RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043121
(169 letters)
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 71.8 bits (177), Expect = 7e-17
Identities = 26/46 (56%), Positives = 35/46 (76%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKN 72
+ +DT++ SGPG Q+ NK ESAVRL H+PTG++ E+RSQHKN
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKN 59
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 71.8 bits (177), Expect = 2e-15
Identities = 27/59 (45%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHAS 75
+E+ +L +DTY+ SG G QH NK +SAVR+ H+PTG++ +RSQH+N AS
Sbjct: 230 IEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKAS 284
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 68.6 bits (169), Expect = 3e-14
Identities = 23/46 (50%), Positives = 33/46 (71%)
Query: 29 EMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
+DT++ SG G QH N +SAVR+ H+PTG++ ++RSQHKN A
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKA 269
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 68.6 bits (168), Expect = 3e-14
Identities = 26/49 (53%), Positives = 35/49 (71%)
Query: 31 DTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNL 79
DTY+ SG G QH NK +SAVR+ H+PTG++ DRSQHKN S++ +
Sbjct: 240 DTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKV 288
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 67.6 bits (166), Expect = 8e-14
Identities = 23/46 (50%), Positives = 33/46 (71%)
Query: 29 EMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
+DT++ SG G QH N +SAVR+ H+PTG++ ++RSQHKN A
Sbjct: 226 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKA 271
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 65.6 bits (160), Expect = 3e-13
Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 4/66 (6%)
Query: 18 ELTDDELLR----ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNH 73
ELTDD+ + + ++DTY+ G G QH NK ESAVR+ H+PTG++ +RSQH N
Sbjct: 184 ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNK 243
Query: 74 ASSVNL 79
+++ +
Sbjct: 244 ETAMKM 249
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 64.2 bits (157), Expect = 6e-13
Identities = 29/59 (49%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHAS 75
+E+ DD+L +DTY+ SG G QH NK +SAVRL H+PTG++ +RSQH N A
Sbjct: 105 IEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKAL 159
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 64.9 bits (158), Expect = 6e-13
Identities = 24/50 (48%), Positives = 35/50 (70%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASS 76
+ +DTY+ SG G QH N +SAVR+ H+PTG++ ++RSQHKN A +
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKA 249
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 64.7 bits (158), Expect = 8e-13
Identities = 22/48 (45%), Positives = 33/48 (68%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
+ +DT++ SG G QH N +SAVR+ H+PTG++ ++RSQHKN
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKD 269
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 60.9 bits (148), Expect = 4e-12
Identities = 26/55 (47%), Positives = 33/55 (60%), Gaps = 4/55 (7%)
Query: 18 ELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKN 72
E T+DE+ E T + SGPG QH NK ESAVR H+ +G+ +RSQH N
Sbjct: 102 EATEDEIRFE----TLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHAN 152
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 58.1 bits (141), Expect = 5e-11
Identities = 22/50 (44%), Positives = 29/50 (58%)
Query: 23 ELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKN 72
E E +T + SGPG QH NK +SAVR H+ +G+ +RSQH N
Sbjct: 104 EQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHAN 153
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 56.2 bits (135), Expect = 6e-10
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 31 DTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLDA 81
D Y+ SG G QH NK ESAVR+ H+PT + RSQH+N +++ + A
Sbjct: 181 DVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLA 231
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 49.0 bits (116), Expect = 2e-07
Identities = 21/53 (39%), Positives = 32/53 (60%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNL 79
+ ++DTY+ SG G QH N +SAVR+ H PT + +RSQ KN ++ +
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKM 250
>gnl|CDD|215735 pfam00126, HTH_1, Bacterial regulatory helix-turn-helix protein,
lysR family.
Length = 60
Score = 29.6 bits (68), Expect = 0.14
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 127 AVEGSVSEAAKLLWLSTGALSRLI 150
A EGS + AA+ L LS A+SR I
Sbjct: 11 AEEGSFTAAAERLGLSQPAVSRQI 34
>gnl|CDD|236402 PRK09191, PRK09191, two-component response regulator; Provisional.
Length = 261
Score = 29.8 bits (68), Expect = 0.58
Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 17/75 (22%)
Query: 101 SEVGPQIGPNNPKFSLGMQALLD----------LIFAVEG-SVSEAAKLLWLSTGALSRL 149
S G F + L L+ A+EG SV EAA++L + L
Sbjct: 65 SSAGANDPEPGSPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEAL 124
Query: 150 ILSDDSHQIAVNELR 164
+ A E+
Sbjct: 125 L------DDARAEIA 133
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 28.6 bits (65), Expect = 0.86
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 36 SGPGSQHRNKRESAVRL 52
SGPG Q+ NK +AV L
Sbjct: 23 SGPGGQNVNKVSTAVEL 39
>gnl|CDD|239831 cd04365, IlGF_relaxin_like, IlGF_like family, relaxin_like
subgroup, specific to vertebrates. Members include a
number of active peptides including (pro)relaxin,
mammalian Leydig cell-specific insulin-like peptide
(gene INSL3), early placenta insulin-like peptide
(ELIP; gene INSL4), and insulin-like peptides 5 (INSL5)
and 6 (INSL6). Members of this subgroup are widely
expressed in testes (INSL3, INSL6), decidua, placenta,
prostate, corpus luteum, brain (various relaxins), GI
tract, and kidney (INSL5) where they serve a variety of
functions in parturition and development. Typically,
the active forms of these peptide hormones are composed
of two chains (A and B) linked by two disulfide bonds;
the arrangement of four cysteines is conserved in the
"A" chain: Cys1 is linked by a disulfide bond to Cys3,
Cys2 and Cys4 are linked by interchain disulfide bonds
to cysteines in the "B" chain. This alignment contains
both chains, plus the intervening linker region,
arranged as found in the propeptide form. Propeptides
are cleaved to yield two separate chains linked
covalently by the two disulfide bonds.
Length = 59
Score = 27.3 bits (61), Expect = 0.91
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 4/37 (10%)
Query: 22 DELLRE----CEMDTYKLSGPGSQHRNKRESAVRLKH 54
EL+R C ++ G + R KR+ + L
Sbjct: 7 RELVRAVIEICGGSRWRRLGLDTHSRKKRQFSRGLSE 43
>gnl|CDD|130539 TIGR01474, ubiA_proteo, 4-hydroxybenzoate polyprenyl transferase,
proteobacterial. This model represents a family of
integral membrane proteins that condenses
para-hydroxybenzoate with any of several
polyprenyldiphosphates. Heterologous expression studies
suggest that for, many but not all members, the activity
seen (e.g. octaprenyltransferase in E. coli) reflects
available host isoprenyl pools rather than enzyme
specificity. A fairly deep split by both clustering
(UPGMA) and phylogenetics (NJ tree) separates this group
(mostly Proteobacterial and mitochondrial), with several
characterized members, from another group (mostly
archaeal and Gram-positive bacterial) lacking
characterized members [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 281
Score = 28.4 bits (64), Expect = 1.5
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 110 NNPKFSL-GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSKV 168
+N K L G+ AL+ L+ A+ G ++ + +L A + L+ QIA ++R +
Sbjct: 202 DNTKPWLGGLYALMILLLALAGLIAGLGPVYYLGLAAAALLL----IRQIATLDIRDPEN 257
Query: 169 C 169
C
Sbjct: 258 C 258
>gnl|CDD|173956 cd08197, DOIS, 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes
carbocycle formation from D-glucose-6-phosphate to
2-deoxy-scyllo-inosose through a multistep reaction in
the biosynthesis of aminoglycoside antibiotics.
2-deoxy-scyllo-inosose synthase (DOIS) catalyzes
carbocycle formation from D-glucose-6-phosphate to
2-deoxy-scyllo-inosose through a multistep reaction in
the biosynthesis of aminoglycoside antibiotics.
2-Deoxystreptamine (DOS)-containing aminoglycoside
antibiotics includes neomycin, kanamycin, gentamicin,
and ribostamycin. They are important antibacterial
agents. DOIS is a homologue of the dehydroquinate
synthase which catalyzes the cyclization of
3-deoxy-D-arabino-heputulosonate-7-phosphate to
dehydroquinate (DHQ) in the shikimate pathway.
Length = 355
Score = 28.4 bits (64), Expect = 1.7
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 50 VRLKHVPTGVIAH--AAEDRSQHKNHASSVNL-DAYSPP------PQLLQILPPK 95
+RL H+PT ++A + Q N NL Y PP ++L+ LP +
Sbjct: 111 IRLVHIPTTLLAQSDSVLSLKQAVNSTYGKNLIGLYYPPSFIFIDTRVLRTLPER 165
>gnl|CDD|149795 pfam08849, DUF1819, Putative inner membrane protein (DUF1819).
These proteins are functionally uncharacterized. Several
are annotated as putative inner membrane proteins.
Length = 191
Score = 26.8 bits (60), Expect = 5.0
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 124 LIFAVEGSVSEAAKLLWLSTGALSRLI 150
L EGS EA +LLW + RL+
Sbjct: 72 LRLLAEGSREEAKQLLWAAACRHYRLV 98
>gnl|CDD|227728 COG5441, COG5441, Uncharacterized conserved protein [Function
unknown].
Length = 401
Score = 27.1 bits (60), Expect = 5.0
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 25/77 (32%)
Query: 89 LQILP---PK---STITSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLS 142
++ LP PK ST+ S +V P +G + D+I SV++ A L
Sbjct: 111 MRRLPLGVPKVMVSTLASGDVAPYVGVS------------DIIMMY--SVTDMAGL---- 152
Query: 143 TGALSRLILSDDSHQIA 159
+SR++LS+ +H IA
Sbjct: 153 -NRISRVVLSNAAHAIA 168
>gnl|CDD|177082 CHL00180, rbcR, LysR transcriptional regulator; Provisional.
Length = 305
Score = 26.9 bits (60), Expect = 5.5
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 127 AVEGSVSEAAKLLWLSTGALSRLI 150
A EGS +AA+ L++S A+S I
Sbjct: 17 ATEGSFKKAAESLYISQPAVSLQI 40
>gnl|CDD|212072 cd11503, SLC5sbd_NIS, Na(+)/iodide cotransporter NIS and related
proteins; solute-binding domain. NIS (product of the
SLC5A5 gene) transports I-, and other anions including
ClO4-, SCN-, and Br-. NIS is expressed in the thyroid,
colon, ovary, and in human breast cancers. It mediates
the active transport and the concentration of iodide
from the blood into thyroid follicular cells, a
fundamental step in thyroid hormone biosynthesis, and is
the basis of radioiodine therapy for thyroid cancer.
Mutation in the SLC5A5 gene can result in a form of
thyroid hormone dysgenesis. Human NIS exists mainly as a
dimer stabilized by a disulfide bridge. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 535
Score = 26.7 bits (59), Expect = 6.3
Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 9/56 (16%)
Query: 82 YSPPPQLLQILP------PKSTITSSEVGPQIGPN---NPKFSLGMQALLDLIFAV 128
Y P Q++ +LP P + +T S G + + AL D +A+
Sbjct: 452 YPPSAQIMGVLPTSAAHCPLTNVTLSTTGSVNASSPPQSSSMDNIRPALADDFYAI 507
>gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and is a member of the
iron-activated alcohol dehydrogenase-like family. They
are distinct from other alcohol dehydrogenases which
contains different protein domain. Proteins of this
family have not been characterized. Their specific
function is unknown. They are mainly found in bacteria.
Length = 374
Score = 26.4 bits (59), Expect = 7.6
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 6 SSSSSSKKKNYLELTDDELLR 26
++ SSS K N + L+D ELL
Sbjct: 351 AAGSSSMKGNPVPLSDAELLE 371
>gnl|CDD|223656 COG0583, LysR, Transcriptional regulator [Transcription].
Length = 297
Score = 26.1 bits (57), Expect = 9.6
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 127 AVEGSVSEAAKLLWLSTGALSRLI 150
A EGS + AA+ L LS A+SR I
Sbjct: 13 AEEGSFTRAAERLGLSQSAVSRQI 36
>gnl|CDD|224916 COG2005, ModE, N-terminal domain of molybdenum-binding protein
[General function prediction only].
Length = 130
Score = 25.7 bits (57), Expect = 9.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 111 NPKFSLGMQALLDLIFAVEGSVSEAAKLLWLS 142
+ + G LL I A GS+S AAK +S
Sbjct: 14 DLRAGPGRIELLKAI-AETGSISAAAKAAGIS 44
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
0.310 0.126 0.355
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,052,302
Number of extensions: 707289
Number of successful extensions: 429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 429
Number of HSP's successfully gapped: 35
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.1 bits)