGISCVLKDLIPDKFDEEEDIDDGDLEKIKEFIEICINKCFSIKNISDITVLCIEP 63
Query: 537 NNLGQKQIKASLN---PHHVN-------EMYINTTLETGLVLPACV-------HSKEDHG 579
N + I + + PH N E + +E + + H E+ G
Sbjct: 64 ANTNKYSISTNHDKNEPHEENDIAMKKIECFFVACIEGSCKINVNIGDREISDHIHENQG 123
Query: 580 YLLDVGVKNTRAFIKYDSVILGQIVTCMISKIKVAASM 617
+++DVG+ D I V I+K +V A +
Sbjct: 124 FIMDVGL---------DHAIDSDNVGLFITKFEVDAHI 152
>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of A0-A2.
This CD includes H. sapiens S1 repeat 6 (hs6) and S.
cerevisiae S1 repeat 5 (sc5). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 70
Score = 28.0 bits (63), Expect = 5.2
Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 17/83 (20%)
Query: 466 ILGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFSIGD 525
G + ++ G I+ N + + +E+S I + F +G
Sbjct: 4 THGTIVKVKPNGCIVSFYNNVKGFLPKSELS--------------EAFIKDPEEHFRVGQ 49
Query: 526 LVVAKILECVTNNLGQKQIKASL 548
+V K+L C + Q+++ S
Sbjct: 50 VVKVKVLSC---DPEQQRLLLSC 69
>gnl|CDD|183941 PRK13277, PRK13277,
5-formaminoimidazole-4-carboxamide-1-(beta)-D-
ribofuranosyl 5'-monophosphate synthetase-like protein;
Provisional.
Length = 366
Score = 30.3 bits (69), Expect = 5.4
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 969 FDGDISGVFPTSAMSQATRTLVYTRF--VIDTVIVCQILKYEDG-ELLLTEADEKLHK 1023
FDG F T A+ Q R Y F ++D VIV + ++L + ++L +
Sbjct: 32 FDGAKDEGFRTIAVCQKGRERTYREFKGIVDEVIV-----LDKFKDILSEKVQDELRE 84
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 30.2 bits (69), Expect = 6.5
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 19/86 (22%)
Query: 464 GRI-LGCVKEITDWGLIIELPNFLSASVHITEISDVYSDLLEKYSNGTIEEIPELSNLFS 522
G + G V I D+G +EL VHI++++ E + ++ ++
Sbjct: 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAK--------------ERVEKVEDVLK 665
Query: 523 IGDLVVAKILECVTNNLGQKQIKASL 548
GD V K++E + G +I+ S+
Sbjct: 666 EGDEVKVKVIE--IDKQG--RIRLSI 687
>gnl|CDD|235614 PRK05807, PRK05807, hypothetical protein; Provisional.
Length = 136
Score = 28.6 bits (64), Expect = 7.9
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 464 GRIL-GCVKEITDWGLIIELPNFLSASVHITEISDVY 499
G IL G V IT++G +E+ + VHI+E++D Y
Sbjct: 6 GSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTY 41
>gnl|CDD|235130 PRK03557, PRK03557, zinc transporter ZitB; Provisional.
Length = 312
Score = 29.7 bits (67), Expect = 8.9
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 12 SCLLLRYA------SQNSLDESSQKQV-----QNNGTREKPPYRNVHH 48
S L+LR A S N L E + + + RE P RNVHH
Sbjct: 194 SVLVLRSAWRLLKESVNELLEGAPVSLDIAELKRRLCREIPEVRNVHH 241
>gnl|CDD|217574 pfam03463, eRF1_1, eRF1 domain 1. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif at
an exposed tip of domain 2 suggests that the Gln residue
coordinates a water molecule to mediate the hydrolytic
activity at the peptidyl transferase centre. A conserved
groove on domain 1, 80 A from the GGQ motif, is proposed
to form the codon recognition site. This family also
includes other proteins for which the precise molecular
function is unknown. Many of them are from
Archaebacteria. These proteins may also be involved in
translation termination but this awaits experimental
verification.
Length = 133
Score = 28.3 bits (64), Expect = 9.0
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 7/36 (19%)
Query: 503 LEKYSNGTIEEIPE-------LSNLFSIGDLVVAKI 531
+EKY G I+ +PE L +L GD V++
Sbjct: 8 IEKYGKGLIKLLPETLGDLWHLISLIIPGDRVISDT 43
>gnl|CDD|132813 cd07280, PX_YPT35, The phosphoinositide binding Phox Homology
domain of the fungal protein YPT35. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions such as cell signaling,
vesicular trafficking, protein sorting, and lipid
modification, among others. This subfamily is composed
of YPT35 proteins from the fungal subkingdom Dikarya.
The PX domain is involved in targeting of proteins to
PI-enriched membranes, and may also be involved in
protein-protein interaction. The PX domain of YPT35
binds to phosphatidylinositol 3-phosphate (PI3P). It
also serves as a protein interaction domain, binding to
members of the Yip1p protein family, which localize to
the ER and Golgi. YPT35 is mainly associated with
endosomes and together with Yip1p proteins, may be
involved in a specific function in the endocytic
pathway.
Length = 120
Score = 28.1 bits (63), Expect = 9.2
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 474 TDWGLIIELPNFLSASVHI----TEISDVYSDLLEKYSNGTIEEIPEL 517
W + IE + + +S+ +E + LL+++ EIP+L
Sbjct: 23 VVWKITIETKDLIGSSIVAYKRYSEFVQLREALLDEFPRHKRNEIPQL 70
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 29.2 bits (66), Expect = 9.5
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 13/82 (15%)
Query: 764 EKSSRNAELSTIGVGGYDGISRQCLSSVEMYSPERNTWEPVKDMLYKRSGAGVGVLDNIL 823
E + N E T+ + GY VE+ SP + E +K L G ++ +
Sbjct: 166 EIARENIEPPTVKIRGY----------VEVTSPAPDGVEKIKKALKAAEDNGEEEVELKV 215
Query: 824 YAVGGHDGPLVRKSVEAYDPET 845
Y VG P R V+A D +
Sbjct: 216 YYVG---APRYRIDVQAPDYKK 234
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 0.391
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 50,999,355
Number of extensions: 4998034
Number of successful extensions: 3904
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3851
Number of HSP's successfully gapped: 132
Length of query: 1026
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 919
Effective length of database: 6,191,724
Effective search space: 5690194356
Effective search space used: 5690194356
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: 64 (28.5 bits)