RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780784|ref|YP_003065197.1| polynucleotide
phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str.
psy62]
(699 letters)
>gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 886 bits (2292), Expect = 0.0
Identities = 380/694 (54%), Positives = 507/694 (73%), Gaps = 4/694 (0%)
Query: 1 MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT 60
MF+ IEW GR L LETG+IARQ++GAVL YG+TVVLATVV + K+GQDFFPLT
Sbjct: 1 MFNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKEGQDFFPLT 59
Query: 61 VNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQH 120
VNY+E+TYA GKIPGG+ +RE RP+E EIL SR+IDR IRPLF K ++NE Q++ V+
Sbjct: 60 VNYEEKTYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSV 119
Query: 121 DLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDE-DQGSLDLFVS 179
D E+ P +++MV ASAAL LSG+PF GP+ +V YI+G +VLNP L+E ++ LDL V+
Sbjct: 120 DPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVA 179
Query: 180 GTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDF-S 238
GT+DAV MVE EA++L E+V+L+A+ FGH + VI A +LA K+ ++
Sbjct: 180 GTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDE 239
Query: 239 KLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDI 298
+LE ++ + +++L+ + I EK R +D +K+K+ S E S + EI ++ E +
Sbjct: 240 ELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEES-SLKEIKAILEKL 298
Query: 299 QAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTRE 358
+ K VR ++L+ KVR+DGR + VR I +VG+L RTHGS+LF RG+TQA+VVVTLGT
Sbjct: 299 EKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPR 358
Query: 359 DEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQ 418
D Q +D L G + F++HYNF P + GE RMG+P RREIGHG LA RA+ PVLP +
Sbjct: 359 DAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEEE 418
Query: 419 FPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSD 478
FPYT+R+VSEI ES+GSSSMA+VCG SLALMDAGVPI PVAGIAMGL+K+GD + +LSD
Sbjct: 419 FPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLSD 478
Query: 479 ISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKV 538
I GDEDHLG MDFKVAGTD GITA+QMD+KI GI++ IM AL+QAK RLHIL M++
Sbjct: 479 ILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEA 538
Query: 539 LSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS 598
+SE R +L + PR+E + I PD+IR+VIG GGK I+ I E+TG K++I+DDGTVKIA+S
Sbjct: 539 ISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAAS 598
Query: 599 SLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA 658
+ A+E I +IT EV ++Y+G VV+++DFGAFV +DGLVHISQL+ ERV
Sbjct: 599 DGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVE 658
Query: 659 KTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ 692
K DV+KEGD V VK+++ D +G+I+LS+K V +
Sbjct: 659 KVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVLE 692
>gnl|CDD|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide
nucleotidyltransferase [General function prediction
only].
Length = 760
Score = 575 bits (1483), Expect = e-164
Identities = 277/706 (39%), Positives = 417/706 (59%), Gaps = 31/706 (4%)
Query: 6 TVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQE 65
+VEI + R + ETG++AR ++G+V+ GET V+ TVV Q F PL V+YQE
Sbjct: 48 SVEIPFGNREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPPQ-FLPLVVDYQE 106
Query: 66 RTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESS 125
+ AVG+IPG ++RRE R + EIL R+IDR IRPLF K + +ETQ++ NV+ D
Sbjct: 107 KFAAVGRIPGNFMRREGRTKDKEILTGRLIDRPIRPLFPKGFYHETQILCNVLSSDGVHD 166
Query: 126 PHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGS-LDLFVSGTQDA 184
P V+++ AASAAL LS +P+ GP+ ++ I+G++V+NP E S L+L V+GT+
Sbjct: 167 PDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGTKSQ 226
Query: 185 VLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAK---EPIVIDSKDFSKLE 241
+M+E +N + + +L AI G E + +I+ I +LAK K EP + D +L
Sbjct: 227 TVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPD-PELV 285
Query: 242 EEMSQMIKEDLRVSCFIPE--KYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQ 299
+ + ++ E L K R + ++ ++ E EI+ F +
Sbjct: 286 KHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRLDDEDKVKEEFPEQEPSEIIESFNTVS 345
Query: 300 AKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTRED 359
KV R+ +L++ R DGRD + +R+IS +V +L+ HGS+LF RG TQ + VTL + E
Sbjct: 346 KKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLES 405
Query: 360 EQYVDSLSGT-QRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQ 418
Q +DSL G +FM+HY F P AT EV ++G +RRE+GHG LA +A+ PVLP+
Sbjct: 406 AQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLPVLPE--D 463
Query: 419 FPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGD------- 471
FP+T+R+ SE+ ES+GSSSMA+VCG SLALMDAGVP+S VAG+A+GLV D
Sbjct: 464 FPFTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKGEIE 523
Query: 472 DFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHI 531
D+ IL+DI G ED+ G MDFK+AGT+ G+TA+ + +K I++ ALQ+A+ RL I
Sbjct: 524 DYRILTDILGIEDYNGDMDFKIAGTNDGVTALGIPLK-------IVMEALQKAREARLQI 576
Query: 532 LNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDG 591
L+ M K ++ R E++P +E + + P + +IG GG + + I +TGA + D+G
Sbjct: 577 LDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-DEG 635
Query: 592 TVKIASSSLAEIEAAREMIRSITDVP-----EVNKIYKGQVVKVMDFGAFVHFCGARDGL 646
T I + + A +E A+E I I E +Y + ++ D G V + GL
Sbjct: 636 TFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGL 695
Query: 647 VHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ 692
+H SQL E++AK SD+++ G + VK ++ D RG I LS + +
Sbjct: 696 LHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLP 741
>gnl|CDD|144653 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 128
Score = 121 bits (307), Expect = 5e-28
Identities = 54/136 (39%), Positives = 80/136 (58%), Gaps = 13/136 (9%)
Query: 13 GRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP--LTVNYQERTYAV 70
RP+++ETG + Q+DG+ L G+T VLATV + +DFFP LTV Y+E+ +A
Sbjct: 2 LRPIEIETG-VLSQADGSALVELGDTKVLATVTGPIEPPNERDFFPGELTVEYEEKPFAS 60
Query: 71 GKIPGGYLRRESRPTENEILISRMIDRSIRPLF--SKCYKNETQVIINVMQHDLESSPHV 128
G+ P G RP+E EI +SR+IDR++RP F + E ++ I V+ D S
Sbjct: 61 GERPEG------RPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSDD--GSLLD 112
Query: 129 VSMVAASAALMLSGLP 144
++ AAS AL +G+P
Sbjct: 113 AAINAASLALADAGIP 128
Score = 115 bits (291), Expect = 3e-26
Identities = 47/132 (35%), Positives = 62/132 (46%), Gaps = 6/132 (4%)
Query: 323 RDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLP 382
R I + G+L + GS+L GDT+ + VT G E D G + Y P
Sbjct: 3 RPIEIETGVLSQADGSALVELGDTKVLATVT-GPIEPPNERDFFPGE----LTVEYEEKP 57
Query: 383 CATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVC 442
A+GE G PS REI RL RA+ P P + +RI + DGS A +
Sbjct: 58 FASGERPE-GRPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSDDGSLLDAAIN 116
Query: 443 GSSLALMDAGVP 454
+SLAL DAG+P
Sbjct: 117 AASLALADAGIP 128
>gnl|CDD|88437 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 = 102 bits (257), Expect = 3e-22
Identities = 41/68 (60%), Positives = 51/68 (75%)
Query: 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD 679
KIY+G+VVK+ DFGAFV +DGLVHIS+LS ERV K DV+K GD V VK+++ DD
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60
Query: 680 RGKIKLSM 687
RG+I LS
Sbjct: 61 RGRISLSR 68
>gnl|CDD|31033 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 96.9 bits (241), Expect = 2e-20
Identities = 68/239 (28%), Positives = 110/239 (46%), Gaps = 16/239 (6%)
Query: 307 MLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSL 366
+ +R DGR + +R I G+L+ GSSL G+T+ I V+ G RE L
Sbjct: 3 ESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVS-GPREPVPR--FL 59
Query: 367 SGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIV 426
GT + Y LP +T E + A R RL RA+ V+ P + +
Sbjct: 60 RGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVI-DLELLPESTIDI 118
Query: 427 S-EITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDH 485
++ ++DG + A++ G+SLAL DAG+P+ VA I++G+V I+ D+ +ED
Sbjct: 119 DCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDGV----IVLDLDYEEDS 174
Query: 486 LGHMDFKVAGTDSG----ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLS 540
D V T +G I + D G +E+ ++ L A +G + + L+
Sbjct: 175 AAEADMNVVMTGNGGLVEIQGLAED---GPFTEDELLELLDLAIKGCNELRELQREALA 230
Score = 56.8 bits (137), Expect = 2e-08
Identities = 49/217 (22%), Positives = 89/217 (41%), Gaps = 12/217 (5%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKI 73
RP+K+ G + ++G+ L +G T V+ TV ++ F T G +
Sbjct: 19 RPIKITRGVLKH-AEGSSLIEFGNTKVICTVS---GPREPVPRFLRGTGKGWLTAEYGML 74
Query: 74 PGGYLRRESRPTEN--EILISRMIDRSIRPLFSKCYKNETQVII--NVMQHDLESSPHVV 129
P R+ R + ISR+I R++R + E+ + I +V+Q D
Sbjct: 75 PRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADG--GTRTA 132
Query: 130 SMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSL-DLFVSGTQDAVLMV 188
S+ AS AL +G+P V V ++G VL+ +ED + D+ V T + +V
Sbjct: 133 SITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVMTGNG-GLV 191
Query: 189 ELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMC 225
E++ D ++ + + +L +
Sbjct: 192 EIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREA 228
>gnl|CDD|29003 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA in prokaryotes and plant chloroplasts. The
C-terminal region of PNPase contains domains homologous
to those in other RNA binding proteins: a KH domain and
an S1 domain. KH domains bind single-stranded RNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA..
Length = 61
Score = 86.7 bits (215), Expect = 2e-17
Identities = 35/60 (58%), Positives = 47/60 (78%)
Query: 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMI 610
PR+E M IPPD+IR+VIG GGK I+ I+E+TG K++I+DDGTV IA+S E A++MI
Sbjct: 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60
>gnl|CDD|88439 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1
domain of human ATP-dependent RNA helicase DHX8, a DEAH
(Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA
helicases are thought to play key roles in pre-mRNA
splicing and DHX8 facilitates nuclear export of spliced
mRNA by releasing the RNA from the spliceosome. DHX8 is
also known as HRH1 (human RNA helicase 1) in Homo
sapiens and PRP22 in Saccharomyces cerevisiae..
Length = 79
Score = 85.6 bits (212), Expect = 4e-17
Identities = 47/80 (58%), Positives = 54/80 (67%), Gaps = 5/80 (6%)
Query: 620 NKIYKGQVVKVMDFGAFVHFCGAR---DGLVHISQLSTE-RVAKTSDVVKEGDTVWVKLL 675
KIYKG+V +MDFG FV G + +GLVHISQLS E RVA SDVVK G V VK++
Sbjct: 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60
Query: 676 DFDDRGKIKLSMKVVDQNTG 695
GKI LSMK VDQ+TG
Sbjct: 61 SI-QNGKISLSMKDVDQDTG 79
>gnl|CDD|88447 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 = 75.7 bits (186), Expect = 4e-14
Identities = 34/67 (50%), Positives = 45/67 (67%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRG 681
+ +G V ++ FGAFV G GLVHISQ++ +RV DV+KEGD V VK+L D RG
Sbjct: 3 VVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG 62
Query: 682 KIKLSMK 688
+I LS+K
Sbjct: 63 RISLSIK 69
>gnl|CDD|31295 COG1098, VacB, Predicted RNA binding protein (contains ribosomal
protein S1 domain) [Translation, ribosomal structure and
biogenesis].
Length = 129
Score = 75.3 bits (185), Expect = 6e-14
Identities = 30/81 (37%), Positives = 47/81 (58%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLD 676
+V KG++ + +GAFV G + GLVHIS+++ V D +K G V VK+LD
Sbjct: 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLD 62
Query: 677 FDDRGKIKLSMKVVDQNTGKP 697
D+ GKI LS++ +++ K
Sbjct: 63 IDENGKISLSIRKLEEEPEKQ 83
>gnl|CDD|88441 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain.
pNO40 is a nucleolar protein of unknown function with an
N-terminal S1 RNA binding domain, a CCHC type zinc
finger, and clusters of basic amino acids representing a
potential nucleolar targeting signal. pNO40 was
identified through a yeast two-hybrid interaction screen
of a human kidney cDNA library using the pinin (pnn)
protein as bait. pNO40 is thought to play a role in
ribosome maturation and/or biogenesis..
Length = 73
Score = 73.4 bits (180), Expect = 2e-13
Identities = 32/73 (43%), Positives = 48/73 (65%), Gaps = 1/73 (1%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTERVAKTSDVVKEGDTVWVKLL 675
P + +I+KG+V V ++GAFV G R GLVH S +S+ RV S+VV G+ VWVK++
Sbjct: 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVI 60
Query: 676 DFDDRGKIKLSMK 688
+ + K+KLS+
Sbjct: 61 GREMKDKMKLSLS 73
>gnl|CDD|36286 KOG1068, KOG1068, KOG1068, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp41 and related exoribonucleases [Translation,
ribosomal structure and biogenesis].
Length = 245
Score = 69.2 bits (169), Expect = 4e-12
Identities = 56/243 (23%), Positives = 101/243 (41%), Gaps = 14/243 (5%)
Query: 309 DKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSG 368
++ +R DGR +R I A++G+L + GS+ +G+T+ + V G RE S
Sbjct: 10 EEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVY-GPREIRGK--SARR 66
Query: 369 TQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYT-LRIVS 427
+ + +TG+ + RRE + ++A PV+ +P + + I
Sbjct: 67 PDKAVLNCEVSSAQFSTGDRKKRPKGDRREKELSLMLQQAFEPVI-LLELYPRSQIDIYV 125
Query: 428 EITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLG 487
++ E DGS+ A + ++LAL DAG+P+ + GL L D++ E+
Sbjct: 126 QVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGLADG----TPLLDLTSLEESAR 181
Query: 488 HMDFKVA--GTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQ 545
VA I +Q+D + + + L+ A G + + VL E
Sbjct: 182 APGLTVAALPNREEIALLQLD---ERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKN 238
Query: 546 LGE 548
Sbjct: 239 AES 241
Score = 36.8 bits (85), Expect = 0.022
Identities = 42/220 (19%), Positives = 89/220 (40%), Gaps = 10/220 (4%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT--VNYQERTYAVG 71
R + G + Q+DG+ G T VL V R ++ P +N + +
Sbjct: 24 RRIYARIG-VLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCE---VSSA 79
Query: 72 KIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSM 131
+ G ++ + E +S M+ ++ P+ +Q+ I V + + S ++
Sbjct: 80 QFSTGDRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAI 139
Query: 132 VAASAALMLSGLPFEGPVVGAQVDYINGQYVLNP-RLDEDQGSLDLFVS--GTQDAVLMV 188
AA+ AL +G+P + +G +L+ L+E + L V+ ++ + ++
Sbjct: 140 NAATLALADAGIPMYDLITACTAGLADGTPLLDLTSLEESARAPGLTVAALPNREEIALL 199
Query: 189 ELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKE 228
+L+ +L D + + CK V E + + + K
Sbjct: 200 QLD-ERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKN 238
>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
structure and biogenesis].
Length = 541
Score = 68.8 bits (168), Expect = 5e-12
Identities = 44/148 (29%), Positives = 74/148 (50%), Gaps = 11/148 (7%)
Query: 549 FTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAARE 608
F P + P + +IG K + + + +D + S E E
Sbjct: 131 FLPGSLVDVRPVRDLDPLIG---KELEFKILE------LDKKRNNVVLSRRAVLEEERSE 181
Query: 609 MIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGD 668
+ + EV ++ +G V + D+GAFV G DGL+HIS++S +RV S+VVK GD
Sbjct: 182 QREELLNKLEVGEVVEGVVKNITDYGAFVD-IGGVDGLLHISEISWKRVDHPSEVVKVGD 240
Query: 669 TVWVKLLDFD-DRGKIKLSMKVVDQNTG 695
V VK++ D +RG++ LS+K ++++
Sbjct: 241 EVKVKVISLDEERGRVSLSLKQLEEDPW 268
Score = 67.6 bits (165), Expect = 1e-11
Identities = 30/77 (38%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
V +G+V + D+GAFV +GLVH+S++S + S+VVK G V VK+LD
Sbjct: 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDI 335
Query: 678 D-DRGKIKLSMKVVDQN 693
D +R +I L +K + +N
Sbjct: 336 DPERRRISLGLKQLKEN 352
Score = 48.3 bits (115), Expect = 7e-06
Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 1/72 (1%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
V + +G+V + DFGAFV G DGLVH+S LS +R + ++ K+GD V K+L
Sbjct: 362 PVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAV 421
Query: 678 D-DRGKIKLSMK 688
D ++ +I L +K
Sbjct: 422 DKEKERISLGIK 433
Score = 43.3 bits (102), Expect = 2e-04
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 615 DVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674
+ + + KG+V V D GAFV G +GL+ +S+LS DV+K GD V +
Sbjct: 445 EKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELS-------RDVLKVGDEVEAVV 497
Query: 675 LDFDDR-GKIKLSMKVVDQ 692
+ D + KI LS+K +++
Sbjct: 498 VSIDKKNRKILLSIKALER 516
Score = 39.9 bits (93), Expect = 0.003
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLL- 675
E + KG VV + G V G +G++ IS+ S E V DVV+ GD V V +L
Sbjct: 19 FEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVE---DVVQVGDEVEVLVLR 75
Query: 676 DFDDRGKIKLSMK 688
D G++ LS +
Sbjct: 76 VEDGEGELVLSRR 88
>gnl|CDD|144242 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 = 64.6 bits (158), Expect = 9e-11
Identities = 30/73 (41%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLD 676
PE + KG V +V GAFV +G + IS++S +RV +V+K GD V VK+L
Sbjct: 2 PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLK 61
Query: 677 FD-DRGKIKLSMK 688
D +RG+I LS++
Sbjct: 62 VDKERGRIILSIR 74
>gnl|CDD|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: 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 3 (ec3) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog..
Length = 68
Score = 64.0 bits (156), Expect = 1e-10
Identities = 31/67 (46%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 621 KIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-D 679
+ +G V + DFGAFV G DGL+HIS +S RV S+VV GD V VK+L D +
Sbjct: 3 DVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKE 61
Query: 680 RGKIKLS 686
R +I L
Sbjct: 62 RKRISLG 68
>gnl|CDD|32366 COG2183, Tex, Transcriptional accessory protein [Transcription].
Length = 780
Score = 64.1 bits (156), Expect = 1e-10
Identities = 40/92 (43%), Positives = 57/92 (61%), Gaps = 2/92 (2%)
Query: 607 REMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKE 666
E + SITD+ + I +G V V+DFGAFV +DGLVHISQLS + V ++VVK
Sbjct: 647 DEGVESITDL-KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKV 705
Query: 667 GDTVWVKLLDFD-DRGKIKLSMKVVDQNTGKP 697
GD V VK+++ D R +I LSM++ ++
Sbjct: 706 GDIVKVKVIEVDTARKRIALSMRLDEEEGKLN 737
>gnl|CDD|31290 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 62.2 bits (151), Expect = 4e-10
Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 609 MIRSITDVPEVNKIYKGQVVKVMDFGAFVHF--CGARDGLVHISQLSTERVAKTSDVVKE 666
M + PE +I G V +V D+GA+V ++G +HIS++++ V D VKE
Sbjct: 1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKE 60
Query: 667 GDTVWVKLLDFD-DRGKIKLSMKVVDQN 693
G V K+L D RG I LS+K V ++
Sbjct: 61 GQKVVAKVLRVDPKRGHIDLSLKRVTEH 88
>gnl|CDD|88440 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a
transcription accessory factor called Tex, which has
been characterized in Bordetella pertussis and
Pseudomonas aeruginosa. The tex gene is essential in
Bortella pertusis and is named for its role in toxin
expression. Tex has two functional domains, an
N-terminal domain homologous to the Escherichia coli
maltose repression protein, which is a poorly defined
transcriptional factor, and a C-terminal S1 RNA-binding
domain. Tex is found in prokaryotes, eukaryotes, and
archaea..
Length = 68
Score = 58.3 bits (141), Expect = 7e-09
Identities = 31/66 (46%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-DR 680
+ +G V V DFGAFV +DGL+HIS+++ V+ SDVV GD V VK++ D +R
Sbjct: 3 VLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEER 62
Query: 681 GKIKLS 686
G+I LS
Sbjct: 63 GRISLS 68
>gnl|CDD|143804 pfam00013, KH_1, KH domain. KH motifs can bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;.
Length = 57
Score = 57.9 bits (141), Expect = 9e-09
Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMI 610
E + IP + +IG GG I+ I E+TGAK+ I D TV I S + +E A+E+I
Sbjct: 1 TEEILIPSSLVGRIIGKGGSNIKEIREETGAKIRIPDRDTVTI-SGTPEAVEKAKELI 57
>gnl|CDD|88416 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 = 57.7 bits (139), Expect = 1e-08
Identities = 30/65 (46%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 623 YKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR-G 681
G+VV + FG FV +GLVHIS+LS + V S+V K GD V VK+L+ D G
Sbjct: 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60
Query: 682 KIKLS 686
+I LS
Sbjct: 61 RISLS 65
>gnl|CDD|88418 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of
translation Initiation Factor 2, S1-like RNA-binding
domain. S1-like RNA-binding domains are found in a wide
variety of RNA-associated proteins. Eukaryotic and
archaeal Initiation Factor 2 (e- and aIF2, respectively)
are heterotrimeric proteins with three subunits (alpha,
beta, and gamma). IF2 plays a crucial role in the
process of translation initiation. The IF2 gamma subunit
contains a GTP-binding site. The IF2 beta and gamma
subunits together are thought to be responsible for
binding methionyl-initiator tRNA. The ternary complex
consisting of IF2, GTP, and the methionyl-initiator tRNA
binds to the small subunit of the ribosome, as part of a
pre-initiation complex that scans the mRNA to find the
AUG start codon. The IF2-bound GTP is hydrolyzed to GDP
when the methionyl-initiator tRNA binds the AUG start
codon, at which time the IF2 is released with its bound
GDP. The large ribosomal subunit then joins with the
small subunit to complete the initiation complex, which
is competent to begin translation. The IF2a subunit is a
major site of control of the translation initiation
process, via phosphorylation of a specific serine
residue. This alpha subunit is well conserved in
eukaryotes and archaea but is not present in bacteria.
IF2 is a cold-shock-inducible protein..
Length = 76
Score = 55.1 bits (133), Expect = 7e-08
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674
PE ++ V + D GA+V G +G++ +S+LS R+ +VK G VK+
Sbjct: 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60
Query: 675 LDFD-DRGKIKLSMK 688
+ D ++G I LS K
Sbjct: 61 IRVDKEKGYIDLSKK 75
>gnl|CDD|88427 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 = 54.4 bits (131), Expect = 9e-08
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 606 AREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVK 665
+ + +D+ + + G V + +G FV F G GL S +S E V S K
Sbjct: 2 EGTLPTNFSDL-KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFK 60
Query: 666 EGDTVWVKLLDFD-DRGKIKLSM 687
+G +V K+ D ++ + LS+
Sbjct: 61 KGQSVTAKVTSVDEEKQRFLLSL 83
>gnl|CDD|146390 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA
binding domain. This family contains the RNA binding
domain of Polyribonucleotide nucleotidyltransferase
(PNPase) PNPase is involved in mRNA degradation in a
3'-5' direction.
Length = 80
Score = 51.9 bits (125), Expect = 6e-07
Identities = 28/80 (35%), Positives = 49/80 (61%)
Query: 239 KLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDI 298
+LEE+++ + +E L + I K R +D++K +V+ F+ E +E EI +F+ +
Sbjct: 1 ELEEKVAALAEERLSEAYTITGKQERYAALDEIKADVVAAFAEEEDEEDEKEIKDIFKAL 60
Query: 299 QAKVVRTVMLDKKVRMDGRD 318
+ KVVR+ +LD R+DGRD
Sbjct: 61 EKKVVRSRILDGGPRIDGRD 80
>gnl|CDD|88463 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 = 51.4 bits (123), Expect = 8e-07
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTERVAKTSDVVKEGDTVWVKLLD 676
+V + G V +V D+G F+ G GL H S++S RVA S + + GD V K+L
Sbjct: 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLK 60
Query: 677 FD-DRGKIKLSMK 688
D ++ +I L +K
Sbjct: 61 IDAEKKRISLGLK 73
>gnl|CDD|146389 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 67
Score = 51.4 bits (124), Expect = 8e-07
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 147 GPVVGAQVDYINGQYVLNPRLDED---QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDA 203
GPV V I+G+ VL+P L+E+ L + V+GT D V +++ L+E+ +L+A
Sbjct: 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGDIVALMKEGGGGLTEEELLEA 60
Query: 204 IIFGH 208
+ H
Sbjct: 61 LELAH 65
Score = 42.6 bits (101), Expect = 3e-04
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 458 PVAGIAMGLVKDGDDFIILSDISGDEDHLGH--MDFKVAGTDSGITAMQMDMKIGGISEN 515
PVA + +G + + ++ D + +E+ L + VAGT + M+ GG++E
Sbjct: 2 PVAAVTVGKI--DGELVL--DPTLEEESLADSDLTIVVAGTGDIVALMKEG--GGGLTEE 55
Query: 516 IMVMALQQAKRG 527
++ AL+ A +G
Sbjct: 56 ELLEALELAHKG 67
>gnl|CDD|36287 KOG1069, KOG1069, KOG1069, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp46 [Translation, ribosomal structure and
biogenesis].
Length = 217
Score = 51.5 bits (123), Expect = 8e-07
Identities = 52/229 (22%), Positives = 91/229 (39%), Gaps = 24/229 (10%)
Query: 319 SETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHY 378
+E +R I+ ++ +L R GSS F +GDT+ I V G + R +
Sbjct: 2 AERLRGIACEISILSRPDGSSEFSQGDTKVICSVY-GPID---------VKARQED---- 47
Query: 379 NFLPCATGEVS---RMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTL-RIVSEITESDG 434
AT EV + G E R+ R+ + + +P T ++ ++ E DG
Sbjct: 48 --PEKATLEVIWRPKSGVNGTVEKVLERIIRKTLSKAIILEL-YPRTTIQVSIQVVEDDG 104
Query: 435 SSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDE-DHLGHMDFKV 493
S+ + + LAL+DAG+P+ I+ L +DG ++L + E
Sbjct: 105 STLACAINAACLALVDAGIPLRSMFCAISCALHEDGV--LVLDPTAKQEKISTARATLSF 162
Query: 494 AGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSES 542
G G + + G SE+ + L+ A+ + +VL
Sbjct: 163 EGGSLGEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRK 211
>gnl|CDD|32306 COG2123, COG2123, RNase PH-related exoribonuclease [Translation,
ribosomal structure and biogenesis].
Length = 272
Score = 49.5 bits (118), Expect = 3e-06
Identities = 46/264 (17%), Positives = 96/264 (36%), Gaps = 40/264 (15%)
Query: 308 LDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLS 367
L K +R+DGR + R + + G++ + +GS+L G+TQ +V V E + D+
Sbjct: 19 LKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEI--GEPFPDT-- 74
Query: 368 GTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVL--------PQTAQF 419
+++ P A G P I R+ R + + +
Sbjct: 75 -PNEGVLVVNVELSPLA-SPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKK 132
Query: 420 PYTLRIVSEITESDGSSSMATVCGSSLALMDAGVP----------------------ISK 457
+ + + + + DG+ A + AL++ VP +S
Sbjct: 133 VWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSN 192
Query: 458 PVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIM 517
P + + + +++ D S +E+ + + + G + G I+E+ +
Sbjct: 193 PPISVTFAKIGN----VLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDL 248
Query: 518 VMALQQAKRGRLHILNEMSKVLSE 541
AL+ A + + + L E
Sbjct: 249 EKALKTALSKAEKLREALKEALKE 272
Score = 40.7 bits (95), Expect = 0.002
Identities = 52/249 (20%), Positives = 97/249 (38%), Gaps = 50/249 (20%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVV--YDRSLKDGQDFFPLTVNYQERTYAVG 71
RPL++ETG I + ++G+ L G T V+ V D + L VN + A
Sbjct: 34 RPLEIETGVIPK-ANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASP 92
Query: 72 KIPGGYLRRESRPTENEILISRMIDRSIRP------------LFSKCYKNETQVIINVMQ 119
G P E I +SR++DR +R K + V ++V+
Sbjct: 93 SFEPG------PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWV--VFVDVHVLD 144
Query: 120 HDLESSPHVVSMVAASAALMLSGLP----------------------FEGPVVGAQVDYI 157
+D + + +AA AAL+ + +P P + I
Sbjct: 145 YD--GNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKI 202
Query: 158 NGQYVLNPRLDED---QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPV 214
V++P L+E+ G L + V+ + V + ++ ++E + A+ ++ + +
Sbjct: 203 GNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTALSKAEKL 262
Query: 215 IEAISKLAK 223
EA+ + K
Sbjct: 263 REALKEALK 271
>gnl|CDD|29002 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension..
Length = 64
Score = 47.1 bits (112), Expect = 2e-05
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 7/64 (10%)
Query: 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD------DGTVKIASSSLAEIEAA 606
E + +P + +IG GG I+ I E+TGAK+ I D + V I + + +E A
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTI-TGTPEAVEKA 59
Query: 607 REMI 610
+E+I
Sbjct: 60 KELI 63
>gnl|CDD|88445 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 = 46.4 bits (110), Expect = 2e-05
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 624 KGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLDFD-DRG 681
G++ + DFG FV G DGLVHIS +S T+RV S++ K+G V +L+ D +R
Sbjct: 5 SGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERE 64
Query: 682 KIKL 685
+I L
Sbjct: 65 RISL 68
>gnl|CDD|88438 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the
archaea-specific RecJ-like exonuclease. The function of
this family is not fully understood. In Escherichia
coli, RecJ degrades single-stranded DNA in the 5'-3'
direction and participates in homologous recombination
and mismatch repair..
Length = 77
Score = 45.1 bits (107), Expect = 6e-05
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 612 SITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVW 671
++ D+ EV K+YKG+V V +G FV GL+H S L + + GD V
Sbjct: 10 TMEDL-EVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD--------YEVGDEVI 60
Query: 672 VKLLDFDDRGKIKLS 686
V++ D + G I L
Sbjct: 61 VQVTDIPENGNIDLI 75
>gnl|CDD|88453 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 = 44.8 bits (106), Expect = 8e-05
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 625 GQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-DRGKI 683
G +VKV G V F G + S+LS + + + G V VK+L D ++ ++
Sbjct: 6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRL 65
Query: 684 KLSMK 688
LS K
Sbjct: 66 LLSCK 70
>gnl|CDD|88442 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: 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 1 of the Escherichia coli and Homo sapiens
RPS1 (ec1 and hs1, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog..
Length = 70
Score = 44.4 bits (105), Expect = 1e-04
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR- 680
I KG VV V D V +G++ IS+ S + + D VK GD V V +L +D
Sbjct: 3 IVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEE 62
Query: 681 GKIKLSMK 688
G + LS +
Sbjct: 63 GNVVLSKR 70
>gnl|CDD|88426 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. RpoE is subunit E of
archaeal RNA polymerase. Archaeal cells contain a single
RNA polymerase made up of 12 subunits, which are
homologous to the 12 subunits (RPB1-12) of eukaryotic
RNA polymerase II. RpoE is homologous to Rpa43 of
eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA
polymerase II, and Rpc25 of eukaryotic RNA polymerase
III. RpoE is composed of two domains, the N-terminal RNP
(ribonucleoprotein) domain and the C-terminal S1 domain.
This S1 domain binds ssRNA and ssDNA. This family is
classified based on the C-terminal S1 domain. The
function of RpoE is not fully understood. In eukaryotes,
RPB7 and RPB4 form a heterodimer that reversibly
associates with the RNA polymerase II core..
Length = 99
Score = 43.3 bits (102), Expect = 2e-04
Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 18/84 (21%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------KTSDVVKEGDTV 670
+ +G+VV+V+DFGAFV G DGL+HISQ+ + ++ +T V+K GD V
Sbjct: 2 VVEGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVV 60
Query: 671 WVKL--LDFDDR----GKIKLSMK 688
++ + +R KI L+M+
Sbjct: 61 RARIVAVSLKERRPRESKIGLTMR 84
>gnl|CDD|36288 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 [RNA
processing and modification].
Length = 1710
Score = 43.1 bits (101), Expect = 3e-04
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD 679
KI KG + + + GAFV F G G +S++S + V S+ G TV K+++ DD
Sbjct: 600 GKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDD 659
Query: 680 -RGKIKLSMKVVD 691
+ ++ L ++
Sbjct: 660 EKRRMPLGLRASS 672
>gnl|CDD|38127 KOG2916, KOG2916, KOG2916, Translation initiation factor 2, alpha
subunit (eIF-2alpha) [Translation, ribosomal structure
and biogenesis].
Length = 304
Score = 42.2 bits (99), Expect = 4e-04
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674
PEV +I V + + GA+V +G++ +S+LS R+ +++ G V +
Sbjct: 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVV 73
Query: 675 LDFD-DRGKIKLSMKVVDQN 693
L D ++G I LS + V
Sbjct: 74 LRVDKEKGYIDLSKRRVSPE 93
>gnl|CDD|88444 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: 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 (ec4) of the Escherichia coli RPS1.
Autoantibodies to double-stranded DNA from patients with
systemic lupus erythematosus cross-react with the human
RPS1 homolog..
Length = 72
Score = 41.2 bits (96), Expect = 0.001
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLL 675
PE +++ G+V + D+G FV +GLVH+S++ T + S VV GD V V +L
Sbjct: 2 PEGTRLF-GKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVL 60
Query: 676 DFD-DRGKIKL 685
D D +R +I L
Sbjct: 61 DIDEERRRISL 71
>gnl|CDD|36889 KOG1676, KOG1676, KOG1676, K-homology type RNA binding proteins
[RNA processing and modification].
Length = 600
Score = 40.0 bits (93), Expect = 0.002
Identities = 32/134 (23%), Positives = 61/134 (45%), Gaps = 26/134 (19%)
Query: 492 KVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLG--EF 549
++A SGI + + G EN+ + AK ++ E V+S R G +
Sbjct: 88 QIAADPSGIG--YRSVDLTGSPENV-----EVAK----QLIGE---VVSRGRPPGGFPDN 133
Query: 550 TPRVEI---MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS-------S 599
VE + IP ++ +IG GG+ I+ + EQ+G K+ + DG++ +
Sbjct: 134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD 193
Query: 600 LAEIEAAREMIRSI 613
++E A++++ I
Sbjct: 194 PDKVEQAKQLVADI 207
Score = 38.9 bits (90), Expect = 0.005
Identities = 45/192 (23%), Positives = 75/192 (39%), Gaps = 32/192 (16%)
Query: 431 ESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMD 490
E GS A V G A + VP SK GI +G K G+ L + +G + +
Sbjct: 214 EVPGSGGHAGVRGGGSATREVKVPRSK--VGIIIG--KGGEMIKKLQNETGAK-----IQ 264
Query: 491 FKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFT 550
FK D ++ + +I G + I A ++NE+
Sbjct: 265 FK---PDDDPSSPERPAQIIGTVDQIEHAA---------ELINEIIAEAEAGAGGGMGGG 312
Query: 551 PRVEI----MAIPPDQIRNVIGMGGKVIRGIVEQTGAKV-------NIDDDGTVKIASSS 599
+ M +P D+ VIG GG+ I+ I +Q+GA+ N + +
Sbjct: 313 APGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGD 372
Query: 600 LAEIEAAREMIR 611
+I+ A+++IR
Sbjct: 373 KRQIDHAKQLIR 384
Score = 32.3 bits (73), Expect = 0.49
Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 10/91 (10%)
Query: 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREM 609
T + E +P + + VIG GG I+ I +++G +V I D S +
Sbjct: 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAAD------PSGIGY---RSVD 102
Query: 610 IRSITDVPEVNKIYKGQVV-KVMDFGAFVHF 639
+ + EV K G+VV + G F
Sbjct: 103 LTGSPENVEVAKQLIGEVVSRGRPPGGFPDN 133
>gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 39.8 bits (93), Expect = 0.003
Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 18/95 (18%)
Query: 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------K 659
R++ P ++ +G+VV+V++FGAFV G DGLVH+SQ+ + + +
Sbjct: 73 RALVFKPFRGEVVEGEVVEVVEFGAFVRI-GPLDGLVHVSQIMDDYIDYDEKNKVLIGEE 131
Query: 660 TSDVVKEGDTVWVKL--LDFDDRG----KIKLSMK 688
T V+K GD V ++ + R KI L+M+
Sbjct: 132 TKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMR 166
>gnl|CDD|29004 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA..
Length = 62
Score = 39.4 bits (92), Expect = 0.003
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI----DDDGTVKIASSSLAEIEAARE 608
E + IP R +IG G IR I+E+TG K+ T+ I + +E A+E
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITI-TGPKENVEKAKE 59
Query: 609 MIR 611
I
Sbjct: 60 EIL 62
>gnl|CDD|30903 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 39.2 bits (91), Expect = 0.004
Identities = 26/82 (31%), Positives = 34/82 (41%), Gaps = 13/82 (15%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTE-----------RVAKTSDVVKE 666
V + + G V V FG FV +GLVHIS L + K+ V +
Sbjct: 622 VGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRL 681
Query: 667 GDTVWVKLLDFD-DRGKIKLSM 687
GD V VK+ D D KI +
Sbjct: 682 GDEVKVKVTSVDLDERKIDFEL 703
>gnl|CDD|31291 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 37.5 bits (87), Expect = 0.011
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 547 GEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASSSLAE--- 602
E + IP D+I +IG G+V + I E+TG K+ ID G+V I ++ E
Sbjct: 3 EFAEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPL 62
Query: 603 -IEAAREMIRSIT 614
+ AR+++++I
Sbjct: 63 ALLKARDVVKAIG 75
>gnl|CDD|37401 KOG2190, KOG2190, KOG2190, PolyC-binding proteins alphaCP-1 and
related KH domain proteins [RNA processing and
modification, General function prediction only].
Length = 485
Score = 37.4 bits (86), Expect = 0.012
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 550 TPRVEI-MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD 590
P V + +P Q+ ++IG GG +I+ I E+TGAK+ + D
Sbjct: 135 GPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD 176
Score = 30.1 bits (67), Expect = 2.0
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 9/65 (13%)
Query: 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI--------DDDGTVKIASSSLAEIEAAR 607
+ +P D I +IG GG I I ++TGA ++I + V+I + L E A+
Sbjct: 342 LLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQI-TGMLREDLLAQ 400
Query: 608 EMIRS 612
+IR+
Sbjct: 401 YLIRA 405
>gnl|CDD|88419 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like
RNA-binding domain. RNase E is an essential
endoribonuclease in the processing and degradation of
RNA. In addition to its role in mRNA degradation, RNase
E has also been implicated in the processing of rRNA,
and the maturation of tRNA, 10Sa RNA and the M1
precursor of RNase P. RNase E associates with PNPase (3'
to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and
enolase (glycolytic enzyme) to form the RNA
degradosome. RNase E tends to cut mRNA within
single-stranded regions that are rich in A/U
nucleotides. The N-terminal region of RNase E contains
the catalytic site. Within the conserved N-terminal
domain of RNAse E and RNase G, there is an S1-like
subdomain, which is an ancient single-stranded
RNA-binding domain. S1 domain is an RNA-binding module
originally identified in the ribosomal protein S1. The
S1 domain is required for RNA cleavage by RNase E. RNase
G is paralogous to RNase E with an N-terminal catalytic
domain that is highly homologous to that of RNase E.
RNase G not only shares sequence similarity with RNase
E, but also functionally overlaps with RNase E. In
Escherichia coli, RNase G is involved in the maturation
of the 5' end of the 16S rRNA. RNase G plays a secondary
role in mRNA decay..
Length = 88
Score = 37.5 bits (87), Expect = 0.013
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 617 PEVNKIYKGQVVKVMDF--GAFVHFCGARDGLVHISQLSTE---RVAKTSDVVKEGDTVW 671
P V IY G+V K++ AFV ++G +H+S + + K + ++KEG +
Sbjct: 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEIL 64
Query: 672 V 672
V
Sbjct: 65 V 65
>gnl|CDD|88446 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 = 36.7 bits (85), Expect = 0.020
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRG 681
I G+V +V GA V +G + ++LS +RV ++ K GD V K+ + D +
Sbjct: 3 IVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKN 62
Query: 682 -KIKLSMKVVD 691
KI LS+K +
Sbjct: 63 RKISLSIKAKE 73
>gnl|CDD|29006 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA..
Length = 65
Score = 35.1 bits (81), Expect = 0.063
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD 590
+ +P Q ++IG GG I+ I E+TGAK+ +
Sbjct: 4 LLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS 38
>gnl|CDD|48406 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is
an essential multifunctional transcription elongation
factor that is universally conserved among prokaryotes
and archaea. NusA anti-termination function plays an
important role in the expression of ribosomal rrn
operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices..
Length = 61
Score = 33.6 bits (77), Expect = 0.21
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 548 EFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI 587
+ + + +P DQ+ IG GG+ +R + G K++I
Sbjct: 21 DDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60
>gnl|CDD|37928 KOG2717, KOG2717, KOG2717, Uncharacterized conserved protein with
similarity to embryogenesis protein H beta 58 and VPS26
[General function prediction only].
Length = 313
Score = 33.4 bits (76), Expect = 0.23
Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 6/97 (6%)
Query: 511 GISENIMVMALQQAKRGRLH--ILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNV-- 566
G+ NI + KRG LH + M ++ + L E P + I I PD +++
Sbjct: 112 GVFINIQYLLTCDIKRGYLHKPLTKTMEFIVESGPVDLPERPPEIVIFYITPDTLQHPLK 171
Query: 567 --IGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLA 601
I G ++ G ++ T + G + + +S A
Sbjct: 172 ERIKTPGFLVTGKLDATQCSLTDPLTGELTVEASEAA 208
>gnl|CDD|88436 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 = 33.1 bits (76), Expect = 0.29
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 13/82 (15%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTE-----------RVAKTSDVVKE 666
V + + G + V FG FV +GLVH+S L + +T V +
Sbjct: 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRL 60
Query: 667 GDTVWVKLLDFD-DRGKIKLSM 687
GD V V+++ D DR KI +
Sbjct: 61 GDKVKVRVVRVDLDRRKIDFEL 82
>gnl|CDD|36825 KOG1612, KOG1612, KOG1612, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp42 [Translation, ribosomal structure and
biogenesis].
Length = 288
Score = 32.7 bits (74), Expect = 0.35
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 312 VRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVV---VTLGTREDEQ 361
+R DGR R I + +L T+GS+ GD I+V +G+ +DE
Sbjct: 21 IRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDET 73
>gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 32.2 bits (73), Expect = 0.57
Identities = 33/167 (19%), Positives = 63/167 (37%), Gaps = 12/167 (7%)
Query: 514 ENIMVMALQQA------KRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVI 567
E ++V+ +++ K I E+ + L +++ ++ +P I VI
Sbjct: 443 EQVVVVPVKEEEESPALKLAEEEIEREIKRYLP-GDVEVEVVGDGRAVVKVPEKYIPKVI 501
Query: 568 GMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQV 627
G GGK I+ I ++ G K+++ + EIE + I K +
Sbjct: 502 GKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKVPVEIEEKGKHIVLYVGPDFAGKPVRIYA 561
Query: 628 VKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674
F A V +R G+V I +E + + + G + L
Sbjct: 562 GDEYLFTATV----SRKGVVKIR-KDSEVGKEIEEAIDNGRDIRASL 603
>gnl|CDD|30544 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 31.7 bits (72), Expect = 0.68
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589
V I+ +PPDQ+ IG GG+ +R + TG +++I+
Sbjct: 142 HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179
>gnl|CDD|88452 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: 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 5 (hs5) and S.
cerevisiae S1 repeat 5 (sc5). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea..
Length = 69
Score = 31.3 bits (71), Expect = 1.0
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-DR 680
+ KG + K+ G FV GLV L+ R+ K G V ++L + +R
Sbjct: 3 VVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPER 62
Query: 681 GKIKLSM 687
++ L++
Sbjct: 63 KRLVLTL 69
>gnl|CDD|36110 KOG0892, KOG0892, KOG0892, Protein kinase ATM/Tel1, involved in
telomere length regulation and DNA repair [Signal
transduction mechanisms, Chromatin structure and
dynamics, Replication, recombination and repair, Cell
cycle control, cell division, chromosome partitioning].
Length = 2806
Score = 30.8 bits (69), Expect = 1.2
Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 272 KKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGL 331
K + + ++N ++ VR +M ++ ++DG + T+ + AQV
Sbjct: 2726 LKALKKQKEEDEENFNLSGNITEDASNDRNAVRALMRAQR-KLDGVEQGTMLSVEAQVQE 2784
Query: 332 L 332
L
Sbjct: 2785 L 2785
>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 30.7 bits (69), Expect = 1.3
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 612 SITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVW 671
++ DV E K YKG V +V +G FV GL+H L + GD +
Sbjct: 116 TMEDV-EAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDP------DYAVGDEII 168
Query: 672 VKLLDF-DDRGKIKLSMKVVD 691
V++ D ++G+I +D
Sbjct: 169 VQVSDVRPEKGEIDFEPVGLD 189
>gnl|CDD|34549 COG4941, COG4941, Predicted RNA polymerase sigma factor containing
a TPR repeat domain [Transcription].
Length = 415
Score = 30.7 bits (69), Expect = 1.3
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 403 RLARRAIHPVLPQTAQFPYTLRIVSEITESD-------GSSSMAT-VCGSSLALMDAGVP 454
RL HP LP + TLR+V ++ ++ ++MA + + + +AG+P
Sbjct: 111 RLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKARIREAGIP 170
Query: 455 ISKP 458
P
Sbjct: 171 FEVP 174
>gnl|CDD|32705 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfB [Energy production and conversion].
Length = 198
Score = 30.7 bits (69), Expect = 1.4
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 209 NECKPVIEA-ISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSC 256
N C P EA I K+A++ EP D + + + M +I E + C
Sbjct: 72 NRCAPGGEAVIRKIAELLGVEPPPADGSEHGEEQARMVALIDEANCIGC 120
>gnl|CDD|36826 KOG1613, KOG1613, KOG1613, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp43 [Translation, ribosomal structure and
biogenesis].
Length = 298
Score = 30.7 bits (69), Expect = 1.5
Identities = 18/67 (26%), Positives = 28/67 (41%)
Query: 292 VSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVV 351
VF+ I ++ L + +R DGR RD + G + +GS+L G T I
Sbjct: 16 PEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICG 75
Query: 352 VTLGTRE 358
+ E
Sbjct: 76 IKAEIAE 82
>gnl|CDD|37490 KOG2279, KOG2279, KOG2279, Kinase anchor protein AKAP149, contains
KH and Tudor RNA-binding domains [Signal transduction
mechanisms].
Length = 608
Score = 30.5 bits (68), Expect = 1.8
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 536 SKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGT--- 592
K + L E TP E +++P + +IG GG+ IR I + +GAK+ D +G
Sbjct: 124 CKAKAAIHQILTENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGL 183
Query: 593 --VKIASSSLAEIEAAREMI 610
+ S E+ AA+ +I
Sbjct: 184 SRLIKISGQQKEVAAAKHLI 203
Score = 29.3 bits (65), Expect = 3.8
Identities = 24/118 (20%), Positives = 51/118 (43%), Gaps = 8/118 (6%)
Query: 510 GGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEI---MAIPPDQIRNV 566
S + + ++ + + R Q E P+ +I M +P + ++ +
Sbjct: 23 IPASATVAYILYRKYRNDEEERDSGGQLTFVGIRGQTEEQKPQKDIEIEMVVPQEAVKLI 82
Query: 567 IGMGGKVIRGIVEQTGAKVNIDD----DGTVKIASSSLAEIEAAR-EMIRSITDVPEV 619
IG G I+ + +QTGAK+++D D V + S ++ A+ + + +T+ V
Sbjct: 83 IGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTENTPV 140
>gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing
and modification].
Length = 674
Score = 30.2 bits (68), Expect = 1.9
Identities = 24/118 (20%), Positives = 38/118 (32%), Gaps = 10/118 (8%)
Query: 589 DDGTVKIASSSLAEIEAAREMIRSIT-----DVPEVNKIYKGQVVKVMDFGAFV-HFCGA 642
G + + + EIEAA E++R D PE+ G + F G
Sbjct: 257 PPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGK 316
Query: 643 RD-GLVHISQLSTERVAKTSDVVKEGDTVWVKL---LDFDDRGKIKLSMKVVDQNTGK 696
R L ++ + VV G K D + +S +Q G+
Sbjct: 317 RKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGR 374
>gnl|CDD|88464 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 = 30.1 bits (68), Expect = 1.9
Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKT----SDVVKEGDTVW 671
+PEV + G+V +V V D ++ +S+++ R + + EGD +
Sbjct: 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIV 62
Query: 672 VKLLDFDDRGKIKLSMKVVDQNTGK 696
++ D G + L + GK
Sbjct: 63 AEVQSVDSDGSVSLHTR--SLKYGK 85
>gnl|CDD|31293 COG1096, COG1096, Predicted RNA-binding protein (consists of S1
domain and a Zn-ribbon domain) [Translation, ribosomal
structure and biogenesis].
Length = 188
Score = 29.9 bits (67), Expect = 2.8
Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%)
Query: 602 EIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARD----------GLVHISQ 651
+ + + +P+ I G+V V + A V G +H+SQ
Sbjct: 47 NRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQ 106
Query: 652 LSTERVAKTSDVVKEGDTVWVKLLDFDDR 680
+ V K SD + GD V +++ D
Sbjct: 107 VRDGYVEKLSDAFRIGDIVRARVISTGDP 135
>gnl|CDD|147130 pfam04816, DUF633, Family of unknown function (DUF633). This
family of proteins are uncharacterized have no known
function.
Length = 204
Score = 29.6 bits (67), Expect = 3.0
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 557 AIPPDQIRNVI---GMGGKVIRGIVEQTGAKVN 586
I + +VI GMGG +I I+EQ K+
Sbjct: 60 VIEELDLIDVIVIAGMGGTLIADILEQGKNKLA 92
>gnl|CDD|88451 cd05696, S1_Rrp5_repeat_hs4, S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is
found in eukaryotes but not in prokaryotes or archaea..
Length = 71
Score = 29.4 bits (66), Expect = 3.3
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 626 QVVKVM-DFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
+V KV D GA G VHIS LS ++V + K G T +++ +
Sbjct: 8 KVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGY 60
>gnl|CDD|32239 COG2056, COG2056, Predicted permease [General function prediction
only].
Length = 444
Score = 29.4 bits (66), Expect = 3.5
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 434 GSSSMATVC--GSSLALMDAGVPISKPVAGIAMGLVKDG 470
G S +AT+ G++ AL DAG P S G GL DG
Sbjct: 375 GFSPLATIALIGTAAALGDAGSPASDSTLGPTSGLNADG 413
>gnl|CDD|38893 KOG3689, KOG3689, KOG3689, Cyclic nucleotide phosphodiesterase
[Signal transduction mechanisms].
Length = 707
Score = 29.2 bits (65), Expect = 3.5
Identities = 27/136 (19%), Positives = 43/136 (31%), Gaps = 26/136 (19%)
Query: 569 MGGKVIRGIVEQTGAKVNIDD-------DGTVKIASSSLAEIEA--AREMIRSITDVPEV 619
+ +RG V TG +NI + D V + + I + + V ++
Sbjct: 243 LLDYGLRGYVASTGEGLNISNAIADPRFDKQVDEDGTGIRPILCIPIKNKKGEVIGVQQL 302
Query: 620 NKIYKGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAK--------------TSD 662
G D F AF FCG H+ + + +
Sbjct: 303 VNKEDGNPFSRNDEDLFEAFTIFCGLSIHNTHMYSKINKSEPRQGVALEFLSYHAKALEE 362
Query: 663 VVKEGDTVWVKLLDFD 678
V+ G +KLLDF
Sbjct: 363 EVQWGPATILKLLDFF 378
>gnl|CDD|48083 cd03466, Nitrogenase_NifN_2, Nitrogenase_nifN_2: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco). This
group also contains the Clostidium fused NifN-NifB
protein..
Length = 429
Score = 29.5 bits (66), Expect = 3.7
Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 195 LSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRV 254
+ E+ ++ +I +E K + E + + K ++ +++D DF +E ++L++
Sbjct: 319 VLENGMVPVLIATGSESKKLKEKLEEDLKEYVEKCVILDGADFFDIESYA-----KELKI 373
Query: 255 SCFIPEKY 262
I Y
Sbjct: 374 DVLIGNSY 381
>gnl|CDD|38225 KOG3015, KOG3015, KOG3015, F1-ATP synthase assembly protein [Energy
production and conversion].
Length = 283
Score = 29.2 bits (65), Expect = 3.8
Identities = 11/68 (16%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 248 IKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVM 307
+ L V + + KQ + K+ + + SS + W + +++ V+ +
Sbjct: 169 FENRLGVKLQPSDNILGGKQAEKDKEAIDKWLSS-LNFWALAGLEFAVASLKSFVIALGI 227
Query: 308 LDKKVRMD 315
++ K+ +D
Sbjct: 228 IEGKLDVD 235
>gnl|CDD|113841 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 29.0 bits (65), Expect = 4.4
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 205 IFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIK 249
IFG N+ + VI S L ++ K I D FS++ +++ ++ K
Sbjct: 389 IFGQNKSEKVITLSSSLFELANK--IDYDEIKFSEISDDVFELSK 431
>gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 29.1 bits (65), Expect = 4.4
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 205 IFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVS 255
++ PVIE + I +D K+E+EM ++ KE+L +
Sbjct: 44 LYPDVTIGPVIEEGFYYDFDVKEP---ITPEDLLKIEKEMKEIAKENLPIE 91
>gnl|CDD|30316 cd02784, MopB_CT_PHLH, The MopB_CT_PHLH CD includes a group of
related uncharacterized putative hydrogenase-like
homologs (PHLH) of molybdopterin binding proteins. This
CD is of the PHLH region homologous to the conserved
molybdopterin-binding C-terminal (MopB_CT) region
present in many, but not all, MopB homologs..
Length = 137
Score = 28.8 bits (64), Expect = 4.8
Identities = 18/73 (24%), Positives = 24/73 (32%), Gaps = 9/73 (12%)
Query: 7 VEIEWAGRPLKLETGRIARQSDGAVLAT--YGETVVLATV------VYDRSLKDGQDF-F 57
V I GR ++L ++G VL YG T Y D DF
Sbjct: 58 VRIRRGGRTIELPVWIQPGHAEGVVLLALGYGRTHAGKVGNGVGHNAYPFRTSDVPDFVA 117
Query: 58 PLTVNYQERTYAV 70
+ V R Y +
Sbjct: 118 GVEVTKTGRKYPL 130
>gnl|CDD|111045 pfam02106, Fanconi_C, Fanconi anaemia group C protein.
Length = 559
Score = 29.1 bits (65), Expect = 4.9
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 5/28 (17%)
Query: 413 LPQTAQFPYTLRIVSEI-----TESDGS 435
LPQ A P RIV EI E+DG+
Sbjct: 282 LPQAACHPAIFRIVDEIFRNALLETDGA 309
>gnl|CDD|146704 pfam04204, HTS, Homoserine O-succinyltransferase.
Length = 298
Score = 29.0 bits (66), Expect = 5.1
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 15/49 (30%)
Query: 513 SENIMVMALQQAKRG-----RLHILNEMSK----------VLSESRLQL 546
SENI VM ++A R R+ ILN M K +L + LQ+
Sbjct: 16 SENIFVMDEERAARQDIRPLRIGILNLMPKKIETETQLLRLLGNTPLQV 64
>gnl|CDD|37403 KOG2192, KOG2192, KOG2192, PolyC-binding hnRNP-K protein
HRB57A/hnRNP, contains KH domain [RNA processing and
modification, General function prediction only].
Length = 390
Score = 28.5 bits (63), Expect = 6.2
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589
+ IP D ++IG GG+ I+ I ++GA + ID+
Sbjct: 319 VTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE 352
>gnl|CDD|146056 pfam03233, Cauli_AT, Aphid transmission protein. This protein is
found in various caulimoviruses. It codes for an 18 kDa
protein (PII), which is dispensable for infection but
which is required for aphid transmission of the virus.
This protein interacts with the PIII protein.
Length = 163
Score = 28.2 bits (63), Expect = 7.3
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 260 EKYVRCKQIDDLKKKMVSYFSSEHSS 285
+K VR K ++ YFSS+ +
Sbjct: 14 DKIVRLKPLELSSNDRSYYFSSQKGN 39
>gnl|CDD|173880 cd08515, PBP2_NikA_DppA_OppA_like_10, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 460
Score = 28.3 bits (64), Expect = 8.1
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 555 IMAIPPDQIRNVIGMGGKVIRG 576
I +PPDQ + G + G
Sbjct: 216 ITNVPPDQAERLKSSPGLTVVG 237
>gnl|CDD|88574 cd05134, RasGAP_RASA3, RASA3 (or GAP1_IP4BP) is a member of the
GAP1 family and has been shown to specifically bind
1,3,4,5-tetrakisphosphate (IP4). Thus, RASA3 may
function as an IP4 receptor. The members of GAP1 family
are characterized by a conserved domain structure
comprising N-terminal tandem C2 domains, a highly
conserved central RasGAP domain, and a C-terminal
pleckstrin-homology domain that is associated with a
Bruton's tyrosine kinase motif. Purified RASA3
stimulates GAP activity on Ras with about a five-fold
lower potency than p120RasGAP, but shows no
GAP-stimulating activity at all against Rac or Rab3A..
Length = 310
Score = 28.1 bits (62), Expect = 9.5
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 190 LEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVI-DSKDFSKLEEEMSQMI 248
L + + E + L + + KP+I+ I + K C +P+ + D ++ E + Q +
Sbjct: 78 LTSKCIDETMKLAGMHYLQVTLKPIIDEICQEHKPCEIDPVKLKDGENLENNRENLRQYV 137
Query: 249 KEDLRVSCFIPEKYVRCKQI 268
RV I + V C +
Sbjct: 138 DRIFRV---ITKSGVSCPTV 154
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.135 0.380
Gapped
Lambda K H
0.267 0.0631 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,111,522
Number of extensions: 436186
Number of successful extensions: 1273
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1225
Number of HSP's successfully gapped: 99
Length of query: 699
Length of database: 6,263,737
Length adjustment: 101
Effective length of query: 598
Effective length of database: 4,081,228
Effective search space: 2440574344
Effective search space used: 2440574344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.5 bits)