RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028409
(209 letters)
>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 = 197 bits (502), Expect = 8e-65
Identities = 76/183 (41%), Positives = 100/183 (54%), Gaps = 14/183 (7%)
Query: 7 PVRVLYCSICSLPAEYCEFGPDFEKCKPWLIKNAPELYPDLLKE---ANEKEAEKVSGQL 63
P+RVLYC +CSLP EYCEF D ++CK WL +NAP+LY L E EA +
Sbjct: 1 PLRVLYCGVCSLPPEYCEFSGDLKRCKVWLSENAPDLYAKLYGTDSPTAEAEAVTIGEAQ 60
Query: 64 QLFGLSSGGADGATSGQTSSSKQEEVKRLPGGKIKKKERQEVVIEKVVRNKRKCITIVKG 123
+ G G Q + GGK KKK Q+V I++ R KRK +T++KG
Sbjct: 61 EEKGEKD--LLGIQKAQEAR---------EGGKKKKKLPQKVTIKREPRTKRKFVTVIKG 109
Query: 124 LDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDISYDIVEFITDTWPAVISLS 183
L+ F + L ASK +KFATG SV K T KE+I +QGD+ DI ++I + WP V
Sbjct: 110 LETFDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKWPEVGDKD 169
Query: 184 IFF 186
I
Sbjct: 170 IKD 172
>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 = 125 bits (316), Expect = 1e-37
Identities = 38/84 (45%), Positives = 55/84 (65%)
Query: 103 QEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQG 162
+V I+++ RNKRK +T V GL+ FG+ L A+K KKFA GASV KG K++I +QG
Sbjct: 1 SKVTIKRISRNKRKFVTTVTGLETFGIDLKKAAKLFAKKFACGASVTKGAEGKDEIVIQG 60
Query: 163 DISYDIVEFITDTWPAVISLSIFF 186
D++ DIV+ I + WP + +I
Sbjct: 61 DVTDDIVDLILEKWPEIDEDNIEI 84
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 74.1 bits (183), Expect = 8e-18
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 99 KKERQEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQI 158
KKE Q++ I + R K +T+V GL+LFG+ L +K+L KKF G +V G E+I
Sbjct: 1 KKEDQKIRIRREKRRGGKTVTVVTGLELFGIDLKKLAKELKKKFGCGGTVKDG----EEI 56
Query: 159 DVQGDISYDIVEFITDTW 176
++QGD + + +
Sbjct: 57 EIQGDHRDKVKDLLEKEG 74
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 63.1 bits (154), Expect = 3e-13
Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
Query: 90 KRLPGGKIKKKERQEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVV 149
K L ++ K+ Q V I + R K K +TI++GLDL + L +K+L KK A G +V
Sbjct: 14 KELTCEEVAKEGDQIVRIRRETRRKGKTVTIIEGLDLKDIDLKKLAKELKKKCACGGTVK 73
Query: 150 KGPTEKEQIDVQGDISYDIVEFITD 174
G +I++QGD + E +
Sbjct: 74 DG-----EIEIQGDHRDKVKELLIK 93
>gnl|CDD|211321 cd11608, eIF2D_C, C-terminal domain of eIF2D and related proteins.
eIF2D translation initiation factor (also known as
ligatin) is involved in the recruitment and delivery of
aminoacyl-tRNAs to the P-site of the eukaryotic ribosome
in a GTP-independent manner.
Length = 85
Score = 47.9 bits (115), Expect = 7e-08
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 104 EVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKE--QIDVQ 161
++ E+ NK+ +T++ GL+ FG+ + +K+L KK A SV P +K+ ++ VQ
Sbjct: 3 DITTERRQGNKK--VTLISGLESFGIDPEEFAKELQKKCAASTSVSPLPGKKKGVEVQVQ 60
Query: 162 GDISYDIVEFITDTW 176
G+ + + +T+ +
Sbjct: 61 GNQVKFVAKLLTEKY 75
>gnl|CDD|211318 cd11566, eIF1_SUI1, Eukaryotic initiation factor 1. eIF1/SUI1
(eukaryotic initiation factor 1) plays 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.
Length = 84
Score = 42.9 bits (102), Expect = 6e-06
Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 112 RNKRKCITIVKGL-DLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDISYDIVE 170
RN RK +T V+GL + F +K K K+FA +VV+ P E I +QGD +I E
Sbjct: 10 RNGRKTLTTVQGLPEEFDLKK--ILKAFKKEFACNGTVVEDPEYGEVIQLQGDQRKNIKE 67
Query: 171 FITD 174
F+ +
Sbjct: 68 FLLE 71
>gnl|CDD|179173 PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
Length = 99
Score = 43.0 bits (102), Expect = 7e-06
Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 100 KERQEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQID 159
KE+Q + I+ R K +TI++G+D + L + +KKL K A G +V G +I+
Sbjct: 21 KEQQRIKIKVDKRRYGKEVTIIEGIDPKDIDLKELAKKLKSKLACGGTVKDG-----RIE 75
Query: 160 VQGD 163
+QGD
Sbjct: 76 LQGD 79
>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 = 41.6 bits (98), Expect = 1e-05
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 105 VVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDI 164
+ I+ R+ K +T V+GL + + L + +L KK G SV EK +I++QGD
Sbjct: 2 IHIKVEQRSGGKKVTKVEGLPAY-IDLRKLADELKKKLGCGGSVEG---EKMEIEIQGDH 57
Query: 165 SYDIVEFITDTWPAVISLSI 184
+ I+ + + + +
Sbjct: 58 TDQIIVALEEKGIDKDWVEL 77
>gnl|CDD|130226 TIGR01158, SUI1_rel, translation initation factor SUI1, putative,
prokaryotic. This family of archaeal and bacterial
proteins is homologous to the eukaryotic translation
intiation factor SUI1 involved in directing the ribosome
to the proper start site of translation by functioning
in concert with eIF-2 and the initiator tRNA-Met
[Protein synthesis, Translation factors].
Length = 101
Score = 40.0 bits (94), Expect = 7e-05
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 97 IKKKERQEVVIEKVVRN-KRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEK 155
K KE Q V I++ R K K +TI++GLDL + L + +K+L K G +V G
Sbjct: 18 AKPKEDQVVRIQRETRGRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGTVKDG---- 73
Query: 156 EQIDVQGD 163
I++QGD
Sbjct: 74 -VIEIQGD 80
>gnl|CDD|130228 TIGR01160, SUI1_MOF2, translation initiation factor SUI1,
eukaryotic. Alternate name: MOF2. A similar protein
family (see TIGRFAMs model TIGR01158) is found in
prokaryotes. The human proteins complements a yeast SUI1
mutatation [Protein synthesis, Translation factors].
Length = 110
Score = 39.0 bits (91), Expect = 2e-04
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 112 RNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDISYDIVEF 171
RN RK +T V+GL L K L K+FA +V++ P E I +QGD ++ EF
Sbjct: 35 RNGRKTLTTVQGLPK-EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEF 93
Query: 172 I 172
+
Sbjct: 94 L 94
>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 = 34.4 bits (80), Expect = 0.005
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 109 KVVRNKR----KCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGDI 164
+V KR K +T+++GL L L + +K+L KK G +V + +I++QGD
Sbjct: 4 RVRLEKRGRGGKTVTVIEGLPLSEEDLKELAKELKKKCGCGGTV-----KDGEIELQGDH 58
Query: 165 SYDIVEFITD 174
I E +
Sbjct: 59 REKIKELLEK 68
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 31.6 bits (72), Expect = 0.28
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 38 KNAPELYPDL---LKEANEKEAEKVSGQLQLFGLSSGGADGATSGQTSSSKQEEVKRLPG 94
N +L DL L A+ + ++ SGQ LF L +G + A++ +S+ K V P
Sbjct: 897 ANRAQLIADLDLVLDWASSRARDRASGQGNLFDLLAGSEEEASNDLSSAPKAAPVPDYPP 956
Query: 95 GKIKKKERQ 103
+ K E++
Sbjct: 957 TEKLKLEKE 965
>gnl|CDD|181613 PRK09019, PRK09019, translation initiation factor Sui1; Validated.
Length = 108
Score = 29.6 bits (67), Expect = 0.39
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 114 KRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQGD 163
K K + ++ GLDL +L + +L KK G +V G I++QGD
Sbjct: 43 KGKGVCLITGLDLDDAELKKLAAELKKKCGCGGAVKDG-----VIEIQGD 87
>gnl|CDD|168689 PRK06824, PRK06824, translation initiation factor Sui1; Validated.
Length = 118
Score = 28.9 bits (65), Expect = 0.79
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 12/61 (19%)
Query: 110 VVRNKR-------KCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQIDVQG 162
+VR +R K +T++ G+ L L + +K+L ++ TG ++ G I++QG
Sbjct: 42 IVRVRRETKGRGGKTVTVITGVPLAEDALKELAKELKRRCGTGGTLKDG-----VIEIQG 96
Query: 163 D 163
D
Sbjct: 97 D 97
>gnl|CDD|224235 COG1316, LytR, Transcriptional regulator [Transcription].
Length = 307
Score = 29.7 bits (67), Expect = 1.1
Identities = 11/92 (11%), Positives = 24/92 (26%), Gaps = 15/92 (16%)
Query: 90 KRLPGGKIKKKERQEVVIEKVVRNKRKCITIVKGLDLFG---------VKLSDASKKLGK 140
K L G + + RQ V+ + +I K L + +++ + +
Sbjct: 189 KALARGDLGRAARQREVMTALANKMLSPNSIFKYQSLLNDISSNFKTNITINNLTALMAY 248
Query: 141 KFATGASVVKGPTEKEQIDVQGDISYDIVEFI 172
K Q+ +
Sbjct: 249 KDCLNK------VVSIQLQGVSQMVDGGSYEF 274
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known
are DNA polymerases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 28.9 bits (65), Expect = 2.2
Identities = 13/51 (25%), Positives = 18/51 (35%)
Query: 46 DLLKEANEKEAEKVSGQLQLFGLSSGGADGATSGQTSSSKQEEVKRLPGGK 96
D L + K+ + GQ LFG S G + + K L K
Sbjct: 895 DALDAVSRKKKAEALGQNSLFGALSEGTKPEYVFFPPDEEWPDKKLLALEK 945
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 28.0 bits (63), Expect = 3.8
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 130 KLSDASKKLGKKFATGASVVKGPTEKEQIDVQ----GDI 164
+ SDA KL K + A+++ E E++ V+ GDI
Sbjct: 77 RASDALSKLAKLQPSTATLLTDDGEIEEVPVELLQPGDI 115
>gnl|CDD|188318 TIGR03416, ABC_choXWV_perm, choline ABC transporter, permease
protein.
Length = 267
Score = 27.3 bits (61), Expect = 5.3
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 5 PQPVRVLYCSICSLPAEYCEFGPDFEKCKPW 35
P P+R+ + I S+P E E G F P
Sbjct: 163 PAPIRLTHLGISSVPQELVEAGEAF-GATPS 192
>gnl|CDD|180843 PRK07108, PRK07108, acetyl-CoA acetyltransferase; Provisional.
Length = 392
Score = 27.0 bits (60), Expect = 7.5
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 10/56 (17%)
Query: 34 PWLIKNAPELYPDLLKEANEKEAEKVSGQLQLFGLSSGGAD--GATSGQTSSSKQE 87
WL+++ PE+Y +L+ A E A++ +G+S D G S Q +++ Q
Sbjct: 135 GWLVEHKPEIYWSMLQTA-ENVAKR-------YGISKERQDEYGVQSQQRAAAAQA 182
>gnl|CDD|240529 cd13124, MATE_SpoVB_like, Stage V sporulation protein B, also known
as Stage III sporulation protein F, and related
proteins. The integral membrane protein SpoVB has been
implicated in the biosynthesis of the peptidoglycan
component of the spore cortex in Bacillus subtilis. This
model represents a subfamily of the multidrug and toxic
compound extrusion (MATE)-like proteins. Proteins from
the MATE family are involved in exporting metabolites
across the cell membrane and are often responsible for
multidrug resistance (MDR).
Length = 434
Score = 26.7 bits (60), Expect = 9.7
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 178 AVISLSIFFSFSCVLHKWCIWKTLK 202
A I+ I F + +L+ + K L
Sbjct: 409 AAIATVIGFLVAALLNLRALKKLLG 433
>gnl|CDD|212105 cd10793, GH57N_TLGT_like, N-terminal catalytic domain of
4-alpha-glucanotransferase; glycoside hydrolase family
57 (GH57). 4-alpha-glucanotransferase (TLGT, EC
2.4.1.25) plays a key role in the maltose metabolism.
It catalyzes the disproportionation of amylose and the
formation of large cyclic alpha-1,4-glucan
(cycloamylose) from linear amylose. TLGT functions as a
homodimer. Each monomer is composed of two domains, an
N-terminal catalytic domain with a (beta/alpha)7 barrel
fold and a C-terminal domain with a twisted
beta-sandwich fold. Some family members have been
designated as alpha-amylases, such as the heat-stable
eubacterial amylase from Dictyoglomus thermophilum
(DtAmyA) and the extremely thermostable archaeal
amylase from Pyrococcus furiosus(PfAmyA). However, both
of these proteins are 4-alpha-glucanotransferases.
DtAmyA was shown to have transglycosylating activity
and PfAmyA exhibits 4-alpha-glucanotransferase
activity.
Length = 279
Score = 26.8 bits (60), Expect = 9.9
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 7/33 (21%)
Query: 35 WLIKNAPELYPDLLKEANEKEAEKVSGQLQLFG 67
WL +N PE DLL++ + GQ+++ G
Sbjct: 53 WLEENHPEYL-DLLRKLVD------RGQIEILG 78
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
0.317 0.136 0.407
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,506,955
Number of extensions: 959708
Number of successful extensions: 945
Number of sequences better than 10.0: 1
Number of HSP's gapped: 938
Number of HSP's successfully gapped: 31
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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 (21.6 bits)
S2: 57 (25.8 bits)