RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1231
(151 letters)
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 76.1 bits (187), Expect = 6e-17
Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 35 DEEVKKLLELKNQLKINDEANEDNSTHKFILKTPKGTRDYGPDSTVVRNQVLDKIVKIFK 94
D + L +++K E+NE + + K PKGTRD+ + +R + I +FK
Sbjct: 301 DPKCPGFDSLVDKVKEIVESNEV----RRLPKIPKGTRDFAKEQMAIREKAFSIITSVFK 356
Query: 95 KHGAVTIDTPIFELKEVLTGKYG 117
+HGA +DTP+FEL+E L GKYG
Sbjct: 357 RHGATALDTPVFELRETLMGKYG 379
>gnl|CDD|238605 cd01200, WHEPGMRS_RNA, EPRS-like_RNA binding domain. This short
RNA-binding domain is found in several higher eukaryote
aminoacyl-tRNA synthetases (aaRSs). It is found in
three copies in the mammalian bifunctional EPRS in a
region that separates the N-terminal GluRS from the
C-terminal ProRS. In the Drosophila EPRS, this domain
is repeated six times. It is found at the N-terminus of
TrpRS, HisRS and GlyR and at the C-terminus of MetRS.
This domain consists of a helix- turn- helix structure,
which is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 42
Score = 65.6 bits (161), Expect = 2e-15
Identities = 26/39 (66%), Positives = 29/39 (74%)
Query: 11 QESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLK 49
E I QGD+VRKLK+ KAPKE+ID VKKLL LK Q K
Sbjct: 1 YEKIAEQGDLVRKLKAEKAPKEEIDAAVKKLLALKAQYK 39
>gnl|CDD|215929 pfam00458, WHEP-TRS, WHEP-TRS domain.
Length = 56
Score = 65.0 bits (159), Expect = 4e-15
Identities = 26/40 (65%), Positives = 30/40 (75%)
Query: 10 IQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLK 49
+ E I AQGD+VRKLK+ KAPKE +D VKKLL LK Q K
Sbjct: 1 LYEKIAAQGDLVRKLKAKKAPKEDVDAAVKKLLALKKQYK 40
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 69.6 bits (171), Expect = 9e-15
Identities = 20/53 (37%), Positives = 31/53 (58%)
Query: 65 LKTPKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTGKYG 117
++ P+GTRD+ P+ +R + I K+F+ +G I TPIFE E+ K G
Sbjct: 4 IQRPRGTRDFLPEDMALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSG 56
>gnl|CDD|214960 smart00991, WHEP-TRS, A conserved domain of 46 amino acids,
called WHEP-TRS has been shown.to exist in a number of
higher eukaryote aminoacyl-transfer RNA synthetases.
This domain is present one to six times in the several
enzymes. There are three copies in mammalian
multifunctional aminoacyl-tRNA synthetase in a region
that separates the N-terminal glutamyl-tRNA synthetase
domain from the C-terminal prolyl-tRNA synthetase
domain, and six copies in the intercatalytic region of
the Drosophila enzyme. The domain is found at the
N-terminal extremity of the mammalian tryptophanyl-
tRNA synthetase and histidyl-tRNA synthetase, and the
mammalian, insect, nematode and plant glycyl- tRNA
synthetases. This domain could contain a central
alpha-helical region and may play a role in the
association of tRNA-synthetases into multienzyme
complexes.
Length = 56
Score = 62.7 bits (153), Expect = 3e-14
Identities = 23/39 (58%), Positives = 31/39 (79%)
Query: 11 QESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLK 49
+E++ AQG++VRKLK+ KA K++ID V KLL LK QLK
Sbjct: 1 EEAVAAQGELVRKLKAEKASKDEIDAAVAKLLALKAQLK 39
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 64.8 bits (159), Expect = 4e-13
Identities = 20/53 (37%), Positives = 31/53 (58%)
Query: 65 LKTPKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTGKYG 117
++ P+GTRD P+ + V D I ++F+++G I TPIFE E+ K G
Sbjct: 4 IQAPRGTRDILPEESAKWQYVEDTIREVFERYGFSEIRTPIFEYTELFKRKVG 56
>gnl|CDD|238473 cd00936, WEPRS_RNA, WEPRS_RNA binding domain. This short
RNA-binding domain is found in several higher eukaryote
aminoacyl-tRNA synthetases (aaRSs). It is found in
multiple copies in eukaryotic bifunctional
glutamyl-prolyl-tRNA synthetases (EPRS) in a region
that separates the N-terminal glutamyl-tRNA synthetase
(GluRS) from the C-terminal prolyl-tRNA synthetase
(ProRS). It is also found at the N-terminus of
vertebrate tryptophanyl-tRNA synthetases (TrpRS). This
domain consists of a helix-turn-helix structure, which
is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 50
Score = 58.8 bits (143), Expect = 9e-13
Identities = 24/38 (63%), Positives = 29/38 (76%)
Query: 12 ESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLK 49
+ I AQGD+VR+LK+ KAPKE+ID VKKLL LK K
Sbjct: 3 KKIAAQGDLVRELKAKKAPKEEIDAAVKKLLALKADYK 40
>gnl|CDD|238474 cd00938, HisRS_RNA, HisRS_RNA binding domain. This short
RNA-binding domain is found at the N-terminus of HisRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). This domain consists of a helix- turn- helix
structure, which is similar to other RNA-binding
proteins. It is involved in both protein-RNA
interactions by binding tRNA and protein-protein
interactions, which are important for the formation of
aaRSs into multienzyme complexes.
Length = 45
Score = 57.9 bits (140), Expect = 2e-12
Identities = 27/41 (65%), Positives = 34/41 (82%)
Query: 8 ADIQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQL 48
A ++E++K QG++VRKLK+ KA KEQI EEV KLLELK QL
Sbjct: 1 AKLEEAVKLQGELVRKLKAEKASKEQIAEEVAKLLELKAQL 41
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 63.3 bits (155), Expect = 2e-12
Identities = 18/52 (34%), Positives = 30/52 (57%)
Query: 66 KTPKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTGKYG 117
+ P+GTRD+ P+ + + + I ++F+ +G I TPIFE E+ K G
Sbjct: 1 QAPRGTRDFLPEEMIKWQYIEETIREVFELYGFKEIRTPIFEYTELFARKVG 52
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 55.3 bits (134), Expect = 6e-10
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 79 TVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTGKYG 117
+R + D + ++F+++G IDTP+FE E+ K G
Sbjct: 2 AALRRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSG 40
>gnl|CDD|238475 cd00939, MetRS_RNA, MetRS_RNA binding domain. This short
RNA-binding domain is found at the C-terminus of MetRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). It is repeated in Drosophila MetRS. This
domain consists of a helix-turn-helix structure, which
is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 45
Score = 44.8 bits (106), Expect = 2e-07
Identities = 20/39 (51%), Positives = 27/39 (69%)
Query: 10 IQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQL 48
+++ + QG+ VRKLK+SKA K EV KLL+LK QL
Sbjct: 1 LEKEVAEQGNKVRKLKASKADKSVWQPEVNKLLDLKKQL 39
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 47.0 bits (112), Expect = 6e-07
Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 17/100 (17%)
Query: 7 MADIQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLKINDEANEDNSTHKFILK 66
+A+ Q ++ AQG+ VR LK+SKA K +ID ++KL LK+ A E L+
Sbjct: 9 LAEKQAAVTAQGNAVRALKASKADKAEIDAAIEKL----KALKLEKSALEKE------LQ 58
Query: 67 TPKGTRDYGPDS-----TVVRNQVLDKIVKI--FKKHGAV 99
G G S V N + ++ I FK +G V
Sbjct: 59 AAVGAGGDGAASKEAFRQAVVNTLERRLFYIPSFKIYGGV 98
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 46.3 bits (110), Expect = 1e-06
Identities = 17/56 (30%), Positives = 35/56 (62%)
Query: 62 KFILKTPKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTGKYG 117
++ KGT+DY P+ V+RN++ + +F+++G ++TP + E+++ KYG
Sbjct: 1 MMEMRNVKGTKDYLPEEQVLRNKIKRALEDVFERYGCKPLETPTLNMYELMSSKYG 56
>gnl|CDD|238361 cd00677, S15_NS1_EPRS_RNA-bind, S15/NS1/EPRS_RNA-binding domain.
This short domain consists of a helix-turn-helix
structure, which can bind to several types of RNA. It
is found in the ribosomal protein S15, the influenza A
viral nonstructural protein (NSA) and in several
eukaryotic aminoacyl tRNA synthetases (aaRSs), where it
occurs as a single or a repeated unit. It is involved
in both protein-RNA interactions by binding tRNA and
protein-protein interactions in the formation of
tRNA-synthetases into multienzyme complexes. While this
domain lacks significant sequence similarity between
the subgroups in which it is found, they share similar
electrostatic surface potentials and thus are likely to
bind to RNA via the same mechanism.
Length = 46
Score = 38.3 bits (90), Expect = 6e-05
Identities = 13/45 (28%), Positives = 16/45 (35%), Gaps = 7/45 (15%)
Query: 12 ESIKAQGDVVRKLKSSKA-------PKEQIDEEVKKLLELKNQLK 49
I + +R LK A K +D V K L L LK
Sbjct: 2 VQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46
>gnl|CDD|238472 cd00935, GlyRS_RNA, GlyRS_RNA binding domain. This short
RNA-binding domain is found at the N-terminus of GlyRS
in several higher eukaryote aminoacyl-tRNA synthetases
(aaRSs). This domain consists of a helix-turn-helix
structure , which is similar to other RNA-binding
proteins. It is involved in both protein-RNA
interactions by binding tRNA and protein-protein
interactions, which are important for the formation of
aaRSs into multienzyme complexes.
Length = 51
Score = 37.9 bits (88), Expect = 1e-04
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 7 MADIQESIKAQGDVVRKLKSSKAPKEQIDEEV------KKLLELK 45
+A ++ ++K QGD+VRKLK AP I + V KKLLE K
Sbjct: 1 LAPLRAAVKEQGDLVRKLKEEGAPDVDIKKAVAELKARKKLLEDK 45
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 39.5 bits (93), Expect = 2e-04
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 81 VRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTG 114
+RN + + I ++ K++G +DTPI E KE+ G
Sbjct: 1 LRNALENFIRELLKRYGYQEVDTPILEPKELWEG 34
>gnl|CDD|226228 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 38.1 bits (89), Expect = 7e-04
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 68 PKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVL 112
P+G RD P + ++ D+++ +F+ G ++TP E + L
Sbjct: 6 PEGIRDVLPLEARRKEEIRDQLLALFRAWGYERVETPTLEPADPL 50
>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type.
This model describes a glycyl-tRNA synthetase distinct
from the two alpha and two beta chains of the tetrameric
E. coli glycyl-tRNA synthetase. This enzyme is a
homodimeric class II tRNA synthetase and is recognized
by pfam model tRNA-synt_2b, which recognizes His, Ser,
Pro, and this set of glycyl-tRNA synthetases [Protein
synthesis, tRNA aminoacylation].
Length = 551
Score = 34.4 bits (79), Expect = 0.017
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 70 GTRDYGPDSTVVRNQVLDKIVKIF-KKHGAVTIDTPIFELKEVL 112
G DYGP V++N + + K F K + IDTPI +EVL
Sbjct: 28 GFWDYGPLGAVLKNNIKNAWRKFFIKNERVLEIDTPIITPEEVL 71
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 33.9 bits (78), Expect = 0.023
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 49 KINDEANEDNSTHKFI-LKTPKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFE 107
+ I + PKGTRD+ P+ +RN + D ++ + G +D P+ E
Sbjct: 53 GTTAPPSVQEDGKPKIDVNPPKGTRDFPPEDMRLRNWLFDHFREVSRLFGFEEVDAPVLE 112
Query: 108 LKEVLTGKYG 117
+E+ K G
Sbjct: 113 SEELYIRKAG 122
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 32.1 bits (74), Expect = 0.088
Identities = 11/46 (23%), Positives = 23/46 (50%)
Query: 68 PKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLT 113
P+G RD P+ ++ +++ +F++ G + TP E + L
Sbjct: 6 PEGIRDLLPEEARKIEEIRRRLLDLFRRWGYEEVITPTLEYLDTLL 51
>gnl|CDD|232978 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase,
regulatory subunit. Apparant second copies of
histidyl-tRNA synthetase, found in Bacillus subtilis,
Synechocystis sp., Aquifex aeolicus, and others, are in
fact a regulatory subunit of ATP
phosphoribosyltransferase, and usually encoded by a gene
adjacent to that encoding the catalytic subunit [Amino
acid biosynthesis, Histidine family].
Length = 313
Score = 31.8 bits (73), Expect = 0.088
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 72 RDYGP-DSTVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLT 113
RD P ++ + ++ +F+ G I TP E + L+
Sbjct: 1 RDLLPEEAARKEE-IERQLQDVFRSWGYQEIITPTLEYLDTLS 42
>gnl|CDD|222097 pfam13393, tRNA-synt_His, Histidyl-tRNA synthetase. This is a
family of class II aminoacyl-tRNA synthetase-like and
ATP phosphoribosyltransferase regulatory subunits.
Length = 308
Score = 31.8 bits (73), Expect = 0.10
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 8/52 (15%)
Query: 70 GTRDYGPDS----TVVRNQVLDKIVKIFKKHGAVTIDTPIFELKEVLTGKYG 117
G RD P +R ++LD +F+ G + P+ E E L G
Sbjct: 1 GIRDLLPPEARRIEELRRRLLD----LFRSWGYELVIPPLLEYLESLLTGAG 48
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 31.0 bits (70), Expect = 0.22
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 69 KGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFE 107
+GT+D PD + DK + + I TPIFE
Sbjct: 8 RGTKDILPDEINYWQFIHDKALTLLSLANYSEIRTPIFE 46
>gnl|CDD|223500 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 558
Score = 30.4 bits (69), Expect = 0.36
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 69 KGTRDYGPDSTVVRNQVLDKIVKIF--KKHGAVTIDTPIFELKEVL 112
G DYGP ++N + + K F ++ V IDTPI +EV
Sbjct: 30 AGFYDYGPLGVELKNNIKEAWRKSFVTEREDVVEIDTPIILPEEVW 75
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 30.3 bits (68), Expect = 0.40
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
Query: 8 ADIQES---IKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLKINDE 53
AD++ + +K +G+VV +LK++KA KE+I V +L K L +E
Sbjct: 235 ADVEAARLIVKERGEVVAQLKAAKASKEEITAAVAELKIAKESLAHIEE 283
>gnl|CDD|221623 pfam12531, DUF3731, DNA-K related protein. This domain family is
found in bacteria, and is approximately 250 amino acids
in length. There are two conserved sequence motifs: RPG
and WRR. The proteins in this family are frequently
annotated as DNA-K related proteins however there is
little accompanying literature to confirm this.
Length = 249
Score = 29.1 bits (66), Expect = 0.78
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 4/35 (11%)
Query: 9 DIQESIKAQGDVVRKLKSSKAPKEQID--EEVKKL 41
D+ E+++ + V+ KLK+SKAP+ I EV +L
Sbjct: 197 DLPEALRER--VLEKLKASKAPESWIAMVREVVEL 229
>gnl|CDD|182775 PRK10847, PRK10847, hypothetical protein; Provisional.
Length = 219
Score = 28.9 bits (65), Expect = 0.86
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 76 PDSTVVRNQVLDKIVKIFKKHGAVTI 101
P+S + R LDK + ++KHG TI
Sbjct: 104 PNSKIFRRSYLDKTHQFYEKHGGKTI 129
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 28.7 bits (64), Expect = 1.1
Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 3 SAAPMADIQESIKAQG--DVVRKLKSSKAPKEQIDEEVKKLLELKNQLKINDEANEDNST 60
SA P D ++ + G + +K K + E +K L E + ++ N +S
Sbjct: 254 SARPSKDKLITLLSLGCKAYLALMKEQKEMFPLLRELIKDLAEEVGEQLLDVPHNPISSA 313
Query: 61 HKFILKTPKGTRDYGP 76
L+T G
Sbjct: 314 --MTLETLDEISKKGR 327
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 28.5 bits (65), Expect = 1.5
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 7/42 (16%)
Query: 15 KAQGDVVR---KLKS----SKAPKEQIDEEVKKLLELKNQLK 49
K + ++ R KL + +KAP+E +++E +KL E + +L
Sbjct: 822 KLEKEIERVEKKLSNEGFVAKAPEEVVEKEREKLAEYEEKLA 863
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.5 bits (64), Expect = 1.7
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 18 GDVVRKLKSSKAPKEQIDEEVKKLLELKNQLK 49
+ ++L+ + KE+I+EE+ K+ +LK
Sbjct: 387 EKLEKELEELEKAKEEIEEEISKITARIGELK 418
>gnl|CDD|224397 COG1480, COG1480, Predicted membrane-associated HD superfamily
hydrolase [General function prediction only].
Length = 700
Score = 28.1 bits (63), Expect = 2.1
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 4/87 (4%)
Query: 32 EQIDEEVKKLLELKNQLKINDEANEDNSTHKFILKTPKGTRDYGPDSTVVRNQVLDKIVK 91
+ I + + + N++K + E NED +T LK K +D T + ++I+
Sbjct: 91 QNIVQLYQNFFDAINEVKRSLEENEDENTEYS-LKQVKQLKDRLLRDTNTVDISEERILT 149
Query: 92 IFKKHGA---VTIDTPIFELKEVLTGK 115
+ + +T DT I E++ +
Sbjct: 150 LLELDSEDLNLTQDTIITEVENAMGNG 176
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 28.0 bits (63), Expect = 2.2
Identities = 17/102 (16%), Positives = 35/102 (34%), Gaps = 4/102 (3%)
Query: 8 ADIQESIKAQGDVVRKLKSSKAPKE--QIDEEVKKLLELKNQLKINDEANEDNSTHKFIL 65
+ + +K G + + + ++ +EV+ + E + K +
Sbjct: 39 GVLTDLLKKLGKLSPLEERKEVGALINELKKEVEDAITELTPELEAAGLWERLAFEKIDV 98
Query: 66 KTPKGTRDYGPDSTVVRNQVLDKIVKIFKKHGAVTIDTPIFE 107
P R P S Q +++I IF G ++ P E
Sbjct: 99 TLP--GRRIYPGSLHPLTQTIEEIEDIFLGMGFTEVEGPEIE 138
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 27.9 bits (62), Expect = 2.5
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 24 LKSSKAPKEQIDEEVKKLLELKNQLKI 50
+K K +++ E V+K+LEL KI
Sbjct: 450 VKKEKEKEKERPEFVEKVLELFKGSKI 476
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase components
[Carbohydrate transport and metabolism].
Length = 338
Score = 27.6 bits (62), Expect = 2.8
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 24 LKSSKAPKEQIDEEVK---KLLELKNQLK 49
LK PK +ID+ VK KLL L++ L
Sbjct: 100 LKLRGVPKAEIDKRVKEVAKLLGLEHLLN 128
>gnl|CDD|206547 pfam14379, Myb_CC_LHEQLE, MYB-CC type transfactor, LHEQLE motif.
This family is found towards the C-terminus of Myb-CC
type transcription factors, and carries a highly
conserved LHEQLE sequence motif.
Length = 51
Score = 25.3 bits (56), Expect = 3.1
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 14/48 (29%)
Query: 9 DIQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLKINDEANE 56
I E+++ Q +V R+L EQ LE++ L+I EA
Sbjct: 3 QITEALRLQMEVQRRLH------EQ--------LEVQRHLQIRIEAQG 36
>gnl|CDD|129165 TIGR00055, uppS, undecaprenyl diphosphate synthase. This enzyme
builds undecaprenyl diphosphate, a molecule that in
bacteria is used a carrier in synthesizing cell wall
components. Alternate name: undecaprenyl pyrophosphate
synthetase. Activity has been demonstrated
experimentally for members of this family from
Micrococcus luteus, E. coli, Haemophilus influenzae, and
Streptococcus pneumoniae [Cell envelope, Biosynthesis
and degradation of surface polysaccharides and
lipopolysaccharides].
Length = 226
Score = 27.4 bits (61), Expect = 3.2
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 4 AAPMADIQESIKAQGDVVRKLKSSKAPKEQIDEEV 38
A E + A + K+KS K E IDEE
Sbjct: 124 AFNYGGRNEILHAVKQIAEKVKSGKLLPEDIDEET 158
>gnl|CDD|223693 COG0620, MetE, Methionine synthase II (cobalamin-independent)
[Amino acid transport and metabolism].
Length = 330
Score = 27.3 bits (61), Expect = 4.0
Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 4/45 (8%)
Query: 72 RDYGPDSTVVRN--QVLDKIVKIFKKHGAVTI--DTPIFELKEVL 112
R Y + ++ L VK + G I D P L
Sbjct: 144 RYYISREELAKDIALALRDEVKDLEDAGIKIIQIDEPALREGLPL 188
>gnl|CDD|217579 pfam03469, XH, XH domain. The XH (rice gene X Homology) domain
is found in a family of plant proteins including gene
X. The molecular function of these proteins is unknown.
However these proteins usually contain an XS domain
that is also found in the PTGS protein SGS3. This
domain contains a conserved glutamate residue that may
be functionally important.
Length = 132
Score = 26.2 bits (58), Expect = 4.5
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 9/52 (17%)
Query: 22 RKLKSSKAPKEQIDEEVKKLLELKNQL---------KINDEANEDNSTHKFI 64
+ +++ + KE +DE+ +KL +LK + K E NE N + ++
Sbjct: 48 KVVETGEIEKEVVDEDDEKLKKLKEEWGEEVYNAVKKALLEMNEYNPSGRYP 99
>gnl|CDD|236904 PRK11387, PRK11387, S-methylmethionine transporter; Provisional.
Length = 471
Score = 27.1 bits (60), Expect = 4.5
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 116 YGVYWT---GYS-TAVGFLMIHSVPSAPLWINW 144
Y + WT G S TA GF M + P P+W W
Sbjct: 101 YWLTWTVALGSSLTAAGFCMQYWFPQVPVWP-W 132
>gnl|CDD|132000 TIGR02955, TMAO_TorT, TMAO reductase system periplasmic protein
TorT. Members of this family are the periplasmic
protein TorT which, together with the the TorS/TorR
histidine kinase/response regulator system, regulates
expression of the torCAD operon for trimethylamine
N-oxide reductase (TMAO reductase). It appears to bind
an inducer for TMAO reductase, and shows homology to a
periplasmic D-ribose binding protein.
Length = 295
Score = 27.0 bits (60), Expect = 4.5
Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 7/53 (13%)
Query: 99 VTIDTPIFELKEVL-----TGKYGV--YWTGYSTAVGFLMIHSVPSAPLWINW 144
+T P+F L + G+ GV Y GY H S P + W
Sbjct: 78 LTKSIPVFALVNQIDSNQVKGRVGVDWYQMGYQAGEYLAQRHPKGSGPTTLAW 130
>gnl|CDD|193319 pfam12845, TBD, TBD domain. The Tbk1/Ikki binding domain (TBD)
is a 40 amino acid domain able to bind kinases, has
been found to be essential for poly(I:C)-induced IRF
activation. The domain is found in SINTBAD, TANK and
NAP1 protein. This domain is predicted to form an
a-helix with residues essential for kinase binding
clustering on one side.
Length = 57
Score = 25.1 bits (55), Expect = 5.3
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 7 MADIQESIKAQGDVVRKLKSSKAPKE 32
+ + K Q D +RKL A K
Sbjct: 20 FSRLCLLAKKQKDHLRKLNQPAAAKS 45
>gnl|CDD|233203 TIGR00946, 2a69, he Auxin Efflux Carrier (AEC) Family. [Transport
and binding proteins, Other].
Length = 321
Score = 26.6 bits (59), Expect = 5.3
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 111 VLTGKYGVYWTGYSTAVGFLMIHSVPSAPLWI 142
VL +Y V STAV + S+ S PL+I
Sbjct: 286 VLATEYEVDVELASTAVTLSTVLSLISLPLFI 317
>gnl|CDD|218647 pfam05591, DUF770, Protein of unknown function (DUF770). This
family consists of several proteins of unknown function
from various bacterial species.
Length = 159
Score = 26.3 bits (59), Expect = 5.4
Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 32 EQIDEEVKKLLELKNQLK 49
Q+ E+KKLLEL+ L
Sbjct: 107 RQV-PELKKLLELREALA 123
>gnl|CDD|234587 PRK00039, ruvC, Holliday junction resolvase; Reviewed.
Length = 164
Score = 26.2 bits (59), Expect = 5.8
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 28 KAPKEQIDEEVKKLLELKNQLKINDEA 54
+A KEQ+ VK+LL L K +D A
Sbjct: 117 RADKEQVQHMVKRLLNLPEIPKPDDAA 143
>gnl|CDD|213361 cd12827, EcCorA_ZntB-like_u2, uncharacterized bacterial subfamily
of the Escherichia coli CorA-Salmonella typhimurium ZntB
family. A uncharacterized subfamily of the Escherichia
coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like)
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes.The EcCorA-ZntB-like
family includes the Mg2+ transporters Escherichia coli
and Salmonella typhimurium CorAs, which can also
transport Co2+, and Ni2+. Structures of the
intracellular domain of EcCorA-ZntB-like family members,
Vibrio parahaemolyticus and Salmonella typhimurium ZntB,
form funnel-shaped homopentamers, the tip of the funnel
is formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA. Natural
variants such as GVN and GIN, such as occur in some ZntB
family proteins, may be associated with the transport of
different divalent cations, such as zinc and cadmium.
The functional diversity of MIT transporters may also be
due to minor structural differences regulating gating,
substrate selection, and transport.
Length = 289
Score = 26.3 bits (59), Expect = 6.7
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 9/44 (20%)
Query: 7 MADIQES-------IKAQGDVVRKLKSSKAPKEQIDEEVKKLLE 43
+ D+++S +K+ V+ KLK S ++DEE K+LLE
Sbjct: 150 LLDLEKSLVYFSTSLKSNEIVLEKLKRS--RSLKLDEEDKELLE 191
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 26.7 bits (59), Expect = 7.4
Identities = 11/56 (19%), Positives = 29/56 (51%)
Query: 1 MSSAAPMADIQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLKINDEANE 56
+ + + +I+E ++A D+ +++ + + + +EEV+ L E + A+E
Sbjct: 736 LDALELLQNIKEKLQAADDLRQRIAAMERDLARFEEEVEALAEAVAPEMLGTPADE 791
>gnl|CDD|224104 COG1183, PssA, Phosphatidylserine synthase [Lipid metabolism].
Length = 234
Score = 26.1 bits (58), Expect = 7.4
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 97 GAVTIDTPIFELKEVLTGKYGVYWTGYSTAVGFLMIHSVP 136
AV + + + TG V +G + LM+ ++P
Sbjct: 134 AAVVVVLLVLLYHSLPTGLATVLLSGILLLLSILMVSNIP 173
>gnl|CDD|234289 TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype
II/NMENI. The CRISPR-associated protein Cas1 is
virtually universal to CRISPR systems. CRISPR, an
acronym for Clustered Regularly Interspaced Short
Palindromic Repeats, is a prokaryotic immunity system
for foreign DNA, mostly from phage. CRISPR systems
belong to different subtypes, distinguished by both
nature of the repeats, the makeup of the cohort of
associated Cas proteins, and by molecular phylogeny
within the more universal Cas proteins such as this one.
This model is of type EXCEPTION and provides more
specific information than the EQUIVALOG model TIGR00287.
It describes the Cas1 variant of the NMENI subtype of
CRISPR/Cas system.
Length = 278
Score = 26.1 bits (58), Expect = 8.5
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 10 IQESIKAQGDVVRKLKSSKAPKEQIDEEVKKLLELKNQLKINDEAN 55
I++ I Q V+ KL +DE+ +KL L N+++ D+ N
Sbjct: 107 IKQKILNQAFVLEKLN--------LDEDSEKLKNLANKVESGDKTN 144
>gnl|CDD|197219 cd09120, PLDc_DNaseII_1, Catalytic domain, repeat 1, of
Deoxyribonuclease II and similar proteins. Catalytic
domain, repeat 1, of Deoxyribonuclease II (DNase II, EC
3.1.22.1), an endodeoxyribonuclease with ubiquitous
tissue distribution. It is essential for accessory
apoptotic DNA fragmentation and DNA clearance during
development, as well as in tissue regeneration in higher
eukaryotes. Unlike the majority of nucleases, DNase II
functions optimally at acidic pH in the absence of
divalent metal ion cofactors. It hydrolyzes the
phosphodiester backbone of DNA by a single strand
cleavage mechanism to generate 3'-phosphate termini. The
majority of family members contain an N-terminal
signal-peptide leader sequence, which is critical for
N-glycosylation and DNase II activity. DNase II is a
monomeric nuclease that contains two copies of a variant
HKD motif, where the aspartic acid residue is not
conserved. The HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) characterizes the
phospholipase D (PLD, EC 3.1.4.4) superfamily. The
catalytic center of DNase II is formed by the two
variant HKD motifs from the N- and C-terminal domains in
a pseudodimeric way. Members of this family are mainly
found in metazoans, and vertebrate proteins have been
further classified into DNase II alpha and beta (also
known as DNase II-like acid DNase, DLAD) subtypes. A few
homologs are found in non-metazoan species, but none are
found in fungi, plants or prokaryotes, with the sole
exception of Burkholderia pseudomallei. Among those
homologs, the Caenorhabditis elegans C07B5.5 ORF
encoding NUC-1 apoptotic nuclease, the uncharacterized
C. elegans crn-6 (cell death related nuclease) gene
encoding protein, and the putative gene CG7780 encoding
Drosophila DNase II (dDNase II) have similar cleavage
activity and specificity to mammalian DNase II enzymes.
They may function like an acid DNase implicated in
degrading DNA from apoptotic cells engulfed by
macrophages. Plancitoxin I, the major lethal factor from
the Acanthaster planci venom, is a unique homolog of
mammalian DNase II. It has potent hepatotoxicity and the
optimum pH for its activity is 7.2, unlike the optimum
acidic PH for mammalian DNase II. Some members of this
family contain substitutions of conserved residues found
in the putative active site, which suggest that these
proteins may have diverged from a canonical DNase II
activity and may perform other functions.
Length = 141
Score = 25.7 bits (57), Expect = 8.6
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 128 GFLMIHSVPSAP 139
GF ++HSVP P
Sbjct: 105 GFWLVHSVPKFP 116
>gnl|CDD|233080 TIGR00665, DnaB, replicative DNA helicase. This model describes
the helicase DnaB, a homohexameric protein required for
DNA replication. The homohexamer can form a ring around
a single strand of DNA near a replication fork. An
intein of > 400 residues is found at a conserved
location in DnaB of Synechocystis PCC6803, Rhodothermus
marinus (both experimentally confirmed), and
Mycobacterium tuberculosis. The intein removes itself by
a self-splicing reaction. The seed alignment contains
inteins so that the model built from the seed alignment
will model a low cost at common intein insertion sites
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 434
Score = 26.2 bits (59), Expect = 8.6
Identities = 15/103 (14%), Positives = 42/103 (40%), Gaps = 24/103 (23%)
Query: 14 IKAQGDVVRK-LKSSKAPKEQIDEEVKKLLELKNQLKINDEANEDNSTHKFILKTPKGTR 72
I+A ++V +E +DE +K+ E+ + +
Sbjct: 111 IQAGTEIVELAYDPEGDVEELLDEAEQKIFEIAES---------------------RTSG 149
Query: 73 DYGPDSTVVRNQVLDKIVKIFKKHGAVT-IDTPIFELKEVLTG 114
+ V+ + +++I +++++ G +T + T +L ++ +G
Sbjct: 150 GFKSIKEVL-KETVEEIEELYERKGGITGVPTGFTDLDKLTSG 191
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 25.8 bits (58), Expect = 9.9
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 81 VRNQVLDKIVKIFKKHGAVTIDTPIF 106
+RN + I + F ++G V +DTPI
Sbjct: 135 IRNTLAQAIHEFFNENGFVWVDTPII 160
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
0.313 0.131 0.379
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,535,940
Number of extensions: 676390
Number of successful extensions: 1090
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1085
Number of HSP's successfully gapped: 112
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
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: 54 (24.6 bits)