RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9114
(98 letters)
>gnl|CDD|216689 pfam01765, RRF, Ribosome recycling factor. The ribosome
recycling factor (RRF / ribosome release factor)
dissociates the ribosome from the mRNA after
termination of translation, and is essential bacterial
growth. Thus ribosomes are "recycled" and ready for
another round of protein synthesis.
Length = 165
Score = 69.1 bits (170), Expect = 3e-16
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFPQLIPVTMKALVDSGMNMNPQ 86
P ++ ++V++ L LA IS +TL+I LI KA++ S + +NPQ
Sbjct: 16 PSLLDGIRVDYYGSPTPLNQLASISVPEARTLLITPWD-KSLIKAIEKAILASDLGLNPQ 74
Query: 87 QEGTTIIIPIPK 98
+G I IPIP
Sbjct: 75 NDGQVIRIPIPP 86
>gnl|CDD|238288 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling
factor dissociates the posttermination complex, composed
of the ribosome, deacylated tRNA, and mRNA, after
termination of translation. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis. RRF is believed to bind the ribosome at the
A-site in a manner that mimics tRNA, but the specific
mechanisms remain unclear. RRF is essential for
bacterial growth. It is not necessary for cell growth
in archaea or eukaryotes, but is found in mitochondria
or chloroplasts of some eukaryotic species.
Length = 179
Score = 60.0 bits (146), Expect = 1e-12
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFPQLIPVTMKALVDSGMNMNPQ 86
P ++S+ VE+ L LA IS P+T++IN I KA+++S + +NP
Sbjct: 30 PALLDSITVEYYGAPTPLNQLASISVPEPRTIVINPFDK-SAIKAIEKAILNSDLGLNPN 88
Query: 87 QEGTTIIIPIPK 98
+G I + +P
Sbjct: 89 NDGAVIRVNLPP 100
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 39.7 bits (94), Expect = 4e-05
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIIN---MSSFPQLIPVTMKALVDSGMNM 83
P ++ +KV++ L +A IS +TL+I S ++ KA+ S + +
Sbjct: 34 PSLLDGIKVDYYGSPTPLNQVASISVPEARTLLIQPWDKS----MLKAIEKAIRASDLGL 89
Query: 84 NPQQEGTTIIIPIP 97
NP +GT I +PIP
Sbjct: 90 NPSNDGTVIRLPIP 103
>gnl|CDD|223311 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal
structure and biogenesis].
Length = 187
Score = 39.5 bits (93), Expect = 5e-05
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSF-PQLIPVTMKALVDSGMNMNP 85
P ++ + VE+ L LA IS +TL+I F ++ KA++ S + +NP
Sbjct: 36 PSLLDRITVEYYGSPTPLNQLASISVPEARTLVI--KPFDKSMVKAIEKAILASNLGLNP 93
Query: 86 QQEGTTIIIPIP 97
+G I +P+P
Sbjct: 94 NNDGNVIRVPLP 105
>gnl|CDD|129587 TIGR00496, frr, ribosome recycling factor. This model finds only
eubacterial proteins. Mitochondrial and/or chloroplast
forms might be expected but are not currently known.
This protein was previously called ribosome releasing
factor. By releasing ribosomes from mRNA at the end of
protein biosynthesis, it prevents inappropriate
translation from 3-prime regions of the mRNA and frees
the ribosome for new rounds of translation.
EGAD|53116|YHR038W is part of the frr superfamily
[Protein synthesis, Translation factors].
Length = 176
Score = 34.7 bits (80), Expect = 0.002
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFPQLIPVTMKALVDSGMNMNPQ 86
P ++ + VE+ L+ LA ++ + +TL+I I KA+ S + +NP
Sbjct: 25 PSLLDRILVEYYGAPTPLRQLASVTVPDARTLVIQPFD-KSNINAIEKAIQRSDLGLNPN 83
Query: 87 QEGTTIIIPIP 97
+G+ I + P
Sbjct: 84 NDGSVIRVNFP 94
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 27.8 bits (62), Expect = 0.73
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 27 PGAIESLKVEFEDDEY----VLQDLAQISRKNPKTLIINMSS 64
GA+E+LK E + + + + Q A + + N I+N++S
Sbjct: 93 EGALEALKQEMDVNVFGLLRLAQAFAPVLKANGGGAIVNLNS 134
>gnl|CDD|222456 pfam13925, Katanin_con80, con80 domain of Katanin. The con80
domain of katanin is the C-terminal region of the
protein that binds to the N-terminal domain of
katanin-p60, the catalytic ATPase. The complex
associates with a specific subregion of the mitotic
spindle leading to increased microtubule disassembly
and targeting of p60 to the spindle poles. The assembly
and function of the mitotic spindle requires the
activity of a number of microtubule-binding proteins.
Katanin, a heterodimeric microtubule-severing ATPase,
is found localized at mitotic spindle poles. A proposed
model is that katanin is targeted to spindle poles
through a combination of direct microtubule binding by
the p60 subunit and through interactions between the
WD40 domain and an unknown protein.
Length = 164
Score = 27.2 bits (61), Expect = 1.1
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 40 DEYVLQDLAQISRKNPKTLIINMSSFPQLIPVTMKAL 76
D VL D+ + ++ K I + L+P+ + L
Sbjct: 42 DLAVLVDVLSVLTQSLKKESITLDLCVDLLPLVEELL 78
>gnl|CDD|187614 cd05356, 17beta-HSD1_like_SDR_c, 17-beta-hydroxysteroid
dehydrogenases (17beta-HSDs) types -1, -3, and -12,
-like, classical (c) SDRs. This subgroup includes
various 17-beta-hydroxysteroid dehydrogenases and
3-ketoacyl-CoA reductase, these are members of the SDR
family, and contain the canonical active site tetrad and
glycine-rich NAD-binding motif of the classical SDRs.
3-ketoacyl-CoA reductase (KAR, aka 17beta-HSD type 12,
encoded by HSD17B12) acts in fatty acid elongation;
17beta- hydroxysteroid dehydrogenases are isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family.
17beta-estradiol dehydrogenase (aka 17beta-HSD type 1,
encoded by HSD17B1) converts estrone to estradiol.
Estradiol is the predominant female sex hormone.
17beta-HSD type 3 (aka testosterone
17-beta-dehydrogenase 3, encoded by HSD17B3) catalyses
the reduction of androstenedione to testosterone, it
also accepts estrogens as substrates. This subgroup also
contains a putative steroid dehydrogenase let-767 from
Caenorhabditis elegans, mutation in which results in
hypersensitivity to cholesterol limitation. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 239
Score = 26.8 bits (60), Expect = 2.0
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 53 KNPKTLIINMSSFPQLIPVTMKA 75
K K I+N+SSF LIP + A
Sbjct: 128 KRKKGAIVNISSFAGLIPTPLLA 150
>gnl|CDD|224199 COG1280, RhtB, Putative threonine efflux protein [Amino acid
transport and metabolism].
Length = 208
Score = 26.4 bits (59), Expect = 2.3
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 54 NPKTLIINMSSFPQLIPVTM 73
NPK ++ ++ PQ +
Sbjct: 124 NPKAILFFLAFLPQFVDPGA 143
>gnl|CDD|216523 pfam01480, PWI, PWI domain.
Length = 74
Score = 25.2 bits (56), Expect = 3.2
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 37 FEDD---EYVLQDLAQISRKNPKTLIINMSSF 65
FEDD +Y+L L +PK + I ++ F
Sbjct: 18 FEDDIVIDYILNLLEDKHNPDPKKIQIQLTGF 49
>gnl|CDD|185406 PTZ00030, PTZ00030, 60S ribosomal protein L20; Provisional.
Length = 121
Score = 25.4 bits (56), Expect = 3.6
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 7/30 (23%)
Query: 49 QISRKNPKTLIINMSSFPQLIPVTMKALVD 78
Q++RK L I P + KALVD
Sbjct: 80 QLNRKILANLAITE-------PFSFKALVD 102
>gnl|CDD|227695 COG5408, COG5408, SPX domain-containing protein [Signal
transduction mechanisms].
Length = 296
Score = 25.6 bits (56), Expect = 4.6
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 34 KVEFEDDEYVLQDLAQISRKNPKTLIINMSSFPQLIPVTMK 74
+V D + QD +++KN T ++++S F I K
Sbjct: 199 EVPSNDQDDEDQDFDYLAKKNDNTALLDLSQFNFKIVKYQK 239
>gnl|CDD|163616 cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal metallophosphatase
domain. Mre11 (also known as SbcD in Escherichia coli)
is a subunit of the MRX protein complex. This complex
includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital
role in several nuclear processes including DNA
double-strand break repair, telomere length maintenance,
cell cycle checkpoint control, and meiotic
recombination, in eukaryotes. During double-strand
break repair, the MRX complex is required to hold the
two ends of a broken chromosome together. In vitro
studies show that Mre11 has 3'-5' exonuclease activity
on dsDNA templates and endonuclease activity on dsDNA
and ssDNA templates. In addition to the N-terminal
phosphatase domain, the eukaryotic MRE11 members of this
family have a C-terminal DNA binding domain (not
included in this alignment model). MRE11-like proteins
are found in prokaryotes and archaea was well as in
eukaryotes. Mre11 belongs to the metallophosphatase
(MPP) superfamily. MPPs are functionally diverse, but
all share a conserved domain with an active site
consisting of two metal ions (usually manganese, iron,
or zinc) coordinated with octahedral geometry by a cage
of histidine, aspartate, and asparagine residues. The
MPP superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 25.4 bits (56), Expect = 5.9
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 12 HSPQPILVNTPLFCIPGAIE 31
H PQ IL P PG+ E
Sbjct: 199 HRPQIILGGGPPIVYPGSPE 218
>gnl|CDD|237689 PRK14359, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 430
Score = 25.3 bits (56), Expect = 6.5
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 10/41 (24%)
Query: 31 ESLKVEFEDDEYVLQDLA----------QISRKNPKTLIIN 61
E++ F + QDL I K+ + LI+N
Sbjct: 60 EAVLEYFPGVIFHTQDLENYPGTGGALMGIEPKHERVLILN 100
>gnl|CDD|187622 cd05364, SDR_c11, classical (c) SDR, subgroup 11. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 253
Score = 25.1 bits (55), Expect = 7.7
Identities = 16/56 (28%), Positives = 19/56 (33%), Gaps = 8/56 (14%)
Query: 17 ILVNTPLFCIPGAIESLKVEFEDDE--------YVLQDLAQISRKNPKTLIINMSS 64
ILVN G E +E D L LA K I+N+SS
Sbjct: 86 ILVNNAGILAKGGGEDQDIEEYDKVMNLNLRAVIYLTKLAVPHLIKTKGEIVNVSS 141
>gnl|CDD|225552 COG3007, COG3007, Uncharacterized paraquat-inducible protein B
[Function unknown].
Length = 398
Score = 24.7 bits (54), Expect = 8.7
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 29 AIESLKVEFEDDEYVLQDLAQISRKNPKT 57
IE++K +F + V+ LA RK+PKT
Sbjct: 121 VIEAIKQDFGKVDLVVYSLASPRRKHPKT 149
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 24.6 bits (54), Expect = 9.3
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 5 ITPQPQRHSPQPILVNTPLFCIPGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMS 63
+TP+PQ +P P + P G + ++ + + VL++L + ++ P+ L I +S
Sbjct: 45 VTPEPQPGNPTPRVFRLP----EGVLNAMGLNNPGLDAVLEELLKRRKEYPRPLGIILS 99
>gnl|CDD|147776 pfam05804, KAP, Kinesin-associated protein (KAP). This family
consists of several eukaryotic kinesin-associated (KAP)
proteins. Kinesins are intracellular multimeric
transport motor proteins that move cellular cargo on
microtubule tracks. It has been shown that the sea
urchin KRP85/95 holoenzyme associates with a KAP115
non-motor protein, forming a heterotrimeric complex in
vitro, called the Kinesin-II.
Length = 708
Score = 24.8 bits (54), Expect = 9.5
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 26 IPGAIESLKVEFEDDEYVLQ 45
I IE L + EDDE+V Q
Sbjct: 574 IDSLIELLNAKQEDDEFVCQ 593
>gnl|CDD|238629 cd01304, FMDH_A, Formylmethanofuran dehydrogenase (FMDH) subunit A;
Methanogenic bacteria and archea derive the energy for
autotrophic growth from methanogenesis, the reduction of
CO2 with molecular hydrogen as the electron donor. FMDH
catalyzes the first step in methanogenesis, the
formyl-methanofuran synthesis. In this step, CO2 is
bound to methanofuran and subsequently reduced to the
formyl state with electrons derived from hydrogen.
Length = 541
Score = 24.7 bits (54), Expect = 9.6
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 39 DDEYVLQDLAQISRKNPKTLI 59
D EY L ++A ++R P L+
Sbjct: 424 DREYSLYEIAIMTRAGPAKLL 444
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 0.134 0.386
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,958,327
Number of extensions: 403334
Number of successful extensions: 436
Number of sequences better than 10.0: 1
Number of HSP's gapped: 432
Number of HSP's successfully gapped: 28
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
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: 53 (24.1 bits)