RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14668
(266 letters)
>gnl|CDD|211320 cd11607, DENR_C, C-terminal domain of DENR and related proteins.
DENR (density regulated protein), together with MCT-1
(multiple copies T cell malignancies), has been shown to
have similar function as eIF2D translation initiation
factor (also known as ligatin), which is involved in the
recruitment and delivery of aminoacyl-tRNAs to the
P-site of the eukaryotic ribosome in a GTP-independent
manner.
Length = 86
Score = 95.3 bits (238), Expect = 3e-25
Identities = 36/56 (64%), Positives = 41/56 (73%), Gaps = 4/56 (7%)
Query: 142 VASKFFGTRFACGSSVTGD----DEIVIQGDVKDDLFDVIPEKWPEIDEDFIEDLG 193
A+K F +FACG+SVT DEIVIQGDV DD+ D+I EKWPEIDED IE LG
Sbjct: 31 KAAKLFAKKFACGASVTKGAEGKDEIVIQGDVTDDIVDLILEKWPEIDEDNIEILG 86
>gnl|CDD|233294 TIGR01159, DRP1, density-regulated protein DRP1. This protein
family shows weak but suggestive similarity to
translation initiation factor SUI1 and its prokaryotic
homologs.
Length = 173
Score = 84.2 bits (208), Expect = 5e-20
Identities = 31/55 (56%), Positives = 37/55 (67%), Gaps = 4/55 (7%)
Query: 142 VASKFFGTRFACGSSV----TGDDEIVIQGDVKDDLFDVIPEKWPEIDEDFIEDL 192
ASK F +FA G SV TG +EIVIQGDV DD+ D I EKWPE+ + I+DL
Sbjct: 119 KASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKWPEVGDKDIKDL 173
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 52.5 bits (127), Expect = 2e-09
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 139 DPIVASKFFGTRFACGSSVTGDDEIVIQGDVKDDLFDVIPEKW 181
D +K +F CG +V +EI IQGD +D + D++ ++
Sbjct: 32 DLKKLAKELKKKFGCGGTVKDGEEIEIQGDHRDKVKDLLEKEG 74
>gnl|CDD|211317 cd00474, eIF1_SUI1_like, Eukaryotic initiation factor 1 and related
proteins. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. eIF1 interacts with 18S rRNA in the 40S
ribosomal subunit during eukaryotic translation
initiation. Point mutations in the yeast eIF1 implicate
the protein in maintaining accurate start-site selection
but its mechanism of action is unknown. The function of
non-eukaryotic family members is also unclear.
Length = 78
Score = 47.0 bits (112), Expect = 2e-07
Identities = 24/73 (32%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 121 KKTVQKTSYTEAQFPLSSDPIVASKFFGTRFACGSSVTGD-DEIVIQGDVKDDLFDVIPE 179
K V K A L + + CG SV G+ EI IQGD D + + E
Sbjct: 12 GKKVTKVEGLPAYIDLRK----LADELKKKLGCGGSVEGEKMEIEIQGDHTDQIIVALEE 67
Query: 180 KWPEIDEDFIEDL 192
K ID+D++E L
Sbjct: 68 KG--IDKDWVELL 78
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 42.7 bits (101), Expect = 2e-05
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 144 SKFFGTRFACGSSVTGDDEIVIQGDVKDDLFDVI-----PEKWPEID 185
+K + ACG +V D EI IQGD +D + +++ K I+
Sbjct: 59 AKELKKKCACGGTVK-DGEIEIQGDHRDKVKELLIKKGFKVKNIGIE 104
>gnl|CDD|211319 cd11567, YciH_like, Homologs of eIF1/SUI1 including Escherichia
coli YciH. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. The function of non-eukaryotic family
members is unclear. Escherichia coli YciH is a
non-essential protein and was reported to be able to
perform some of the functions of IF3 in prokaryotic
initiation.
Length = 76
Score = 33.6 bits (78), Expect = 0.013
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 149 TRFACGSSVTGDDEIVIQGDVKDDL 173
+ CG +V D EI +QGD ++ +
Sbjct: 39 KKCGCGGTVK-DGEIELQGDHREKI 62
>gnl|CDD|236418 PRK09225, PRK09225, threonine synthase; Validated.
Length = 462
Score = 31.3 bits (72), Expect = 0.50
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 162 EIVIQGDVKDD-LFDVIPEKWPEIDEDFIEDLGDLKSPTY-NIAYYVL 207
E V+QG D L+ +PE+ P++ + I+ L L +Y +A+ +L
Sbjct: 17 EAVLQGLAPDGGLY--VPEELPKLSAEEIDALLGL---SYAELAFEIL 59
>gnl|CDD|224266 COG1347, NqrD, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrD [Energy production and conversion].
Length = 208
Score = 30.5 bits (69), Expect = 0.62
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 204 YYVLPTHIIISWVQPNGTLLLTMRSCFTHGFIVLGI 239
+ V PT W QPNG LL + F GF++ G+
Sbjct: 163 FTVFPTIQDGGWYQPNGLFLLAPSAFFLIGFMIWGL 198
>gnl|CDD|225244 COG2369, COG2369, Uncharacterized protein, homolog of phage Mu
protein gp30 [Function unknown].
Length = 432
Score = 30.7 bits (69), Expect = 0.72
Identities = 28/140 (20%), Positives = 43/140 (30%), Gaps = 17/140 (12%)
Query: 79 AKPVGDFREIVLRGSSVSQDMSVSHLLKNKKLASLMGTTPPSKKTVQKTSYTEAQFPLSS 138
P+ D + RG VSQ L+N G K + + +
Sbjct: 250 VIPLSD-SNVEARGLIVSQSEKEVEKLENVAKDKDTGEAREEKVKLISKKRKSMKKGIGW 308
Query: 139 DPIVASKFFGTRFACGSSVTGDDEIVIQ-GDVKDDLFDVIPEKWPEIDEDFIEDLGDLKS 197
D V S FGT D ++ VK+ + I + E+ F + D+
Sbjct: 309 DYNVGSAAFGT----------DMAVIRNLILVKNKRYQEIQQHNNELLRQFAFEEWDM-- 356
Query: 198 PTYNIAYYVLPTHIIISWVQ 217
N PT +S
Sbjct: 357 ---NFLDTRAPTLNSLSIGD 373
>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
prediction only].
Length = 352
Score = 30.4 bits (69), Expect = 0.97
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 11/68 (16%)
Query: 145 KFFGTRFACGSSVTGDDEIVIQGD--VKDDLFDVIPEKWPEIDEDFIEDLGD-------- 194
KFF D I++ G K+D +D + E++PE+ IED
Sbjct: 177 KFFDEIAKALKEYANLDIIIVAGPGFAKEDFYDFLRERYPELANIVIEDTSTGGRAGINE 236
Query: 195 -LKSPTYN 201
LK +
Sbjct: 237 VLKRGAVD 244
>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2. This
domain family is found in eukaryotes, and is typically
between 138 and 153 amino acids in length. The family is
found in association with pfam00493. Mini-chromosome
maintenance (MCM) proteins are essential for DNA
replication. These proteins use ATPase activity to
perform this function.
Length = 145
Score = 29.2 bits (66), Expect = 1.3
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 182 PEIDEDFIEDLGDLKSPTY 200
P +E +EDL D+K+ +
Sbjct: 127 PLEEELSLEDLSDVKAASI 145
>gnl|CDD|226733 COG4283, COG4283, Uncharacterized conserved protein [Function
unknown].
Length = 170
Score = 28.6 bits (64), Expect = 2.0
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 171 DDLFDVIPEKWPEIDEDFIEDLGDLKSPTYNIAYYVLPTHIIISWVQPN 219
L + I E+ D F D K+P N+A+ V +++++W Q
Sbjct: 22 LSLIESISEE--LKDTRFDFVDRD-KNPRDNLAHLVEWHNLLLNWEQDE 67
>gnl|CDD|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function
prediction only].
Length = 351
Score = 28.5 bits (63), Expect = 3.9
Identities = 14/71 (19%), Positives = 22/71 (30%), Gaps = 7/71 (9%)
Query: 74 SHGGCAKPVGDFREIVLR-----GSSVSQDMSVSHLLKNKKLASLMGTTPPSKKTVQKTS 128
KP G ++ +LR D + +K ++SL T P K +
Sbjct: 102 RGSNANKPYGLYKTEMLRSSTEIPYCRYPDKNPF--AHSKAISSLAQTHPKYKTESLEVF 159
Query: 129 YTEAQFPLSSD 139
P S
Sbjct: 160 INPGYVPYSKR 170
>gnl|CDD|130455 TIGR01388, rnd, ribonuclease D. This model describes ribonuclease
D, a 3'-exonuclease shown to act on tRNA both in vitro
and when overexpressed in vivo. Trusted members of this
family are restricted to the Proteobacteria; Aquifex,
Mycobacterial, and eukaryotic homologs are not
full-length homologs. Ribonuclease D is not essential in
E. coli and is deleterious when overexpressed. Its
precise biological role is still unknown [Transcription,
RNA processing].
Length = 367
Score = 28.2 bits (63), Expect = 5.1
Identities = 10/66 (15%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 78 CAKPVGDFREIVLRGSSVSQDMSVSHLLKNKKLASLMGTTPPSKKTVQKTSYTEAQFPLS 137
+ + +RE + +D+ + +LK + L L P + + ++
Sbjct: 212 VLQALAAWRE----REARERDLPRNFVLKEEALWELARQAPGNLTELASLGPKGSEIRKH 267
Query: 138 SDPIVA 143
D ++A
Sbjct: 268 GDTLLA 273
>gnl|CDD|176467 cd01595, Adenylsuccinate_lyase_like, Adenylsuccinate lyase
(ASL)_like. This group contains ASL, prokaryotic-type
3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and
related proteins. These proteins are members of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. ASL catalyzes two steps in the
de novo purine biosynthesis: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and; the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP). pCMLE catalyzes the
cyclization of 3-carboxy-cis,cis-muconate (3CM) to
4-carboxy-muconolactone, in the beta-ketoadipate
pathway. ASL deficiency has been linked to several
pathologies including psychomotor retardation with
autistic features, epilepsy and muscle wasting.
Length = 381
Score = 27.9 bits (63), Expect = 5.7
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 8/37 (21%)
Query: 176 VIPEKWPEIDEDFIEDLGDLKSPTYNIAYYVLPTHII 212
+ K PE++E E LG LK P T I
Sbjct: 184 SLGPKGPEVEERVAEKLG-LKVPPI-------TTQIE 212
>gnl|CDD|107203 cd01560, Thr-synth_2, Threonine synthase catalyzes the final step
of threonine biosynthesis. The conversion of
O-phosphohomoserine into threonine and inorganic
phosphate is pyridoxal 5'-phosphate dependent. The
Thr-synth_1 CD includes members from higher plants,
cyanobacteria, archaebacteria and eubacterial groups.
This CD, Thr-synth_2, includes enzymes from fungi and
eubacterial groups, as well as, metazoan threonine
synthase-like proteins.
Length = 460
Score = 27.6 bits (62), Expect = 7.1
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 11/66 (16%)
Query: 145 KFFGTRFACGSSVTGD-DEIVIQGDVKDD-LFDVIPEKWPEIDEDFIEDLGDLKSPTYN- 201
K+ TR G + E ++ G D L+ +PE+ P++ + I L +Y
Sbjct: 1 KYVSTR---GGNPGVSFSEALLSGLAPDGGLY--VPEELPKLSAEEIASWSGL---SYQE 52
Query: 202 IAYYVL 207
+A+ VL
Sbjct: 53 LAFEVL 58
>gnl|CDD|201826 pfam01493, GXGXG, GXGXG motif. This domain is found in glutamate
synthase, tungsten formylmethanofuran dehydrogenase
subunit c (FwdC) and molybdenum formylmethanofuran
dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G
motif is seen in the alignment.
Length = 198
Score = 27.2 bits (61), Expect = 7.5
Identities = 7/26 (26%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 148 GTRFACGSSVTGDDEIVIQGDVKDDL 173
G F G+ + G + ++GD D +
Sbjct: 42 GQSF--GAFMKGGVTLEVEGDANDYV 65
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 27.7 bits (61), Expect = 8.0
Identities = 26/115 (22%), Positives = 44/115 (38%), Gaps = 11/115 (9%)
Query: 97 QDMSVSHLLKNKKLASLMGTTPPSKKTVQKTSYTEAQFPLSSDPIVASKFFGTRFACGSS 156
+D+ +S LL N+KL P K VQ Q S
Sbjct: 145 KDLFISGLLPNRKL-RYFKNQPGLSKEVQNK--YLKQRIFES---FLKNLRFRVLEVLEV 198
Query: 157 VTGDDEIVIQGDVKDDLFDVIPEKWPEIDED----FIEDLGDLKSPTYNIAYYVL 207
++ D ++ V ++D++ + PE + + FI LGD + + A YV+
Sbjct: 199 LSHDPIQYVKKQVVRLVYDLLEAR-PEQEVNLLHLFINKLGDKRDKVSSKASYVI 252
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
0.323 0.139 0.435
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,643,200
Number of extensions: 1295042
Number of successful extensions: 1036
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1033
Number of HSP's successfully gapped: 21
Length of query: 266
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 171
Effective length of database: 6,723,972
Effective search space: 1149799212
Effective search space used: 1149799212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.1 bits)