RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6189
(539 letters)
>gnl|CDD|201193 pfam00380, Ribosomal_S9, Ribosomal protein S9/S16. This family
includes small ribosomal subunit S9 from prokaryotes and
S16 from eukaryotes.
Length = 121
Score = 164 bits (418), Expect = 6e-49
Identities = 63/121 (52%), Positives = 82/121 (67%), Gaps = 2/121 (1%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIFTDMLNKVDIVASVREG 478
RK A A V + +PG+GKITIN K +YFP+E R +++ PL T L K DIV +V+ G
Sbjct: 3 RKTAVARVWL-KPGSGKITINGKPLEEYFPNETLRMKILEPLELTGTLGKFDIVVTVKGG 61
Query: 479 GHSGQAGAIRWGISWGLRNFVEPEMRERMRLAGLLTRDFRRKERKKPGQARARKKFTWKK 538
G SGQAGAIR I+ L + +PE+R ++ AGLLTRD RRKERKK G +ARK+ + K
Sbjct: 62 GISGQAGAIRLAIARALVAY-DPELRPELKKAGLLTRDPRRKERKKYGLKKARKRPQFSK 120
Query: 539 R 539
R
Sbjct: 121 R 121
>gnl|CDD|223181 COG0103, RpsI, Ribosomal protein S9 [Translation, ribosomal
structure and biogenesis].
Length = 130
Score = 137 bits (348), Expect = 1e-38
Identities = 59/121 (48%), Positives = 78/121 (64%), Gaps = 2/121 (1%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIFTDMLNKVDIVASVREG 478
RK A A V + PG GKIT+N + YFP E R ++M PL+ T + K DI +V+ G
Sbjct: 12 RKSAVARVRLV-PGKGKITVNGRPLELYFPRETLRMKIMQPLLLTGTVGKFDIDVTVKGG 70
Query: 479 GHSGQAGAIRWGISWGLRNFVEPEMRERMRLAGLLTRDFRRKERKKPGQARARKKFTWKK 538
G SGQAGAIR GI+ L + +PE+R ++ AGLLTRD RR ERKK G +AR++ + K
Sbjct: 71 GISGQAGAIRHGIARALVEY-DPELRPALKKAGLLTRDPRRVERKKYGLKKARRRPQFSK 129
Query: 539 R 539
R
Sbjct: 130 R 130
>gnl|CDD|178888 PRK00132, rpsI, 30S ribosomal protein S9; Reviewed.
Length = 130
Score = 136 bits (345), Expect = 3e-38
Identities = 54/121 (44%), Positives = 73/121 (60%), Gaps = 2/121 (1%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIFTDMLNKVDIVASVREG 478
RK A A V + PG+GKIT+N + +YFP E R + PL T+ K D+ +V+ G
Sbjct: 12 RKTAVARVRLK-PGSGKITVNGRDLEEYFPRETLRMVVRQPLELTETEGKFDVYVTVKGG 70
Query: 479 GHSGQAGAIRWGISWGLRNFVEPEMRERMRLAGLLTRDFRRKERKKPGQARARKKFTWKK 538
G SGQAGAIR GI+ L +P++R ++ AG LTRD R ERKK G +AR+ + K
Sbjct: 71 GISGQAGAIRHGIARAL-LEYDPDLRPALKKAGFLTRDARMVERKKYGLKKARRAPQFSK 129
Query: 539 R 539
R
Sbjct: 130 R 130
>gnl|CDD|214357 CHL00079, rps9, ribosomal protein S9.
Length = 130
Score = 92.3 bits (230), Expect = 3e-22
Identities = 51/122 (41%), Positives = 68/122 (55%), Gaps = 3/122 (2%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFP-DENDRQQLMFPLIFTDMLNKVDIVASVRE 477
RK A A V + PG+G+I IN K +Y + N + PL + NK DI+ V+
Sbjct: 11 RKTAVAQVRLV-PGSGEIIINGKPAEEYLQYNPNYLNAIKAPLKLLGLENKYDIIVKVKG 69
Query: 478 GGHSGQAGAIRWGISWGLRNFVEPEMRERMRLAGLLTRDFRRKERKKPGQARARKKFTWK 537
GG +GQA AIR G++ L PE R+ ++ G LTRD R KERKK G +ARK +
Sbjct: 70 GGLTGQAEAIRLGLARALCKI-NPENRKSLKKEGFLTRDARIKERKKYGLKKARKAPQFS 128
Query: 538 KR 539
KR
Sbjct: 129 KR 130
>gnl|CDD|179041 PRK00474, rps9p, 30S ribosomal protein S9P; Reviewed.
Length = 134
Score = 70.3 bits (173), Expect = 1e-14
Identities = 44/121 (36%), Positives = 60/121 (49%), Gaps = 7/121 (5%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIF--TDMLNKVDIVASVR 476
RK A A T+ + G G++ IN + E R ++M PLI D+ +KVDI +V
Sbjct: 11 RKTAIARATI-REGKGRVRINGVP-LELIEPELARLKIMEPLILAGEDLRSKVDIDVNVE 68
Query: 477 EGGHSGQAGAIRWGISWGLRNFV-EPEMRERMRL--AGLLTRDFRRKERKKPGQARARKK 533
GG GQA A R I+ GL + + E+++ LL D RR E KK G AR K
Sbjct: 69 GGGIMGQADAARTAIARGLVEWTGDMELKDAFLAYDRTLLVGDPRRTEPKKWGGKGARAK 128
Query: 534 F 534
Sbjct: 129 R 129
>gnl|CDD|132666 TIGR03627, arch_S9P, archaeal ribosomal protein S9P. This model
describes exclusively the archaeal ribosomal protein
S9P. Homologous eukaryotic and bacterial ribosomal
proteins are excluded from this model [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 130
Score = 69.3 bits (170), Expect = 3e-14
Identities = 49/120 (40%), Positives = 62/120 (51%), Gaps = 6/120 (5%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIFT-DMLNKVDIVASVRE 477
RK A A T+ G G++ IN + +P E R ++M PLI D+ +VDI V
Sbjct: 8 RKTAIARATIR-EGKGRVRIN-GVPVELYPPELARLKIMEPLILAGDIAKEVDIDVKVSG 65
Query: 478 GGHSGQAGAIRWGISWGLRNFV-EPEMRERMRL--AGLLTRDFRRKERKKPGQARARKKF 534
GG GQA A R I+ GL F + E+R+ R LL D RRKE KKPG AR K
Sbjct: 66 GGIMGQADAARTAIARGLVEFTGDKELRDAFRAYDRTLLVNDPRRKEPKKPGGRGARAKR 125
>gnl|CDD|185437 PTZ00086, PTZ00086, 40S ribosomal protein S16; Provisional.
Length = 147
Score = 41.6 bits (98), Expect = 2e-04
Identities = 40/129 (31%), Positives = 57/129 (44%), Gaps = 14/129 (10%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIF--TDMLNKVDIVASVR 476
+K A A V G G I +N D E R ++ PL+ + +++DI VR
Sbjct: 17 KKTAVAVALV-TKGKGLIRVNGVP-LDLINPETLRAKVFEPLLLVGKERFSRLDIRVRVR 74
Query: 477 EGGHSGQAGAIRWGISWGL----RNFVEPEMRERMRLA------GLLTRDFRRKERKKPG 526
GG QA AIR I+ GL + +V+ + ++ LL D RR E KK G
Sbjct: 75 GGGQVAQAYAIRQAIAKGLVAYYQKYVDEATKAELKDKLLAYDRSLLVADPRRCEPKKFG 134
Query: 527 QARARKKFT 535
AR +F
Sbjct: 135 GPGARARFQ 143
>gnl|CDD|177799 PLN00210, PLN00210, 40S ribosomal protein S16; Provisional.
Length = 141
Score = 40.1 bits (94), Expect = 6e-04
Identities = 39/132 (29%), Positives = 58/132 (43%), Gaps = 22/132 (16%)
Query: 419 RKCARADVTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLI------FTDMLNKVDIV 472
+K A A VT + G G I IN + E R + P++ F VD+
Sbjct: 11 KKTAVA-VTYCKRGRGLIKINGCP-IELVQPEILRFKAFEPILLLGRHRFAG----VDMR 64
Query: 473 ASVREGGHSGQAGAIRWGISWGL----RNFVEPEMRERMRLA------GLLTRDFRRKER 522
V+ GGH+ Q AIR I+ L + +V+ + ++ ++ LL D RR E
Sbjct: 65 IRVKGGGHTSQIYAIRQSIAKALVAYYQKYVDEQSKKEIKDILLRYDRTLLVADPRRCEP 124
Query: 523 KKPGQARARKKF 534
KK G AR +F
Sbjct: 125 KKFGGRGARARF 136
>gnl|CDD|220854 pfam10704, DUF2508, Protein of unknown function (DUF2508). This
family is conserved in Firmicutes. Several members are
annotated as being the protein YaaL. The function is not
known.
Length = 71
Score = 29.9 bits (68), Expect = 0.55
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 332 RELYLTNTEWMSQEALERITVEPITKPEYQQFVAVMTRLVNHKYAYLHEEFIFKYRQPKV 391
+ EW S + LE +V+P + YQ T+L KY +L+ E + R+ K
Sbjct: 19 ELIEKAKEEWDSAKQLEENSVDPSEELIYQ------TKLAEAKYFFLYRE--ARKRKVKG 70
>gnl|CDD|215236 PLN02428, PLN02428, lipoic acid synthase.
Length = 349
Score = 32.4 bits (74), Expect = 0.58
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 9 RNCRLSFLARFSSKTPNPPDKPNEPSELAKETA 41
R CR F A +S+TP PPD P+EP +A+ A
Sbjct: 114 RGCR--FCAVKTSRTPPPPD-PDEPENVAEAIA 143
>gnl|CDD|212679 cd10237, HSPA13-like_NBD, Nucleotide-binding domain of human HSPA13
and similar proteins. Human HSPA13 (also called 70-kDa
heat shock protein 13, STCH, "stress 70 protein
chaperone, microsome-associated, 60kD", "stress 70
protein chaperone, microsome-associated, 60kDa"; the
gene encoding HSPA13 maps to 21q11.1) belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). STCH contains an NBD but lacks an SBD.
STCH may function to regulate cell proliferation and
survival, and modulate the TRAIL-mediated cell death
pathway. The HSPA13 gene is a candidate stomach cancer
susceptibility gene; a mutation in the NBD coding region
of HSPA13 has been identified in stomach cancer cells.
The NBD of HSPA13 interacts with the ubiquitin-like
proteins Chap1 and Chap2, implicating HSPA13 in
regulating cell cycle and cell death events. HSPA13 is
induced by the Ca2+ ionophore A23187.
Length = 417
Score = 31.7 bits (72), Expect = 0.95
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 8/39 (20%)
Query: 426 VTVYQPGTGKITINEKHYFDYFPDENDRQQLMFPLIFTD 464
V VYQ GTG+ I PDEN R+ + + FT
Sbjct: 34 VGVYQAGTGETDI--------IPDENGRKSIPSVVAFTP 64
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.0 bits (62), Expect = 2.6
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 251 MPSGLYSKKARPYMKHPEEVFPPKKDAEFDNLGRPYHFLFYTGKPNLYELFHNANVLIRK 310
+P +Y + P + ++ + +FD R Y F+ YT K H A +R+
Sbjct: 9 IPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQK-------HEAKRAVRE 61
Query: 311 LNKME 315
LN E
Sbjct: 62 LNNYE 66
>gnl|CDD|181187 PRK07984, PRK07984, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 262
Score = 29.9 bits (67), Expect = 2.8
Identities = 28/94 (29%), Positives = 41/94 (43%), Gaps = 11/94 (11%)
Query: 63 AYL--KRAEDYTNFMEGEKHSFEVGRRHLANMMGRD---VETFTQKDIDEAIAYLMPSGL 117
+YL +RA N M K S E R++AN MG + V + I L SG+
Sbjct: 145 SYLGAERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAG----PIRTLAASGI 200
Query: 118 YSKKARPYMKHPEEVFPPKKDAEFDNLGRPYHFL 151
K R + H E V P ++ +++G FL
Sbjct: 201 --KDFRKMLAHCEAVTPIRRTVTIEDVGNSAAFL 232
>gnl|CDD|173113 PRK14650, PRK14650, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 302
Score = 29.4 bits (66), Expect = 4.8
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 451 NDRQQLMFPLIFTDMLNKVDI 471
ND +++ FP+I+T LNK++I
Sbjct: 71 NDEEEIDFPIIYTGHLNKIEI 91
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 29.0 bits (65), Expect = 5.3
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 236 ETFTQKDIDEAIAYLMPSGLYSKKARPYMKHPEEVFPPKKDAEFDNLGRPYHFLFYTGK- 294
+ T++DI A+ +P +Y KK + F P+ DA+ R YH+ T K
Sbjct: 69 DRMTEEDIKNAMNANLPDDIYVKKV----FEVPKNFHPRFDAK----KRIYHYFILTSKE 120
Query: 295 PNLY 298
N++
Sbjct: 121 KNVF 124
>gnl|CDD|222607 pfam14225, MOR2-PAG1_C, Cell morphogenesis C-terminal. This family
is the conserved C-terminal region of proteins that are
involved in cell morphogenesis.
Length = 258
Score = 28.7 bits (65), Expect = 7.1
Identities = 25/146 (17%), Positives = 41/146 (28%), Gaps = 41/146 (28%)
Query: 268 EEVFPPKKDAEFDNLGRPYHFLFYTG--KPNLYELFHNANVLIRKLNKMEDEDLRNPKQT 325
PPK + +F+ L L G EL L+ +L + D+ L +
Sbjct: 50 ISGQPPKWEGKFEGL----QPLLLKGLRSSASLELTLE---LLSRLTPLPDDRLIGDSE- 101
Query: 326 QASEASRELY--LTNTEWMSQEALERITVEPITK------------PEYQQFVAVMTRLV 371
SR L+ L N + L+ +P V+
Sbjct: 102 -----SRLLFAVLANLPRLLH-HLDDPNQDPKCVSTAEALAQVAEAQGLSSLARVLDSYS 155
Query: 372 NHKY-----------AYLHEEFIFKY 386
KY +YL + +
Sbjct: 156 KGKYRSKKDFLSQVVSYLRDAYFPDL 181
>gnl|CDD|99981 cd03809, GT1_mtfB_like, This family is most closely related to the
GT1 family of glycosyltransferases. mtfB
(mannosyltransferase B) in E. coli has been shown to
direct the growth of the O9-specific polysaccharide
chain. It transfers two mannoses into the position 3 of
the previously synthesized polysaccharide.
Length = 365
Score = 28.9 bits (65), Expect = 7.8
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 502 EMRERMRLAGLLTRDFRRKERKKPGQARARKKFTWKK 538
+ + LL R+E ++ G ARA+ +F+W+K
Sbjct: 325 ALAAAIE--RLLEDPALREELRERGLARAK-RFSWEK 358
>gnl|CDD|193552 cd05677, M20_dipept_like_DUG2_type, M20 Defective in Utilization of
Glutathione-type peptidases containing WD repeats.
Peptidase M20 family, Defective in Utilization of
Glutathione (DUG2) subfamily. DUG2-type proteins are
metallopeptidases containing WD repeats at the
N-terminus. DUG2 proteins are involved in the
alternative pathway of glutathione (GSH) degradation.
GSH, the major low-molecular-weight thiol compound in
most eukaryotic cells, is normally degraded through the
gamma-glutamyl cycle initiated by gamma-glutamyl
transpeptidase. However, a novel pathway for the
degradation of GSH has been characterized; it requires
the participation of three genes identified in
Saccharomyces cerevisiae as "defective in utilization of
glutathione" genes including DUG1, DUG2, and DUG3. DUG1
encodes a probable di- or tri-peptidase identified as
M20 metallopeptidase, DUG2 gene encodes a protein with a
metallopeptidase domain and a large N-terminal WD40
repeat region, while DUG3 encodes a protein with a
glutamine amidotransferase domain. Although dipeptides
and tripeptides with a normal peptide bond, such as
cys-gly or glu-cys-gly, can be hydrolyzed by the DUG1
protein, the presence of an unusual peptide bond, like
in GSH, requires the participation of the DUG2 and DUG3
proteins as well. These three proteins form a GSH
degradosomal complex.
Length = 434
Score = 28.8 bits (65), Expect = 8.6
Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 352 VEPITKPEYQQFVAVMTRLVNHKYAYLHEEFIFKYRQPKV-IKTMNF 397
V+PIT+ E +F + + + + I K+R+P + I ++N
Sbjct: 242 VKPITEEEEARFRDIASIALIPL-PTTVDSLIAKWRKPSLTIHSVNV 287
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 0.401
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,600,814
Number of extensions: 2840881
Number of successful extensions: 2627
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2612
Number of HSP's successfully gapped: 34
Length of query: 539
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 437
Effective length of database: 6,413,494
Effective search space: 2802696878
Effective search space used: 2802696878
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: 61 (27.1 bits)