RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy961
(118 letters)
>gnl|CDD|153416 cd07962, Anticodon_Ia_Val, Anticodon-binding domain of valyl tRNA
synthetases. This domain is found in valyl tRNA
synthetases (ValRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. ValRS catalyzes the
transfer of valine to the 3'-end of its tRNA.
Length = 135
Score = 93.8 bits (234), Expect = 6e-26
Identities = 26/71 (36%), Positives = 34/71 (47%)
Query: 44 SPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMADGSLI 103
S D WILSRL V +A + Y F+ +A Y + + CD YLE +KP +
Sbjct: 41 SLADRWILSRLNKTVEEVTEALENYRFSEAATALYEFFWNDFCDWYLELVKPRLYGEDEE 100
Query: 104 EKANAARTLVT 114
EK A TL
Sbjct: 101 EKKAARATLYY 111
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 85.8 bits (213), Expect = 7e-21
Identities = 38/94 (40%), Positives = 52/94 (55%), Gaps = 2/94 (2%)
Query: 25 KKQDADVNAALDQASKVKVSP-IDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLY 83
K N+ L + + V+ P D WIL RL A+ + F++Y+F+ T A YN WLY
Sbjct: 688 LKDFNLPNSTLFKPNNVESLPWEDKWILHRLNVAIKEVTEGFKEYDFSEATQATYNFWLY 747
Query: 84 ELCDVYLECIKPVMADGSLIEKAN-AARTLVTSI 116
ELCDVYLE IKP ++ S E+ A L T +
Sbjct: 748 ELCDVYLELIKPRLSKQSDGERKQHAQDVLHTVL 781
>gnl|CDD|219767 pfam08264, Anticodon_1, Anticodon-binding domain of tRNA. This
domain is found mainly hydrophobic tRNA synthetases. The
domain binds to the anticodon of the tRNA.
Length = 148
Score = 71.3 bits (175), Expect = 5e-17
Identities = 24/70 (34%), Positives = 34/70 (48%)
Query: 47 DSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMADGSLIEKA 106
D WILSRL + +A++KY FNT SA Y + +L D YLE K + +
Sbjct: 1 DRWILSRLNKLIKEVTEAYEKYRFNTAASALYEFFWNDLSDWYLELSKDRLYGEAPDSDR 60
Query: 107 NAARTLVTSI 116
+A L +
Sbjct: 61 SAQTVLYEVL 70
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 75.0 bits (185), Expect = 5e-17
Identities = 28/80 (35%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 35 LDQASKVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIK 94
D + +S D WILSRL + V +A Y F+ A Y + CD YLE K
Sbjct: 595 PDDLDLLALSLADRWILSRLNETVKEVTEALDNYRFDEAARALYEFIWNDFCDWYLELAK 654
Query: 95 PVMADGSLIEKANAARTLVT 114
P + G EK A TL
Sbjct: 655 PRLYGGEE-EKRAARATLYY 673
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 70.1 bits (172), Expect = 3e-15
Identities = 26/75 (34%), Positives = 36/75 (48%)
Query: 40 KVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMAD 99
+ K+S D WILS+L + KA KY F A Y + CD Y+E +K + +
Sbjct: 600 EEKLSLADRWILSKLNRTIKEVRKALDKYRFAEAAKALYEFIWNDFCDWYIELVKYRLYN 659
Query: 100 GSLIEKANAARTLVT 114
G+ EK A TL
Sbjct: 660 GNEAEKKAARDTLYY 674
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 66.7 bits (164), Expect = 4e-14
Identities = 28/71 (39%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 44 SPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMADGSLI 103
S D WILSRL VA +A KY F+ A Y E CD YLE KPV+ +
Sbjct: 600 SLADRWILSRLNRTVAEVTEALDKYRFDEAARALYEFIWNEFCDWYLELAKPVLQEA--- 656
Query: 104 EKANAARTLVT 114
K TL
Sbjct: 657 AKRATRATLAY 667
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 58.4 bits (141), Expect = 4e-11
Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 45 PIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMA-DGSLI 103
WILS L A++ + YEF+ S Y+ W Y+ CDV++E IKP A D
Sbjct: 774 FSCKWILSVLNKAISKTVSSLDAYEFSDAASTVYSWWQYQFCDVFIEAIKPYFAGDNPEF 833
Query: 104 EKANAA 109
AA
Sbjct: 834 ASERAA 839
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 54.8 bits (133), Expect = 5e-10
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 45 PIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKP-VMADGSLI 103
P+D WIL++LA V +A + Y+F + + + CD YLE +K +
Sbjct: 610 PLDRWILAKLAKVVEKATEALENYDFAKALEEIESFFWHVFCDDYLELVKSRAYGEDEEE 669
Query: 104 EKANAARTLVTSI 116
E+ +A TL T +
Sbjct: 670 EQKSARYTLYTVL 682
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 49.6 bits (118), Expect = 4e-08
Identities = 24/78 (30%), Positives = 39/78 (50%)
Query: 39 SKVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMA 98
+++ +P D WIL+RL AV +A + + FN +A Y +ELCD Y+E K +A
Sbjct: 614 ARLARTPADRWILARLQRAVNETVEALEAFRFNDAANAVYAFVWHELCDWYIELAKEALA 673
Query: 99 DGSLIEKANAARTLVTSI 116
+ + LV +
Sbjct: 674 SEDPEARRSVQAVLVHCL 691
>gnl|CDD|153414 cd07960, Anticodon_Ia_Ile_BEm, Anticodon-binding domain of
bacterial and eukaryotic mitochondrial isoleucyl tRNA
synthetases. This domain is found in isoleucyl tRNA
synthetases (IleRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. This family includes
bacterial and eukaryotic mitochondrial members. IleRS
catalyzes the transfer of isoleucine to the 3'-end of
its tRNA.
Length = 180
Score = 46.7 bits (112), Expect = 2e-07
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 30 DVNAALDQASKVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVY 89
D + A D ++ +D + L RL + + +A++ YEF+ V A N +L Y
Sbjct: 29 DFDPAKDAVPYEELLELDRYALHRLNELIKEVREAYENYEFHKVYQALNNFCTVDLSAFY 88
Query: 90 LECIK 94
L+ IK
Sbjct: 89 LDIIK 93
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 44.3 bits (106), Expect = 3e-06
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 29 ADVNAALDQASKVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDV 88
D + A D ++ +D W L RLA+ +A++ Y+F+ V +N +L
Sbjct: 657 NDFDPAKDAVPYEELLELDRWALHRLAELQEEILEAYENYDFHKVYQKLHNFCSVDLSAF 716
Query: 89 YLECIK 94
YL+ IK
Sbjct: 717 YLDIIK 722
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 41.0 bits (97), Expect = 4e-05
Identities = 21/69 (30%), Positives = 34/69 (49%)
Query: 29 ADVNAALDQASKVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDV 88
D + D ++ +D WILSRL V +A++ Y+F+ V A N +L +
Sbjct: 667 DDFDPKKDAVLPEELRELDRWILSRLNSLVKEVREAYENYDFHKVVRALMNFVSEDLSNW 726
Query: 89 YLECIKPVM 97
YL+ IK +
Sbjct: 727 YLDIIKDRL 735
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 39.7 bits (93), Expect = 1e-04
Identities = 20/54 (37%), Positives = 28/54 (51%)
Query: 42 KVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKP 95
K D WILSRL V N+A +KY F+ V A + + EL + Y+ I+
Sbjct: 692 KFPEEDRWILSRLNSLVEEVNEALEKYNFHKVLRALQDFIVEELSNWYIRIIRD 745
>gnl|CDD|153415 cd07961, Anticodon_Ia_Ile_ABEc, Anticodon-binding domain of
archaeal, bacterial, and eukaryotic cytoplasmic
isoleucyl tRNA synthetases. This domain is found in
isoleucyl tRNA synthetases (IleRS), which belong to the
class Ia aminoacyl tRNA synthetases. It lies C-terminal
to the catalytic core domain, and recognizes and
specifically binds to the tRNA anticodon. This family
includes bacterial, archaeal, and eukaryotic
cytoplasmic members. IleRS catalyzes the transfer of
isoleucine to the 3'-end of its tRNA.
Length = 183
Score = 34.4 bits (80), Expect = 0.005
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 45 PIDSWILSRLADAVATCNKAFQKYEFNTVTSA 76
+D WILSRL + + + Y+ T A
Sbjct: 47 VLDRWILSRLNSLIKEVTEEMEAYDLYTAVRA 78
>gnl|CDD|153413 cd07959, Anticodon_Ia_Leu_AEc, Anticodon-binding domain of archaeal
and eukaryotic cytoplasmic leucyl tRNA synthetases.
This domain is found in leucyl tRNA synthetases (LeuRS),
which belong to the class Ia aminoacyl tRNA synthetases.
It lies C-terminal to the catalytic core domain. In
contrast to other class Ia enzymes, the anticodon is not
used as an identity element in LeuRS (with exceptions
such as Saccharomyces cerevisiae and some other
eukaryotes). No anticodon-binding site can be defined
for this family, which includes archaeal and eukaryotic
cytoplasmic members. LeuRS catalyzes the transfer of
leucine to the 3'-end of its tRNA.
Length = 117
Score = 32.9 bits (76), Expect = 0.010
Identities = 20/101 (19%), Positives = 34/101 (33%), Gaps = 12/101 (11%)
Query: 12 HLTRWYGHVTELKKKQDADVNAALDQASKVKVSPIDSWILSRLADAVATCNKAFQKYEFN 71
L R+Y EL + + ++ ID W+LSRL + +A++ +F
Sbjct: 12 RLERFYELAEELIETEGELEE----------LTFIDRWLLSRLNRLIKETTEAYENMQFR 61
Query: 72 TVTSACYNLWLYELCDVYLECIKPVMADGSLIEKANAARTL 112
L D Y E + L+ + T
Sbjct: 62 EALKEGLYE-LQNDLDWYRE-RGGAGMNKDLLRRFIEVWTR 100
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 34.0 bits (79), Expect = 0.011
Identities = 14/51 (27%), Positives = 17/51 (33%), Gaps = 7/51 (13%)
Query: 33 AALDQASKVKVSP-------IDSWILSRLADAVATCNKAFQKYEFNTVTSA 76
A LD +D WILSRL V +A Y+ A
Sbjct: 658 ANLDGFDYPPAEDEVDSLNELDRWILSRLNSLVKEVTEALDNYDITKAARA 708
>gnl|CDD|237514 PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional.
Length = 961
Score = 32.6 bits (75), Expect = 0.030
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 45 PIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVM---ADGS 101
++ ++L RL + +A+ Y+F + A N +L Y + K + A S
Sbjct: 711 ELERYMLHRLNELDGLVREAYDAYDFKRIYKALVNFVNVDLSAFYFDIRKDALYCDAPSS 770
Query: 102 LIEKA 106
L +A
Sbjct: 771 LRRRA 775
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 32.4 bits (74), Expect = 0.036
Identities = 11/49 (22%), Positives = 23/49 (46%)
Query: 46 IDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIK 94
ID + L +L + V +++ Y+F + + +L + YL+ K
Sbjct: 701 IDKYALFQLENVVNEIEESYDNYQFFKIFQILQRFTIVDLSNFYLDVAK 749
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 29.8 bits (68), Expect = 0.27
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 14/81 (17%)
Query: 12 HLTRWYGHVTELKKKQDADVNAALDQASKVKVSPIDSWILSRLADAVATCNKAFQKYEFN 71
L R+Y EL + + ++ ID W+LSRL + +A + ++
Sbjct: 627 QLERFYELAKELIEIGGEE-----------ELRFIDKWLLSRLNRIIKETTEAMESFQTR 675
Query: 72 T-VTSACYNLWLYELCDVYLE 91
V A Y L YL
Sbjct: 676 DAVQEAFYE--LLNDLRWYLR 694
>gnl|CDD|215509 PLN02943, PLN02943, aminoacyl-tRNA ligase.
Length = 958
Score = 29.1 bits (65), Expect = 0.60
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 49 WILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIK 94
W++S+L + + + ++ KY F V Y+ + + D Y+E K
Sbjct: 679 WVVSKLHELIDSVTTSYDKYFFGDVGREIYDFFWSDFADWYIEASK 724
>gnl|CDD|219045 pfam06471, NSP11, NSP11. This region of coronavirus polyproteins
encodes the NSP11 protein.
Length = 594
Score = 27.7 bits (62), Expect = 1.3
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 5/36 (13%)
Query: 59 ATCNKAFQKYE-----FNTVTSACYNLWLYELCDVY 89
A C+K +Y +NT+T+A + +W+ + DVY
Sbjct: 479 AVCSKHAAEYREYVEAYNTMTTAGFTIWVPKNFDVY 514
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 27.6 bits (62), Expect = 1.6
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 10/75 (13%)
Query: 6 VSAPYTHLTRWYGHVTELKKKQDADVNAALDQASKVKVSPIDSWILSRLADAVATCNKAF 65
V L R + V E +K ++ + D W+L R V +A
Sbjct: 623 VEGARRFLQRVWNLVKEHLEKLVEELTKEQGKE--------DRWLLHRTIKKVTEDFEAR 674
Query: 66 QKYEFNTVTSACYNL 80
Q FNT +A L
Sbjct: 675 QT--FNTAIAALMEL 687
>gnl|CDD|235425 PRK05349, PRK05349, Na(+)-translocating NADH-quinone reductase
subunit B; Provisional.
Length = 405
Score = 27.5 bits (62), Expect = 1.7
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 1 MLTDRVSAPYTHLTRW-YG 18
M TD VSA +T+ +W YG
Sbjct: 334 MATDPVSASFTNKGKWIYG 352
>gnl|CDD|179207 PRK01024, PRK01024, Na(+)-translocating NADH-quinone reductase
subunit B; Provisional.
Length = 503
Score = 27.0 bits (60), Expect = 2.7
Identities = 10/19 (52%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 1 MLTDRVSAPYTHLTRW-YG 18
M TD VS+P L +W YG
Sbjct: 437 MATDPVSSPTMKLAKWIYG 455
>gnl|CDD|153408 cd07375, Anticodon_Ia_like, Anticodon-binding domain of class Ia
aminoacyl tRNA synthetases and similar domains. This
domain is found in a variety of class Ia aminoacyl tRNA
synthetases, C-terminal to the catalytic core domain.
It recognizes and specifically binds to the anticodon
of the tRNA. Aminoacyl tRNA synthetases catalyze the
transfer of cognate amino acids to the 3'-end of their
tRNAs by specifically recognizing cognate from
non-cognate amino acids. Members include valyl-,
leucyl-, isoleucyl-, cysteinyl-, arginyl-, and
methionyl-tRNA synthethases. This superfamily also
includes a domain from MshC, an enzyme in the mycothiol
biosynthetic pathway.
Length = 117
Score = 26.3 bits (58), Expect = 2.9
Identities = 6/36 (16%), Positives = 13/36 (36%)
Query: 45 PIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNL 80
D +L+RL + + A + + T +
Sbjct: 39 EADRELLARLQEFIKRTTNALEALDPTTAVQELFKF 74
>gnl|CDD|198341 cd10308, GST_C_eEF1b_like, Glutathione S-transferase
C-terminal-like, alpha helical domain of eukaryotic
translation Elongation Factor 1 beta. Glutathione
S-transferase (GST) C-terminal domain family,
eukaryotic translation Elongation Factor 1 beta (eEF1b)
subfamily; eEF1b is a component of the eukaryotic
translation elongation factor-1 (EF1) complex which
plays a central role in the elongation cycle during
protein biosynthesis. EF1 consists of two functionally
distinct units, EF1A and EF1B. EF1A catalyzes the
GTP-dependent binding of aminoacyl-tRNA to the
ribosomal A site concomitant with the hydrolysis of
GTP. The resulting inactive EF1A:GDP complex is
recycled to the active GTP form by the
guanine-nucleotide exchange factor EF1B, a complex
composed of at least two subunits, alpha and gamma.
Metazoan EFB1 contain a third subunit, beta. eEF1b
contains a GST_C-like alpha helical domain at the
N-terminal region and a C-terminal guanine nucleotide
exchange domain. The GST_C-like domain likely functions
as a protein-protein interaction domain, similar to the
function of the GST_C-like domains of EF1Bgamma and
various aminoacyl-tRNA synthetases (aaRSs) from higher
eukaryotes.
Length = 82
Score = 25.5 bits (56), Expect = 3.9
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 10 YTHLTRWYGHVTEL 23
+ HL RWY H+
Sbjct: 69 FPHLARWYRHIASF 82
>gnl|CDD|130992 TIGR01937, nqrB, NADH:ubiquinone oxidoreductase,
Na(+)-translocating, B subunit. This model represents
the NqrB subunit of the six-protein, Na(+)-pumping
NADH-quinone reductase of a number of marine and
pathogenic Gram-negative bacteria. This oxidoreductase
complex functions primarily as a sodium ion pump
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 413
Score = 26.3 bits (58), Expect = 4.7
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 1 MLTDRVSAPYTHLTRW-YG 18
M TD VS+ +T +W YG
Sbjct: 348 MATDPVSSSFTKKGKWIYG 366
>gnl|CDD|217374 pfam03116, NQR2_RnfD_RnfE, NQR2, RnfD, RnfE family. This family of
bacterial proteins includes a sodium-translocating
NADH-ubiquinone oxidoreductase (i.e. a respiration
linked sodium pump). In Vibrio cholerae, it negatively
regulates the expression of virulence factors through
inhibiting (by an unknown mechanism) the transcription
of the transcriptional activator ToxT. The family also
includes proteins involved in nitrogen fixation, RnfD
and RnfE. The similarity of these proteins to
NADH-ubiquinone oxidoreductases was previously noted.
Length = 319
Score = 26.3 bits (59), Expect = 4.8
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 1 MLTDRVSAPYTHLTRW-YG 18
M TD V+AP T+ R +G
Sbjct: 255 MATDPVTAPTTNKGRLIFG 273
>gnl|CDD|238057 cd00109, KU, BPTI/Kunitz family of serine protease inhibitors;
Structure is a disulfide rich alpha+beta fold. BPTI
(bovine pancreatic trypsin inhibitor) is an extensively
studied model structure.
Length = 54
Score = 24.5 bits (54), Expect = 5.9
Identities = 5/25 (20%), Positives = 8/25 (32%)
Query: 53 RLADAVATCNKAFQKYEFNTVTSAC 77
L C +Y ++ T C
Sbjct: 4 SLPPDTGPCKAYIPRYYYDATTKQC 28
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 25.7 bits (57), Expect = 6.4
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 29 ADVNAALDQASKVKVSPIDSWILSR-----LADAVATCNKAFQKYEFNTVTSACYNL 80
ADV A+ + V + D +L R +A A+ K ++ + N + + YN+
Sbjct: 495 ADVGIAIGAGTDVAIEAAD-VVLLRNDLNDVATAIDLSRKTLRRIKQNLLWAFGYNV 550
>gnl|CDD|212570 cd11697, DHR2_DOCK_A, Dock Homology Region 2, a GEF domain, of
Class A Dedicator of Cytokinesis proteins. DOCK
proteins are atypical guanine nucleotide exchange
factors (GEFs) that lack the conventional Dbl homology
(DH) domain. As GEFs, they activate small GTPases by
exchanging bound GDP for free GTP. They are divided
into four classes (A-D) based on sequence similarity
and domain architecture; class A includes Dock1, 2 and
5. Class A DOCKs are specific GEFs for Rac. Dock1
interacts with the scaffold protein Elmo and the
resulting complex functions upstream of Rac in many
biological events including phagocytosis of apoptotic
cells, cell migration and invasion. Dock2 plays an
important role in lymphocyte migration and activation,
T-cell differentiation, neutrophil chemotaxis, and type
I interferon induction. Dock5 functions upstream of
Rac1 to regulate osteoclast function. All DOCKs contain
two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of class A DOCKs,
which contains the catalytic GEF activity for Rac
and/or Cdc42. Class A DOCKs also contain an SH3 domain
at the N-terminal region and a PxxP motif at the
C-terminus.
Length = 400
Score = 25.8 bits (57), Expect = 7.8
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 78 YNLWLYELCDVYLEC 92
Y +LY+LCD++LEC
Sbjct: 3 YIRYLYKLCDLHLEC 17
>gnl|CDD|119336 cd06568, GH20_SpHex_like, A subgroup of the Glycosyl hydrolase
family 20 (GH20) catalytic domain found in proteins
similar to the N-acetylhexosaminidase from Streptomyces
plicatus (SpHex). SpHex catalyzes the hydrolysis of
N-acetyl-beta-hexosaminides. An Asp residue within the
active site plays a critical role in substrate-assisted
catalysis by orienting the 2-acetamido group and
stabilizing the transition state. The GH20
hexosaminidases are thought to act via a catalytic
mechanism in which the catalytic nucleophile is not
provided by solvent or the enzyme, but by the substrate
itself. Proteins belonging to this subgroup lack the
C-terminal PKD (polycystic kidney disease I)-like domain
found in the chitobiases.
Length = 329
Score = 25.4 bits (56), Expect = 8.5
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 3 TDRVSAPYTHLTRWYGHVTELKKKQDADVNAALDQASKVKVSPID 47
R P + +++ DAD AALD+ +KV +SP D
Sbjct: 197 IARADLPAGTVAQYWSDR-----APDADAAAALDKGAKVILSPAD 236
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
0.320 0.130 0.396
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,630,742
Number of extensions: 443633
Number of successful extensions: 399
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 37
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.3 bits)