RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13182
(194 letters)
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 134 bits (340), Expect = 2e-37
Identities = 53/151 (35%), Positives = 86/151 (56%), Gaps = 5/151 (3%)
Query: 2 ESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEKD 61
E +K+SKKA KK A + EK ++ K+A ++E+ + D A YG PL +
Sbjct: 7 EESGEKISKKAAKKAAAKAEKLRREATAKAAAASLEDED---DPLASNYGDVPLEELQSK 63
Query: 62 VD-RDFVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGD-TVS 119
V R++ + L ++ V +RGR+HT R KGK F+V+R+ FT+Q ++ V + TVS
Sbjct: 64 VTGREWTDVSDLGEELAGSEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVS 123
Query: 120 KQMIKYVSQIPKESILDIQAHVQATPTIVES 150
K M+KY Q+ +ES++D++ V V+
Sbjct: 124 KGMVKYAKQLSRESVVDVEGVVSVPKKPVKG 154
>gnl|CDD|239815 cd04320, AspRS_cyto_N, AspRS_cyto_N: N-terminal, anticodon
recognition domain of the type found in Saccharomyces
cerevisiae and human cytoplasmic aspartyl-tRNA
synthetase (AspRS). This domain is a beta-barrel domain
(OB fold) involved in binding the tRNA anticodon
stem-loop. The enzymes in this group are homodimeric
class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs
catalyze the specific attachment of amino acids (AAs) to
their cognate tRNAs during protein biosynthesis. This
2-step reaction involves i) the activation of the AA by
ATP in the presence of magnesium ions, followed by ii)
the transfer of the activated AA to the terminal ribose
of tRNA. In the case of the class2b aaRSs, the
activated AA is attached to the 3'OH of the terminal
ribose. Eukaryotes contain 2 sets of aaRSs, both of
which are encoded by the nuclear genome. One set
concerns with cytoplasmic protein synthesis, whereas the
other exclusively with mitochondrial protein synthesis.
Length = 102
Score = 93.4 bits (233), Expect = 4e-25
Identities = 32/73 (43%), Positives = 50/73 (68%), Gaps = 2/73 (2%)
Query: 80 TVWVRGRLHTSRAKG-KQCFVVIREQNFTIQGILSVGDT-VSKQMIKYVSQIPKESILDI 137
V +R R+HTSRA+G K F+V+R+Q +TIQG+L+ VSKQM+K+ + KESI+D+
Sbjct: 1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDV 60
Query: 138 QAHVQATPTIVES 150
+ V+ ++S
Sbjct: 61 EGTVKKPEEPIKS 73
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 90.1 bits (223), Expect = 3e-21
Identities = 46/136 (33%), Positives = 78/136 (57%), Gaps = 4/136 (2%)
Query: 9 SKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVS--ARLYGKTPLIMSEKDVDRDF 66
A + K+ +K+ +K R A++ +E V ++G P++ S R F
Sbjct: 7 DAGAPAVEKKQSDKEARKAAR-LAEEKARAAEKAALVEKYKDVFGAAPMVQSTTYKSRTF 65
Query: 67 VPIRQLNKD-YVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKY 125
+P+ L+K VDKTV +R R+ T+R KGK F+V+R+ + ++Q + +V V K+MI +
Sbjct: 66 IPVAVLSKPELVDKTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDF 125
Query: 126 VSQIPKESILDIQAHV 141
+ QIP ESI+D++A V
Sbjct: 126 IGQIPTESIVDVEATV 141
>gnl|CDD|239766 cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal, anticodon
recognition domain of class 2b aminoacyl-tRNA
synthetases (aaRSs). This domain is a beta-barrel domain
(OB fold) involved in binding the tRNA anticodon
stem-loop. Class 2b aaRSs include the homodimeric
aspartyl-, asparaginyl-, and lysyl-tRNA synthetases
(AspRS, AsnRS, and LysRS). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the transfer
of the activated AA to the terminal ribose of tRNA. In
the case of the class2b aaRSs, the activated AA is
attached to the 3'OH of the terminal ribose. Eukaryotes
contain 2 sets of aaRSs, both of which are encoded by
the nuclear genome. One set concerns with cytoplasmic
protein synthesis, whereas the other exclusively with
mitochondrial protein synthesis. Included in this group
are archeal and archeal-like AspRSs which are
non-discriminating and can charge both tRNAAsp and
tRNAAsn. E. coli cells have two isoforms of LysRSs (LysS
and LysU) encoded by two distinct genes, which are
differentially regulated. The cytoplasmic and the
mitochondrial isoforms of human LysRS are encoded by a
single gene. Yeast cytoplasmic and mitochondrial LysRSs
participate in mitochondrial import of cytoplasmic
tRNAlysCUU. In addition to their housekeeping role,
human LysRS may function as a signaling molecule that
activates immune cells. Tomato LysRS may participate in
a process possibly connected to conditions of
oxidative-stress conditions or heavy metal uptake. It is
known that human tRNAlys and LysRS are specifically
packaged into HIV-1 suggesting a role for LysRS in tRNA
packaging. AsnRS is immunodominant antigen of the
filarial nematode Brugia malayai and is of interest as a
target for anti-parasitic drug design. Human AsnRS has
been shown to be a pro-inflammatory chemokine which
interacts with CCR3 chemokine receptors on T cells,
immature dendritic cells and macrophages.
Length = 85
Score = 47.6 bits (114), Expect = 1e-07
Identities = 12/66 (18%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQA 139
V + G +H+ R G F+ +R+ + +Q +++ + + ++ ES++ +
Sbjct: 1 EVTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGE--FFEEAEKLRTESVVGVTG 58
Query: 140 HVQATP 145
V P
Sbjct: 59 TVVKRP 64
>gnl|CDD|129550 TIGR00458, aspS_nondisc, nondiscriminating aspartyl-tRNA
synthetase. In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_arch, represents
aspartyl-tRNA synthetases from the eukaryotic cytosol
and from the Archaea. In some species, this enzyme
aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn)
is subsequently transamidated to Asn-tRNA(asn) [Protein
synthesis, tRNA aminoacylation].
Length = 428
Score = 49.4 bits (118), Expect = 3e-07
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 4/80 (5%)
Query: 79 KTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQ 138
+ V G +H R G FV++R++ IQ VSK + K+ ++ ES++ ++
Sbjct: 13 QEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAP-AKKVSKNLFKWAKKLNLESVVAVR 71
Query: 139 AHVQ---ATPTIVESLPMSI 155
V+ P E +P I
Sbjct: 72 GIVKIKEKAPGGFEIIPTKI 91
>gnl|CDD|239811 cd04316, ND_PkAspRS_like_N, ND_PkAspRS_like_N: N-terminal,
anticodon recognition domain of the type found in the
homodimeric non-discriminating (ND) Pyrococcus
kodakaraensis aspartyl-tRNA synthetase (AspRS). This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. P. kodakaraensis
AspRS is a class 2b aaRS. aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation the AA by ATP in the presence
of magnesium ions, followed by ii) the transfer of the
activated AA to the terminal ribose of tRNA. In the
case of the class2b aaRSs, the activated AA is attached
to the 3'OH of the terminal ribose. P. kodakaraensis
ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of
the enzymes in this group may be discriminating, based
on the presence of homologs of asparaginyl-tRNA
synthetase (AsnRS) in their completed genomes.
Length = 108
Score = 41.9 bits (99), Expect = 1e-05
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 79 KTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQ 138
+ V V G +H R G FV++R++ +Q + + V K++ K V ++ +ES++ +
Sbjct: 13 EEVTVAGWVHEIRDLGGIKFVILRDREGIVQ-VTAPKKKVDKELFKTVRKLSRESVISVT 71
Query: 139 AHVQAT---PTIVESLPMSI--LSVGDTV 162
V+A P VE +P I LS T
Sbjct: 72 GTVKAEPKAPNGVEIIPEEIEVLSEAKTP 100
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases [Translation,
ribosomal structure and biogenesis].
Length = 435
Score = 42.2 bits (100), Expect = 8e-05
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 67 VPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYV 126
I+ + + V VRG +H R GK F+V+R+ + IQ ++ V +++ K
Sbjct: 5 TYIKDIKPHVGGQEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNK-VYEELFK-A 62
Query: 127 SQIPKESILDIQAHVQATP 145
++ ES + + V+A+P
Sbjct: 63 KKLTLESSVVVTGIVKASP 81
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 39.7 bits (94), Expect = 4e-04
Identities = 27/86 (31%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 66 FVPIRQ-LNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIK 124
V I+ L YV + V VRG + T R GK F+ +R+ + Q + V +
Sbjct: 3 RVSIKDILKGKYVGQEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQV-----VKDNGEE 57
Query: 125 YVSQIPKESILDIQAHVQATPTIVES 150
Y +I K L + V T T+VES
Sbjct: 58 YFEEIKK---LTTGSSVIVTGTVVES 80
>gnl|CDD|235354 PRK05159, aspC, aspartyl-tRNA synthetase; Provisional.
Length = 437
Score = 39.0 bits (92), Expect = 7e-04
Identities = 19/92 (20%), Positives = 45/92 (48%), Gaps = 5/92 (5%)
Query: 67 VPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYV 126
+L + + V + G +H R G F+++R+++ IQ ++ +++ + +
Sbjct: 5 HLTSELTPELDGEEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVD--EELFETI 62
Query: 127 SQIPKESILDIQAHVQAT---PTIVESLPMSI 155
++ +ES++ + V+A P VE +P I
Sbjct: 63 KKLKRESVVSVTGTVKANPKAPGGVEVIPEEI 94
>gnl|CDD|224111 COG1190, LysU, Lysyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 502
Score = 35.6 bits (83), Expect = 0.009
Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 10/93 (10%)
Query: 69 IRQLNKDYVDKT----------VWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTV 118
L + Y DKT V V GR+ T R GK F +++ + IQ ++ +
Sbjct: 42 SADLREKYADKTKEELEALNIEVSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVG 101
Query: 119 SKQMIKYVSQIPKESILDIQAHVQATPTIVESL 151
+ ++ I+ ++ + T T S+
Sbjct: 102 EEVFEALFKKLDLGDIIGVEGPLFKTKTGELSV 134
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 34.8 bits (81), Expect = 0.016
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRK 30
++ + K KA KK+ K++ K K +
Sbjct: 61 LDKKELKAWHKAQKKKEKQEAKAAKAKSKP 90
Score = 28.3 bits (64), Expect = 2.5
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVE 37
+A + KK LK K Q+KKEK+ + K+A+ +
Sbjct: 57 KAALLDKKELKAWHKAQKKKEKQ-EAKAAKAKSK 89
>gnl|CDD|239818 cd04323, AsnRS_cyto_like_N, AsnRS_cyto_like_N: N-terminal,
anticodon recognition domain of the type found in human
and Saccharomyces cerevisiae cytoplasmic
asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai
AsnRs and, in various putative bacterial AsnRSs. This
domain is a beta-barrel domain (OB fold) involved in
binding the tRNA anticodon stem-loop. The enzymes in
this group are homodimeric class2b aminoacyl-tRNA
synthetases (aaRSs). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the transfer
of the activated AA to the terminal ribose of tRNA. In
the case of the class2b aaRSs, the activated AA is
attached to the 3'OH of the terminal ribose. Eukaryotes
contain 2 sets of aaRSs, both of which are encoded by
the nuclear genome. One set concerns with cytoplasmic
synthesis, whereas the other exclusively with
mitochondrial protein synthesis. AsnRS is
immunodominant antigen of the filarial nematode B.
malayai and of interest as a target for anti-parasitic
drug design. Human AsnRS has been shown to be a
pro-inflammatory chemokine which interacts with CCR3
chemokine receptors on T cells, immature dendritic cells
and macrophages.
Length = 84
Score = 32.2 bits (74), Expect = 0.032
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQA 139
V V G +H R++ K F+V+R+ +Q +LS K ++Q ES +++
Sbjct: 1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQ---ESSVEVTG 57
Query: 140 HVQATP 145
V+ P
Sbjct: 58 EVKEDP 63
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 33.8 bits (78), Expect = 0.041
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 2 ESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQN 35
S A++ KK KKQ K ++K EK++ K+A +
Sbjct: 406 LSPAER--KKLRKKQRKAEKKAEKEEAEKAAAKK 437
Score = 31.1 bits (71), Expect = 0.31
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 2 ESEAQKVSKKALKKQAKE--------QEKKEKKDQRKSAQQNVEESEPVED 44
+E +K+ KK K + K KK+ + K A+ E++ V+
Sbjct: 408 PAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDP 458
Score = 28.0 bits (63), Expect = 4.0
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 2 ESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESE 40
E E +S KK K+Q K EKK +++ A++ + +
Sbjct: 400 EGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKK 438
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 33.4 bits (77), Expect = 0.055
Identities = 31/125 (24%), Positives = 46/125 (36%), Gaps = 20/125 (16%)
Query: 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEK 60
+ ++ + K K A K RKSA + E +P + + RL K + K
Sbjct: 19 AKQAEEEKAAKEEAKAAAAA-AAAKGRSRKSAAADDETMDPTQYRANRL--KKVEALRAK 75
Query: 61 DV-------DRDFVPIRQLNKDYV---------DKTVWVRGRLHTSRAKGKQCFVVIREQ 104
V D +L + Y D +V V GR+ RA GK F +R+
Sbjct: 76 GVEPYPYKFDVTHT-APELQEKYGSLENGEELEDVSVSVAGRIMAKRAFGKLAFYDLRDD 134
Query: 105 NFTIQ 109
IQ
Sbjct: 135 GGKIQ 139
>gnl|CDD|239817 cd04322, LysRS_N, LysRS_N: N-terminal, anticodon recognition domain
of lysyl-tRNA synthetases (LysRS). These enzymes are
homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. aaRSs catalyze
the specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Included in this group are E. coli LysS and LysU. These
two isoforms of LysRS are encoded by distinct genes
which are differently regulated. Eukaryotes contain 2
sets of aaRSs, both of which encoded by the nuclear
genome. One set concerns with cytoplasmic protein
synthesis, whereas the other exclusively with
mitochondrial protein synthesis. Saccharomyces
cerevisiae cytoplasmic and mitochondrial LysRSs have
been shown to participate in the mitochondrial import of
the only nuclear-encoded tRNA of S. cerevisiae
(tRNAlysCUU). The gene for human LysRS encodes both the
cytoplasmic and the mitochondrial isoforms of LysRS. In
addition to their housekeeping role, human lysRS may
function as a signaling molecule that activates immune
cells and tomato LysRS may participate in a
root-specific process possibly connected to conditions
of oxidative-stress conditions or heavy metal uptake. It
is known that human tRNAlys and LysRS are specifically
packaged into HIV-1 suggesting a role for LysRS in tRNA
packaging.
Length = 108
Score = 32.1 bits (74), Expect = 0.058
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILS 113
V V GR+ + R GK F +++++ IQ ++
Sbjct: 1 EVSVAGRIMSKRGSGKLSFADLQDESGKIQVYVN 34
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 32.5 bits (75), Expect = 0.064
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQ 34
++ + K +KA KK K + K EKK +K +
Sbjct: 63 LDKKELKAWEKAEKKAEKAKAKAEKKKAKKEEPK 96
Score = 29.0 bits (66), Expect = 0.82
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLY 50
EA + KK LK K ++K EK K+ ++ ++ E+ RL+
Sbjct: 59 EAALLDKKELKAWEKAEKKAEKAKA-KAEKKKAKK----EEPKPRLF 100
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 32.8 bits (76), Expect = 0.10
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 10/51 (19%)
Query: 69 IRQLNKDYVDK----------TVWVRGRLHTSRAKGKQCFVVIREQNFTIQ 109
+L Y DK V V GR+ R GK F +++ + IQ
Sbjct: 35 AAELRAKYDDKEKEELEELEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQ 85
>gnl|CDD|239812 cd04317, EcAspRS_like_N, EcAspRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia coli
aspartyl-tRNA synthetase (AspRS), the human
mitochondrial (mt) AspRS-2, the discriminating (D)
Thermus thermophilus AspRS-1, and the nondiscriminating
(ND) Helicobacter pylori AspRS. These homodimeric
enzymes are class2b aminoacyl-tRNA synthetases (aaRSs).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. aaRSs catalyze
the specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic synthesis, whereas the other exclusively
with mitochondrial protein synthesis. Human mtAspRS
participates in mitochondrial biosynthesis; this enzyme
been shown to charge E.coli native tRNAsp in addition to
in vitro transcribed human mitochondrial tRNAsp. T.
thermophilus is rare among bacteria in having both a
D_AspRS and a ND_AspRS. H.pylori ND-AspRS can charge
both tRNAASp and tRNAAsn, it is fractionally more
efficient at aminoacylating tRNAAsp over tRNAAsn. The
H.pylori genome does not contain AsnRS.
Length = 135
Score = 31.3 bits (72), Expect = 0.13
Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 71 QLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIP 130
+L + +V + V + G + R G F+ +R++ +Q + + + ++
Sbjct: 7 ELRESHVGQEVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEE---APEFELAEKLR 63
Query: 131 KESILDIQAHVQATP 145
ES++ + V+A P
Sbjct: 64 NESVIQVTGKVRARP 78
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 32.5 bits (75), Expect = 0.13
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 71 QLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIP 130
+L + +V +TV + G +H R G F+ +R++ +Q + S + + S++
Sbjct: 8 ELRESHVGQTVTLSGWVHRRRDHGGLIFIDLRDREGIVQ--VVFDPEDSPEAFEVASRLR 65
Query: 131 KESILDIQAHVQATP 145
E ++ + V+A P
Sbjct: 66 NEFVIQVTGTVRARP 80
>gnl|CDD|219522 pfam07696, 7TMR-DISMED2, 7TMR-DISM extracellular 2. This entry
represents one of two distinct types of extracellular
domain found in the 7TM-DISM (7TM Receptors with Diverse
Intracellular Signalling Modules) bacterial
transmembrane proteins. It is possible that this domain
adopts a jelly roll fold and acts as a receptor for
carbohydrates and their derivatives.
Length = 141
Score = 31.1 bits (71), Expect = 0.18
Identities = 15/62 (24%), Positives = 19/62 (30%), Gaps = 5/62 (8%)
Query: 43 EDVSARLYGKTPLIMSEKDVDRDFVPI--RQLNKDYVDKTVWVRGRLHTSRAKGKQCFVV 100
ED S L T + F PI LN Y W+R L K +
Sbjct: 11 EDPSGSL---TIDDVLAPGAAGQFRPIDEGSLNFGYSRSAYWLRFTLANPSDAQKDWLLE 67
Query: 101 IR 102
+
Sbjct: 68 LA 69
>gnl|CDD|232998 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and
non-spirochete bacterial. This model represents the
lysyl-tRNA synthetases that are class II amino-acyl tRNA
synthetases. It includes all eukaryotic and most
bacterial examples of the enzyme, but not archaeal or
spirochete forms [Protein synthesis, tRNA
aminoacylation].
Length = 496
Score = 31.6 bits (72), Expect = 0.23
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 77 VDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQ 109
+ V + GR+ R+ GK F+ +++++ IQ
Sbjct: 52 KNIEVSIAGRIMARRSMGKATFITLQDESGQIQ 84
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 30.0 bits (68), Expect = 0.42
Identities = 12/32 (37%), Positives = 25/32 (78%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQN 35
E QK+ K+ LK++AK++++K+KK ++K + +
Sbjct: 96 EEQKIVKQVLKEKAKQKKQKKKKKKKKKKKTS 127
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 30.4 bits (69), Expect = 0.48
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSAR 48
A K K K E+++K K+++ + + +EE P ED A
Sbjct: 52 VAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTP-EDELAE 95
Score = 26.9 bits (60), Expect = 6.9
Identities = 7/45 (15%), Positives = 18/45 (40%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSAR 48
+ ++ +K +K + K KK + ++ + E+ R
Sbjct: 38 DEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLR 82
>gnl|CDD|232942 TIGR00366, TIGR00366, TIGR00366 family protein. [Hypothetical
proteins, Conserved].
Length = 438
Score = 30.6 bits (69), Expect = 0.51
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 3 SEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEES 39
E + + K LKK+ +E EKK KK + + + +E S
Sbjct: 213 GELKSIDPKLLKKEKEE-EKKLKKKEDATIAEKLENS 248
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 30.5 bits (69), Expect = 0.56
Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 4/77 (5%)
Query: 69 IRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQ 128
QL +++ +TV + G ++ R G F+ +R+++ +Q V +K
Sbjct: 6 CGQLRTEHLGQTVTLAGWVNRRRDLGGLIFIDLRDRSGIVQ----VVCDPDADALKLAKG 61
Query: 129 IPKESILDIQAHVQATP 145
+ E ++ ++ V A P
Sbjct: 62 LRNEDVVQVKGKVSARP 78
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 29.9 bits (68), Expect = 0.76
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 2 ESEAQKVSKKALKKQAKEQEKKEKKDQRK 30
E + K SKK L K+A+++EK+++K + K
Sbjct: 385 EKKTGKPSKKVLAKRAEKKEKEKEKPKVK 413
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 30.0 bits (67), Expect = 0.94
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIK 124
TV V GR+ + R GK FV IR +Q + VG+ +++ +K
Sbjct: 109 TVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLK 153
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 29.3 bits (66), Expect = 1.2
Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 7/85 (8%)
Query: 66 FVPIRQLNKD---YVDKTVWVRGRLHTSRAKGKQCFVVIREQNF--TIQGILSVGDTVSK 120
I+ L + +V V V G + T R+ K F+ + + + IQ +++ +
Sbjct: 1 SAAIKDLLQQVYKFVGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVIN--GEDNP 58
Query: 121 QMIKYVSQIPKESILDIQAHVQATP 145
+ + + + S + + V +P
Sbjct: 59 YLFQLLKSLTTGSSVSVTGKVVESP 83
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 28.8 bits (65), Expect = 1.7
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRK 30
E +K KKA+ K+ K+ K+EK+ +
Sbjct: 95 EEEKEKKKAMSKEEKKAIKEEKEKLEE 121
>gnl|CDD|111553 pfam02667, SCFA_trans, Short chain fatty acid transporter. This
family consists of two sequences annotated as short
chain fatty acid transporters, however, there are no
references giving details of experimental
characterisation of this function.
Length = 453
Score = 29.0 bits (65), Expect = 1.7
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 3 SEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEES 39
E + + K LKK+ +E EKK K + + + +E S
Sbjct: 216 GELKSIDPKLLKKEKEE-EKKLKSKKDATIAEKLENS 251
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 29.1 bits (65), Expect = 2.0
Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 24/97 (24%)
Query: 10 KKALKKQAKEQEKKEKKDQRKS--AQQNVEESEPVEDVSARL----------YGKTPL-- 55
KK KK++KE++KK+ ++ K A +N+EE + +G++P+
Sbjct: 685 KKKKKKKSKEKKKKKNREASKQIHALENIEEGIEGSNNEKSSETPQLKLEKKFGQSPVFV 744
Query: 56 ---IMSEKDVDRDFVP-------IRQLNKDYVDKTVW 82
++ V R+ P I+ ++ Y DKT W
Sbjct: 745 ASTLLENGGVPRNASPASLLREAIQVISCGYEDKTEW 781
>gnl|CDD|217286 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 27.9 bits (63), Expect = 2.4
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQ 28
EA+K KKA+ K+ K+ K+EK
Sbjct: 96 EAEKEKKKAMSKEEKKAIKEEKDKL 120
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 28.4 bits (63), Expect = 2.8
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 2 ESEAQKVSKKALK-KQAKEQEKKEKKDQRKSAQQNVEESEP--VEDVSARLYGKTPLIMS 58
+ E + S + +++E+K A NV++ +P V++++ L ++ I
Sbjct: 808 DKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPYKVDNMTRILPQQSRYISF 867
Query: 59 EKDVDRDFVPIRQL 72
KD DR FVP+R+
Sbjct: 868 IKD-DR-FVPVRKF 879
>gnl|CDD|224958 COG2047, COG2047, Uncharacterized protein (ATP-grasp superfamily)
[General function prediction only].
Length = 258
Score = 27.7 bits (62), Expect = 3.2
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 7 KVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVED 44
++ +AL+++AKE E+ +K + Q +E +P E+
Sbjct: 215 EIDMEALEERAKEMEEIIEKLKEMEEMQEAQEPKPGEE 252
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 28.0 bits (63), Expect = 3.5
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 12/74 (16%)
Query: 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQ---QNVEES-EPVEDVSARLYGKTPLI 56
+ + + L K+ KE + +K QR +VEE E VE+V++R++ KTP
Sbjct: 92 DVEKRNRSYRLYLDKKRKELQALSEK-QRHVLHYHNPSVEELKEMVENVNSRIWEKTPE- 149
Query: 57 MSEKDVDRDFVPIR 70
DF+ +R
Sbjct: 150 ------HHDFLHVR 157
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.9 bits (63), Expect = 3.7
Identities = 13/38 (34%), Positives = 25/38 (65%), Gaps = 4/38 (10%)
Query: 4 EAQKVSKKALKKQA---KEQEKKEKKDQRKSAQQNVEE 38
EA+K+ K+ L+++ +E+E K ++ K AQQ ++E
Sbjct: 545 EAEKL-KEELEEKKEKLQEEEDKLLEEAEKEAQQAIKE 581
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 26.5 bits (59), Expect = 5.4
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEP 41
+ +K +KK K+Q K+Q+KK+KK +K ++ +E
Sbjct: 76 KRKDEEKTAKKRAKRQKKKQKKKKKKKAKKGNKKEEKEGSK 116
>gnl|CDD|226280 COG3757, Acm, Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell
envelope biogenesis, outer membrane].
Length = 269
Score = 27.0 bits (60), Expect = 5.5
Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 7/70 (10%)
Query: 27 DQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEKDVDRDFVPIRQLNKDYVDKTVWVR-- 84
D R + +Q D +L GK P I + D D L + D +W+
Sbjct: 162 DVRPNMEQMNAGVLAFLDKLEKLGGKKPGIYTGVDFYDD-----NLIGTFKDYPLWIASY 216
Query: 85 GRLHTSRAKG 94
H S
Sbjct: 217 ATDHPSEPYV 226
>gnl|CDD|239814 cd04319, PhAsnRS_like_N, PhAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Pyrococcus
horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS).
This domain is a beta-barrel domain (OB fold) involved
in binding the tRNA anticodon stem-loop. The archeal
enzymes in this group are homodimeric class2b
aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the
specific attachment of amino acids (AAs) to their
cognate tRNAs during protein biosynthesis. This 2-step
reaction involves i) the activation of the AA by ATP in
the presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Length = 103
Score = 26.3 bits (58), Expect = 5.6
Identities = 15/65 (23%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 81 VWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAH 140
V + G ++ R GK+ F+V+R+ +Q + S ++++ + ++ ES + ++
Sbjct: 2 VTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFS--KDLNEEAYREAKKVGIESSVIVEGA 59
Query: 141 VQATP 145
V+A P
Sbjct: 60 VKADP 64
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 27.4 bits (60), Expect = 6.5
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 2 ESEAQKVSKKALKKQAKEQEKK------EKKDQRKSAQQNVEESE 40
E K+ K+A+E +KK ++D++K+A+ +E+E
Sbjct: 1655 AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAE 1699
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 26.8 bits (60), Expect = 6.5
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSA 47
EA +KA +++ K + K +K ++ AQ+ + PV D+S
Sbjct: 123 EAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDISE 166
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 26.7 bits (59), Expect = 6.5
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 2 ESEAQKVSKKALKKQAKEQE---KKEKKDQRKSAQQNVEESEPVE 43
+SE K +K KK+ E + KK+KK+++K +++ E V
Sbjct: 133 DSEGLKGHEKKHKKKKHEDDKERKKKKKEKKKKKKRHSPEHPGVG 177
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 26.9 bits (60), Expect = 6.6
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKK 26
+AQK KKA+ K+ K+ K EK+
Sbjct: 95 KAQKEEKKAMSKEEKKAIKAEKE 117
>gnl|CDD|227594 COG5269, ZUO1, Ribosome-associated chaperone zuotin [Translation,
ribosomal structure and biogenesis / Posttranslational
modification, protein turnover, chaperones].
Length = 379
Score = 26.9 bits (59), Expect = 6.6
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 2 ESEAQK-VSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDV 45
E EA+ S A+KK+AKE KK K ++K+ + ++++ D
Sbjct: 273 EIEAEALASATAVKKKAKEVMKKALKMEKKAIKNAAKDADYFGDA 317
>gnl|CDD|218427 pfam05093, CIAPIN1, Cytokine-induced anti-apoptosis inhibitor 1,
Fe-S biogenesis. Anamorsin, subsequently named CIAPIN1
for cytokine-induced anti-apoptosis inhibitor 1, in
humans is the homologue of yeast Dre2, a conserved
soluble eukaryotic Fe-S cluster protein, that functions
in cytosolic Fe-S protein biogenesis. It is found in
both the cytoplasm and in the mitochondrial
intermembrane space (IMS). CIAPIN1 is found to be
up-regulated in hepatocellular cancer, is considered to
be a downstream effector of the receptor tyrosine
kinase-Ras signalling pathway, and is essential in
mouse definitive haematopoiesis. Dre2 has been found to
interact with the yeast reductase Tah18, forming a
tight cytosolic complex implicated in the response to
high levels of oxidative stress.
Length = 97
Score = 25.8 bits (57), Expect = 6.9
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 18 KEQEKKEKKDQRKSAQQN 35
E+E++EKKD+ + QQ
Sbjct: 33 AEEEEQEKKDKSAAQQQK 50
>gnl|CDD|173630 cd05044, PTKc_c-ros, Catalytic domain of the Protein Tyrosine
Kinase, C-ros. Protein Tyrosine Kinases (PTK) family;
C-ros and Drosophila Sevenless proteins; catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. The
proto-oncogene c-ros encodes an orphan receptor tyr
kinase (RTK) with an unknown ligand. RTKs contain an
extracellular ligand-binding domain, a transmembrane
region, and an intracellular tyr kinase domain. RTKs
are usually activated through ligand binding, which
causes dimerization and autophosphorylation of the
intracellular tyr kinase catalytic domain. C-ros is
expressed in embryonic cells of the kidney, intestine
and lung, but disappears soon after birth. It persists
only in the adult epididymis. Male mice bearing
inactive mutations of c-ros lack the initial segment of
the epididymis and are infertile. The Drosophila
protein, Sevenless, is required for the specification
of the R7 photoreceptor cell during eye development.
Length = 269
Score = 26.7 bits (59), Expect = 7.8
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 3 SEAQKVSKKALKKQAKEQEKKE 24
S +V+ K L+K A +QEKKE
Sbjct: 24 SGPIRVAVKTLRKGATDQEKKE 45
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 26.1 bits (58), Expect = 8.1
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 2 ESEAQKVSKKALKKQAKEQEKKEKKDQRK 30
E E K KK K+ KE+EK+ K+ ++
Sbjct: 94 EHERNKQEKKKRSKEKKEEEKERKRQLKQ 122
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 26.6 bits (59), Expect = 8.3
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARL 49
E QK K K + K+ + K+KKD +K + ++ + ED L
Sbjct: 80 EKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDL 125
Score = 26.2 bits (58), Expect = 8.8
Identities = 10/46 (21%), Positives = 23/46 (50%)
Query: 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVS 46
E + + KK K+ K+++K +K D++ + +E E + +
Sbjct: 78 YEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLE 123
>gnl|CDD|145910 pfam03012, PP_M1, Phosphoprotein. This family includes the M1
phosphoprotein non-structural RNA polymerase alpha
subunit, which is thought to be a component of the
active polymerase, and may be involved in template
binding.
Length = 298
Score = 26.6 bits (59), Expect = 8.7
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 134 ILDIQAHVQATPTIVESLP--MSILSVGDTVSKQ 165
I D QAH+Q P V+SLP MS L + D Q
Sbjct: 32 IEDNQAHLQGEPIEVDSLPEDMSRLQISDAKPSQ 65
>gnl|CDD|217092 pfam02538, Hydantoinase_B, Hydantoinase B/oxoprolinase. This
family includes N-methylhydaintoinase B which converts
hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase
EC:3.5.2.9 which catalyzes the formation of L-glutamate
from 5-oxo-L-proline. These enzymes are part of the
oxoprolinase family and are related to pfam01968.
Length = 527
Score = 26.6 bits (59), Expect = 8.7
Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 4/73 (5%)
Query: 125 YVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIK----YVSQIPKESILD 180
Y S+ P+ +I D++A + A ++ + I G + + K I
Sbjct: 172 YPSRNPECNIGDLKAQIAANQKGIDRIGKLIDEYGLETVLGYMAHIQDNAEEAIKRKIAK 231
Query: 181 IQAHVQATPTIVE 193
+ A V
Sbjct: 232 LDEPYGAYDYGVC 244
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving DNA
bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 26.4 bits (59), Expect = 9.0
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 2 ESEAQKVSKKALKKQAKEQEKKEKKDQRKS 31
E A+K ++K L Q K+ K ++ Q++
Sbjct: 99 EINAKKTAEKLLASQLKKSAVKSQQQQQER 128
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
0.312 0.127 0.335
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,116,063
Number of extensions: 816937
Number of successful extensions: 2119
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1943
Number of HSP's successfully gapped: 229
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
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 (21.9 bits)
S2: 56 (25.2 bits)