RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10357
(252 letters)
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 192 bits (489), Expect = 7e-59
Identities = 76/225 (33%), Positives = 123/225 (54%), Gaps = 4/225 (1%)
Query: 30 SGQMGQNLKEPVGPEICTWWKGGAFIPFIDALPSLNRKMDGPFLMPVVEKF--KDMGTVV 87
SG G NL + E W+KG + +D L R +D P +P+ + + +GTV
Sbjct: 192 SGFKGDNLTKKS--ENMPWYKGPTLLEALDQLEPPERPLDKPLRLPIQDVYSISGIGTVP 249
Query: 88 MGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPG 147
+G+VESG K GQ + MP V + EE+S PG+N+ ++G+E++D+ G
Sbjct: 250 VGRVESGVIKPGQKVTFMPAGVVGEVKSIEMHHEEISQAEPGDNVGFNVRGVEKNDIRRG 309
Query: 148 FVLCDPNNPARTARVFDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTG 207
V+ +NP + F AQI++L H II +GY+ V+H H + L+ +D +TG
Sbjct: 310 DVIGHSDNPPTVSPEFTAQIIVLWHPGIITSGYTPVLHAHTAQVACRIAELLSKLDPRTG 369
Query: 208 EKSKTRPRFVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRDE 252
+K + P+F+K+ AI+++E +CL++ PQ+GRF LRD
Sbjct: 370 KKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQLGRFALRDM 414
>gnl|CDD|239675 cd03704, eRF3c_III, This family represents eEF1alpha-like
C-terminal region of eRF3 homologous to the domain III
of EF-Tu. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. The C-terminal region is
responsible for translation termination activity and is
essential for viability. Saccharomyces cerevisiae eRF3
(Sup35p) is a translation termination factor which is
divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation termination.
Sup35NM is a non-pathogenic prion-like protein with
the property of aggregating into polymer-like fibrils.
Length = 108
Score = 159 bits (404), Expect = 4e-50
Identities = 62/95 (65%), Positives = 70/95 (73%), Gaps = 1/95 (1%)
Query: 159 TARVFDAQIVILEHK-SIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFV 217
F+AQI ILE K SII AGYSAV+HIH EEV +K LI LIDKKTG+KSK RPRFV
Sbjct: 2 VVTEFEAQIAILELKRSIITAGYSAVLHIHTAVEEVTIKKLIALIDKKTGKKSKKRPRFV 61
Query: 218 KQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRDE 252
K I RLE G ICL++F+ FPQ+GRFTLRDE
Sbjct: 62 KSGMKVIARLETTGPICLEKFEDFPQLGRFTLRDE 96
>gnl|CDD|239756 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). In eukaryotes, translation
termination is mediated by two interacting release
factors, eRF1 and eRF3, which act as class I and II
factors, respectively. eRF1 functions as an omnipotent
release factor, decoding all three stop codons and
triggering the release of the nascent peptide catalyzed
by the ribsome. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. Sequence comparison of class
II release factors with elongation factors shows that
eRF3 is more similar to eEF1alpha whereas prokaryote RF3
is more similar to EF-G, implying that their precise
function may differ. Only eukaryote RF3s are found in
this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
translation termination factor which is divided into
three regions N, M and a C-terminal eEF1a-like region
essential for translation termination. Sup35NM is a
non-pathogenic prion-like protein with the property of
aggregating into polymer-like fibrils.
Length = 82
Score = 136 bits (345), Expect = 2e-41
Identities = 47/82 (57%), Positives = 66/82 (80%)
Query: 71 PFLMPVVEKFKDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPGE 130
P +P+++K+KDMGTVV+GKVESG KKG L++MPN+T V V ++++D EV PGE
Sbjct: 1 PLRLPIIDKYKDMGTVVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARPGE 60
Query: 131 NIKVKLKGIEEDDVSPGFVLCD 152
N++++LKGIEE+D+SPGFVLC
Sbjct: 61 NVRLRLKGIEEEDISPGFVLCS 82
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 138 bits (351), Expect = 1e-38
Identities = 74/232 (31%), Positives = 117/232 (50%), Gaps = 14/232 (6%)
Query: 27 ISPSGQMGQNLKEPVGPEICTWWKGGAFIPFIDALPSLNRKMDGPFLMPV--VEKFKDMG 84
I S G N+ + E W+ G + +D L + D P +P+ V +G
Sbjct: 183 IPVSAFEGDNVVKK--SENMPWYNGPTLLEALDNLKPPEKPTDKPLRIPIQDVYSISGVG 240
Query: 85 TVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDV 144
TV +G+VE+G K G +V MP V + EE+ PG+NI ++G+ + D+
Sbjct: 241 TVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQAEPGDNIGFNVRGVGKKDI 300
Query: 145 SPGFVLCDPNNPARTARVFDAQIVILEHKSIICAGYSAVMHIH-----CVAEEVNVKALI 199
G V P+NP A F AQIV+L+H S I GY+ V H H C EE+ K
Sbjct: 301 KRGDVCGHPDNPPTVAEEFTAQIVVLQHPSAITVGYTPVFHAHTAQVACTFEELVKK--- 357
Query: 200 CLIDKKTGEKSKTRPRFVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRD 251
+D +TG+ ++ P+F+K AI++++ + +++ K PQ+GRF +RD
Sbjct: 358 --LDPRTGQVAEENPQFIKTGDAAIVKIKPTKPLVIEKVKEIPQLGRFAIRD 407
>gnl|CDD|239669 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of
the eukaryotic class II release factor (eRF3). In
eukaryotes, translation termination is mediated by two
interacting release factors, eRF1 and eRF3, which act as
class I and II factors, respectively. eRF1 functions as
an omnipotent release factor, decoding all three stop
codons and triggering the release of the nascent peptide
catalyzed by the ribsome. eRF3 is a GTPase, which
enhances the termination efficiency by stimulating the
eRF1 activity in a GTP-dependent manner. Sequence
comparison of class II release factors with elongation
factors shows that eRF3 is more similar to eEF1alpha
whereas prokaryote RF3 is more similar to EF-G, implying
that their precise function may differ. Only eukaryote
RF3s are found in this group. Saccharomyces cerevisiae
eRF3 (Sup35p) is a translation termination factor which
is divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation termination.
Sup35NM is a non-pathogenic prion-like protein with
the property of aggregating into polymer-like fibrils.
This group also contains proteins similar to S.
cerevisiae Hbs1, a G protein known to be important for
efficient growth and protein synthesis under conditions
of limiting translation initiation and, to associate
with Dom34. It has been speculated that yeast Hbs1 and
Dom34 proteins may function as part of a complex with a
role in gene expression.
Length = 83
Score = 120 bits (303), Expect = 4e-35
Identities = 44/83 (53%), Positives = 62/83 (74%), Gaps = 1/83 (1%)
Query: 71 PFLMPVVEKFKD-MGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPG 129
PF +P+ +K+KD GTVV GKVESG +KG +L++MP++ V V ++ DDEEV G
Sbjct: 1 PFRLPISDKYKDQGGTVVSGKVESGSIQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVAG 60
Query: 130 ENIKVKLKGIEEDDVSPGFVLCD 152
EN+++KLKGI+E+D+SPG VLC
Sbjct: 61 ENVRLKLKGIDEEDISPGDVLCS 83
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 125 bits (316), Expect = 1e-33
Identities = 64/206 (31%), Positives = 104/206 (50%), Gaps = 2/206 (0%)
Query: 48 WWKGGAFIPFIDALPSLNRKMDGPFLMPV--VEKFKDMGTVVMGKVESGEAKKGQSLVLM 105
W+KG + +DAL + D P +P+ V +GTV +G+VE+G K G +V
Sbjct: 204 WYKGKTLLEALDALEPPEKPTDKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFE 263
Query: 106 PNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDA 165
P V + E++ PG+NI ++G+ + D+ G V P+NP + A+ F A
Sbjct: 264 PAGVSGEVKSIEMHHEQIEQAEPGDNIGFNVRGVSKKDIRRGDVCGHPDNPPKVAKEFTA 323
Query: 166 QIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIM 225
QIV+L+H I GY+ V H H L+ D +TG+ + P+F+K AI+
Sbjct: 324 QIVVLQHPGAITVGYTPVFHCHTAQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIV 383
Query: 226 RLEAAGVICLDQFKLFPQMGRFTLRD 251
+ + + ++ K P +GRF +RD
Sbjct: 384 KFKPTKPMVIEAVKEIPPLGRFAIRD 409
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 118 bits (297), Expect = 7e-31
Identities = 68/230 (29%), Positives = 116/230 (50%), Gaps = 15/230 (6%)
Query: 30 SGQMGQNLKEPVGPEICTWWKGGAFIPFIDALPSLNRKMDGPFLMPV--VEKFKDMGTVV 87
SG G N+ E + W+KG + +D L R +D P +P+ V K +GTV
Sbjct: 194 SGWQGDNMIEK--SDNMPWYKGPTLLEALDTLEPPKRPVDKPLRLPLQDVYKIGGIGTVP 251
Query: 88 MGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPG 147
+G+VE+G K G + P+ V + E+++ PG+N+ +K + D+ G
Sbjct: 252 VGRVETGILKPGMVVTFAPSGVTTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSVKDIKRG 311
Query: 148 FVLCDP-NNPARTARVFDAQIVILEHKSIICAGYSAVM-----HIHCVAEEVNVKALICL 201
+V D N+PA+ F AQ+++L H I GY+ V+ HI C E+ K
Sbjct: 312 YVASDSKNDPAKECADFTAQVIVLNHPGQIKNGYTPVLDCHTAHIACKFAEIESK----- 366
Query: 202 IDKKTGEKSKTRPRFVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRD 251
ID+++G+ + P+ +K AI+++ +C++ F +P +GRF +RD
Sbjct: 367 IDRRSGKVLEENPKAIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRD 416
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 104 bits (259), Expect = 1e-25
Identities = 55/207 (26%), Positives = 103/207 (49%), Gaps = 3/207 (1%)
Query: 48 WWKGGAFIPFIDALPSLNRKMDGPFLMPV--VEKFKDMGTVVMGKVESGEAKKGQSLVLM 105
W+KG + +D + R D P +P+ V K +GTV +G+VE+G K G +
Sbjct: 210 WYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFG 269
Query: 106 PNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDP-NNPARTARVFD 164
P V + E + PG+N+ +K + D+ G+V + ++PA+ A F
Sbjct: 270 PTGLTTEVKSVEMHHESLQEALPGDNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFT 329
Query: 165 AQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAI 224
+Q++I+ H I GY+ V+ H V ++ ID+++G++ + P+F+K
Sbjct: 330 SQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGF 389
Query: 225 MRLEAAGVICLDQFKLFPQMGRFTLRD 251
+++ + ++ F +P +GRF +RD
Sbjct: 390 VKMIPTKPMVVETFSEYPPLGRFAVRD 416
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 90.6 bits (225), Expect = 9e-21
Identities = 59/188 (31%), Positives = 90/188 (47%), Gaps = 21/188 (11%)
Query: 55 IPFIDALPSLNRKMD-GPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLMPNRT-- 109
F LP R D GPFLM + + + +GTVV G V+SG G +++L P +
Sbjct: 331 DEFFLLLPKRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGK 390
Query: 110 --PVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDAQI 167
V+V + V S G I + LKG+E++++ G VL +P + R FDA++
Sbjct: 391 FREVVVKSIEMHHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADP-KAVREFDAEV 449
Query: 168 VILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDK---KTGEKS------KTRPRFVK 218
++L H + I AGY V H + E V + IDK G++ K RP V+
Sbjct: 450 LVLRHPTTIRAGYEPVFHYETIREAVYFEE----IDKGFLMPGDRGVVRMRFKYRPHHVE 505
Query: 219 QDQIAIMR 226
+ Q + R
Sbjct: 506 EGQKFVFR 513
>gnl|CDD|239760 cd04093, HBS1_C, HBS1_C: this family represents the C-terminal
domain of Hsp70 subfamily B suppressor 1 (HBS1) which is
homologous to the domain III of EF-1alpha. This group
contains proteins similar to yeast Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation and, to associate with Dom34. It has been
speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 107
Score = 80.3 bits (199), Expect = 2e-19
Identities = 29/93 (31%), Positives = 48/93 (51%)
Query: 158 RTARVFDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFV 217
++ F+A+I+ I G + H + E + L+ ++DK TGE SK +PR +
Sbjct: 1 PSSTRFEARILTFNVDKPILPGTPFELFRHSLKEPATITKLVSILDKSTGEVSKKKPRCL 60
Query: 218 KQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLR 250
+ Q AI+ +E I L+ FK ++GR LR
Sbjct: 61 TKGQTAIVEIELERPIPLELFKDNKELGRVVLR 93
>gnl|CDD|239676 cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation
factor 1 (EF-1) is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to ribosomes. EF-1 is
composed of four subunits: the alpha chain, which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This family is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea (aEF-1
alpha) and eukaryotes (eEF-1 alpha).
Length = 104
Score = 78.4 bits (194), Expect = 8e-19
Identities = 27/89 (30%), Positives = 48/89 (53%)
Query: 163 FDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQI 222
F AQ+++L H I GY+ V+ H ++ ID +TG+K + P+F+K
Sbjct: 6 FTAQVIVLNHPGQIKPGYTPVLDCHTAHVACRFAEILSKIDPRTGKKLEENPKFLKSGDA 65
Query: 223 AIMRLEAAGVICLDQFKLFPQMGRFTLRD 251
AI+++ + ++ F +P +GRF +RD
Sbjct: 66 AIVKIVPQKPLVVETFSEYPPLGRFAVRD 94
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 72.8 bits (179), Expect = 8e-15
Identities = 42/152 (27%), Positives = 65/152 (42%), Gaps = 13/152 (8%)
Query: 58 IDALPSLNRKMDGPFLMPV--VEKFKDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQ 115
ID L + R PF + + K +GTVV G V SGE K G L L P V V
Sbjct: 158 IDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRS 217
Query: 116 LWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARV-FDAQIVILEHKS 174
+ + D +V G+ + + LKG+E++++ G L P T R+ + +I L K+
Sbjct: 218 IQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVELEIDPLFKKT 277
Query: 175 IICAGYSAVMHIH-------CVAEEVNVKALI 199
+ +HIH + A +
Sbjct: 278 L---KQGQPVHIHVGLRSVTGRIVPLEKNAEL 306
>gnl|CDD|217387 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain.
Elongation factor Tu consists of three structural
domains, this is the third domain. This domain adopts a
beta barrel structure. This the third domain is involved
in binding to both charged tRNA and binding to EF-Ts
pfam00889.
Length = 91
Score = 66.8 bits (164), Expect = 2e-14
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 19/96 (19%)
Query: 156 PARTARVFDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPR 215
P + F AQ+ IL H + I GY V + H G+K
Sbjct: 1 PIKPHTKFKAQVYILNHPTPIFNGYRPVFYCHTADVTGKF--------ILPGKK-----E 47
Query: 216 FVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRD 251
FV AI+ +E I +++ + RF +R+
Sbjct: 48 FVMPGDNAIVTVELIKPIAVEKGQ------RFAIRE 77
>gnl|CDD|238771 cd01513, Translation_factor_III, Domain III of Elongation factor
(EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Experimental data
showed that: (1) intrinsic GTPase activity of EF-G is
influenced by excision of its domain III; (2) that EF-G
lacking domain III has a 1,000-fold decreased GTPase
activity on the ribosome and, a slightly decreased
affinity for GTP; and (3) EF-G lacking domain III does
not stimulate translocation, despite the physical
presence of domain IV which is also very important for
translocation. These findings indicate an essential
contribution of domain III to activation of GTP
hydrolysis. Domains III and V of EF-G have the same fold
(although they are not completely superimposable), the
double split beta-alpha-beta fold. This fold is observed
in a large number of ribonucleotide binding proteins and
is also referred to as the ribonucleoprotein (RNP) or
RNA recognition (RRM) motif. This domain III is found
in several elongation factors, as well as in peptide
chain release factors and in GT-1 family of GTPase
(GTPBP1).
Length = 102
Score = 64.0 bits (156), Expect = 2e-13
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 163 FDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQI 222
F A+I +L+H + GY V+++ + L+ +D KT + K P F+K +
Sbjct: 6 FVAEIYVLDHPEPLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKT--EEKKPPEFLKSGER 63
Query: 223 AIMRLEAAGVICLDQFKLFPQMGRFTLRD 251
I+ +E + L+ F + GRF LRD
Sbjct: 64 GIVEVELQKPVALETFSENQEGGRFALRD 92
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 60.4 bits (147), Expect = 3e-12
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 72 FLMPVVEKFKD--MGTVVMGKVESGEAKKGQSLVLMPNRTPV--IVDQLWSDDEEVSSVG 127
V + FKD GTV G+VESG KKG + + P V V L EV
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 128 PGENIKVKLKGIEEDDVSPGFVLCD 152
G+ + + LK ++DD+ G L D
Sbjct: 61 AGDIVGIVLK--DKDDIKIGDTLTD 83
>gnl|CDD|239664 cd03693, EF1_alpha_II, EF1_alpha_II: this family represents the
domain II of elongation factor 1-alpha (EF-1a) that is
found in archaea and all eukaryotic lineages. EF-1A is
very abundant in the cytosol, where it is involved in
the GTP-dependent binding of aminoacyl-tRNAs to the A
site of the ribosomes in the second step of translation
from mRNAs to proteins. Both domain II of EF1A and
domain IV of IF2/eIF5B have been implicated in
recognition of the 3'-ends of tRNA. More than 61% of
eukaryotic elongation factor 1A (eEF-1A) in cells is
estimated to be associated with actin cytoskeleton. The
binding of eEF1A to actin is a noncanonical function
that may link two distinct cellular processes,
cytoskeleton organization and gene expression.
Length = 91
Score = 60.6 bits (148), Expect = 3e-12
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 2/90 (2%)
Query: 69 DGPFLMPV--VEKFKDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSV 126
D P +P+ V K +GTV +G+VE+G K G + P V + E +
Sbjct: 2 DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMHHEPLEEA 61
Query: 127 GPGENIKVKLKGIEEDDVSPGFVLCDPNNP 156
PG+N+ +K + + D+ G V D N
Sbjct: 62 LPGDNVGFNVKNVSKKDIKRGDVAGDSKND 91
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 63.1 bits (154), Expect = 2e-11
Identities = 45/207 (21%), Positives = 86/207 (41%), Gaps = 7/207 (3%)
Query: 48 WWKGGAFIPFIDALPSLNRKMDGPFLMPV--VEKFKDMGTVVMGKVESGEAKKGQSLVLM 105
W+KG + ++ + + + F PV V + G + SG K G +V++
Sbjct: 200 WYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRPNLDFRGYAGTIASGSVKVGDEVVVL 259
Query: 106 PNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDA 165
P+ V ++ + D E++ GE + + L +E D+S G ++ + P A FDA
Sbjct: 260 PSGKTSRVKRIVTFDGELAQASAGEAVTLVLA--DEIDISRGDLIVAADAPPAVADAFDA 317
Query: 166 QIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIM 225
+V ++ + + G S + I V+ + +D T E + + ++I +
Sbjct: 318 DVVWMD-EEPLLPGRSYDLKIATRTVRARVEEIKHQLDVNTLE--QEGAESLPLNEIGRV 374
Query: 226 RLEAAGVICLDQFKLFPQMGRFTLRDE 252
R+ I D + G F L D
Sbjct: 375 RISFDKPIAFDAYAENRATGSFILIDR 401
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 56.1 bits (136), Expect = 8e-11
Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 84 GTVVMGKVESGEAKKGQSLVLMPNRTP--VIVDQLWSDDEEVSSVGPGENIKVKLKGIEE 141
GTV G+VESG KKG +V+ PN T V L ++ G N + L GI
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 142 DDVSPGFVLC 151
D+ G L
Sbjct: 61 KDIKRGDTLT 70
>gnl|CDD|239667 cd03696, selB_II, selB_II: this subfamily represents the domain of
elongation factor SelB, homologous to domain II of
EF-Tu. SelB may function by replacing EF-Tu. In
prokaryotes, the incorporation of selenocysteine as the
21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3' or 5' non-coding elements of mRNA have been found as
probable structures for directing selenocysteine
incorporation.
Length = 83
Score = 54.4 bits (132), Expect = 5e-10
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 72 FLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPG 129
F +P+ F K GTVV G V SG K G + ++P V + ++V G
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAG 60
Query: 130 ENIKVKLKGIEEDDVSPGFVLCD 152
+ + + L G++ D+ G VL
Sbjct: 61 DRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 56.9 bits (138), Expect = 2e-09
Identities = 34/109 (31%), Positives = 57/109 (52%), Gaps = 5/109 (4%)
Query: 66 RKMDGPFLMPVVEKFK--DMGTVVMGKVESGEAKKGQSLVLMPNRTP--VIVDQLWSDDE 121
R +D PFLMPV + F GTVV G+VE G K G+ + ++ + V + +
Sbjct: 205 RDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIKETQKTTVTGVEMFRK 264
Query: 122 EVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDAQIVIL 170
+ G+N+ V L+G++ +DV G VL P + + F+A++ +L
Sbjct: 265 LLDEGQAGDNVGVLLRGVKREDVERGQVLAKPGS-IKPHTKFEAEVYVL 312
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 55.9 bits (135), Expect = 4e-09
Identities = 34/116 (29%), Positives = 62/116 (53%), Gaps = 5/116 (4%)
Query: 59 DALPSLNRKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQ--SLVLMPNRTPVIVD 114
+ +P+ R+ D PFLMP+ + F GTVV G+VE G K G+ +V + + V
Sbjct: 198 EYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIVGLKDTRKTTVT 257
Query: 115 QLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDAQIVIL 170
+ +E+ G+N+ + L+GI+ +++ G VL P + + F+A++ +L
Sbjct: 258 GVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVLAKPGS-IKPHTKFEAEVYVL 312
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 55.6 bits (134), Expect = 5e-09
Identities = 36/118 (30%), Positives = 66/118 (55%), Gaps = 11/118 (9%)
Query: 61 LPSLNRKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLM------PNRTPVI 112
+P R +D PFLMP+ + F + GTV G+VE G K G+ + ++ P +T V
Sbjct: 251 IPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVT 310
Query: 113 VDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDAQIVIL 170
+++ + + G+N+ + L+G++ +DV G V+C P + +T + F+A+I +L
Sbjct: 311 GVEMFK--KILDQGQAGDNVGLLLRGLKREDVQRGQVICKPGS-IKTYKKFEAEIYVL 365
>gnl|CDD|239668 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
Elongation factors Tu (EF-Tu) are three-domain GTPases
with an essential function in the elongation phase of
mRNA translation. The GTPase center of EF-Tu is in the
N-terminal domain (domain I), also known as the
catalytic or G-domain. The G-domain is composed of about
200 amino acid residues, arranged into a predominantly
parallel six-stranded beta-sheet core surrounded by
seven a-helices. Non-catalytic domains II and III are
beta-barrels of seven and six, respectively,
antiparallel beta-strands that share an extended
interface. Either non-catalytic domain is composed of
about 100 amino acid residues. EF-Tu proteins exist in
two principal conformations: in a compact one,
EF-Tu*GTP, with tight interfaces between all three
domains and a high affinity for aminoacyl-tRNA, and in
an open one, EF-Tu*GDP, with essentially no
G-domain-domain II interactions and a low affinity for
aminoacyl-tRNA. EF-Tu has approximately a 100-fold
higher affinity for GDP than for GTP.
Length = 87
Score = 49.4 bits (119), Expect = 3e-08
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 72 FLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLM---PNRTPVIVDQLWSDDEEVSSV 126
FLMP+ + F GTVV G++E G K G + ++ + + + +
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTG-IEMFRKTLDEA 59
Query: 127 GPGENIKVKLKGIEEDDVSPGFVLCDPN 154
G+N+ V L+G++ +DV G VL P
Sbjct: 60 EAGDNVGVLLRGVKREDVERGMVLAKPG 87
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 52.9 bits (128), Expect = 3e-08
Identities = 37/132 (28%), Positives = 51/132 (38%), Gaps = 51/132 (38%)
Query: 66 RKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEV 123
R +D PFLMP+ + F GTVV G+VE G K G +EV
Sbjct: 207 RAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVKVG---------------------DEV 245
Query: 124 SSVG-----------------------PGENIKVKLKGIEEDDVSPGFVLCDPN--NPAR 158
VG G+N+ V L+G + +DV G VL P P
Sbjct: 246 EIVGIKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKPGSIKPHT 305
Query: 159 TARVFDAQIVIL 170
F+A++ +L
Sbjct: 306 K---FEAEVYVL 314
>gnl|CDD|239679 cd03708, GTPBP_III, Domain III of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse tissues
revealed that GTPBP1 is expressed in some neurons and
smooth muscle cells of various organs as well as
macrophages. Immunofluorescence analyses revealed that
GTPBP1 is localized exclusively in cytoplasm and shows a
diffuse granular network forming a gradient from the
nucleus to the periphery of the cells in smooth muscle
cell lines and macrophages. No significant difference
was observed in the immune response to protein antigen
between mutant mice and wild-type mice, suggesting
normal function of antigen-presenting cells of the
mutant mice. The absence of an eminent phenotype in
GTPBP1-deficient mice may be due to functional
compensation by GTPBP2, which is similar to GTPBP1 in
structure and tissue distribution.
Length = 87
Score = 49.5 bits (119), Expect = 4e-08
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 161 RVFDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDK---KTGEKSKTRPRFV 217
F+A+I++L H + I GY A +HI + + A I IDK +TG+++ R RF+
Sbjct: 4 WEFEAEILVLHHPTTISPGYQATVHIGSIRQ----TARIVSIDKDVLRTGDRALVRFRFL 59
Query: 218 KQ 219
Sbjct: 60 YH 61
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 52.6 bits (127), Expect = 5e-08
Identities = 37/124 (29%), Positives = 58/124 (46%), Gaps = 25/124 (20%)
Query: 61 LPSLNRKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQS---LVLMPNRTPVI--- 112
+P+ R D PFLMPV + F GTVV G+VE G K G + + + V+
Sbjct: 200 IPTPERDTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIKETQKTVVTGV 259
Query: 113 ------VDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDAQ 166
+D+ + G+N+ V L+G++ D+V G VL P + + F A+
Sbjct: 260 EMFRKLLDEGQA----------GDNVGVLLRGVDRDEVERGQVLAKPGS-IKPHTKFKAE 308
Query: 167 IVIL 170
+ IL
Sbjct: 309 VYIL 312
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 51.6 bits (124), Expect = 1e-07
Identities = 46/228 (20%), Positives = 84/228 (36%), Gaps = 17/228 (7%)
Query: 30 SGQMGQNLKEPVGPEICTWWKGGAFIPFIDALPSLNRKMDGPFLMPVV------EKFKDM 83
S G N+ E W+ G + ++ + D P PV F+
Sbjct: 178 SALKGDNVVSR--SESMPWYSGPTLLEILETVEVERDAQDLPLRFPVQYVNRPNLDFRGY 235
Query: 84 GTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDD 143
G + SG G +V++P+ V ++ + D ++ G+ + + L +E D
Sbjct: 236 A----GTIASGSVHVGDEVVVLPSGRSSRVARIVTFDGDLEQARAGQAVTLTLD--DEID 289
Query: 144 VSPGFVLCDPNNPARTARVFDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLID 203
+S G +L ++ A F A +V + + ++ G S + + +V A+ +D
Sbjct: 290 ISRGDLLAAADSAPEVADQFAATLVWMAEEPLL-PGRSYDLKLGTRKVRASVAAIKHKVD 348
Query: 204 KKTGEKSKTRPRFVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRD 251
T EK + I + L I D + G F L D
Sbjct: 349 VNTLEKGAA-KSLELNE-IGRVNLSLDEPIAFDPYAENRTTGAFILID 394
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 51.1 bits (123), Expect = 2e-07
Identities = 29/127 (22%), Positives = 58/127 (45%), Gaps = 12/127 (9%)
Query: 48 WWKGGAFIPFIDALPSLNRKMDGPFLMPV--VEK----FKDMGTVVMGKVESGEAKKGQS 101
W++G + + ++ + + + F PV V + F+ G V SG + G
Sbjct: 218 WYEGPSLLEHLETVEIASDRNLKDFRFPVQYVNRPNLDFRG----FAGTVASGVVRPGDE 273
Query: 102 LVLMPNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTAR 161
+V++P+ V ++ + D ++ G+ + + L +E D+S G +L +N A
Sbjct: 274 VVVLPSGKTSRVKRIVTPDGDLDEAFAGQAVTLTLA--DEIDISRGDMLARADNRPEVAD 331
Query: 162 VFDAQIV 168
FDA +V
Sbjct: 332 QFDATVV 338
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 50.2 bits (121), Expect = 4e-07
Identities = 38/132 (28%), Positives = 51/132 (38%), Gaps = 51/132 (38%)
Query: 66 RKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEV 123
R +D PFLMP+ + F GTVV G+VE G K G EEV
Sbjct: 207 RAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVG---------------------EEV 245
Query: 124 SSVG-----------------------PGENIKVKLKGIEEDDVSPGFVLCDPN--NPAR 158
VG G+N+ L+GI+ +DV G VL P P
Sbjct: 246 EIVGIRDTQKTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVLAKPGSITPHT 305
Query: 159 TARVFDAQIVIL 170
F+A++ +L
Sbjct: 306 K---FEAEVYVL 314
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 49.6 bits (119), Expect = 6e-07
Identities = 38/121 (31%), Positives = 61/121 (50%), Gaps = 19/121 (15%)
Query: 61 LPSLNRKMDGPFLMPVVEKFK--DMGTVVMGKVESGEAKKGQS--LV-LMPNRTPVIVD- 114
+P+ R D PFLM + + F GTV G++E G K G + +V L +T +
Sbjct: 210 IPTPERDTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKTTTVTGL 269
Query: 115 ---QLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPN--NPARTARVFDAQIVI 169
Q + DE ++ G+N+ + L+GI+++D+ G VL P P F+AQ+ I
Sbjct: 270 EMFQK-TLDEGLA----GDNVGILLRGIQKEDIERGMVLAKPGTITPHTK---FEAQVYI 321
Query: 170 L 170
L
Sbjct: 322 L 322
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 46.4 bits (110), Expect = 7e-06
Identities = 39/147 (26%), Positives = 63/147 (42%), Gaps = 14/147 (9%)
Query: 65 NRKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEE 122
+++ P M + F K GTVV G SGE K G +L L+P V V + + +++
Sbjct: 170 IKRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQAQNQD 229
Query: 123 VSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPA-RTARVFDAQIVILEHKSIICAGYS 181
V G+ I + L +E + + G ++ P +P R F A++ +LE +
Sbjct: 230 VEIAYAGQRIALNLMDVEPESLKRGLLILTPEDPKLRVVVKFIAEVPLLELQ-------- 281
Query: 182 AVMHIHCVAEEVNVKALICLIDKKTGE 208
HI K I L+DK
Sbjct: 282 -PYHIAHGMSVTTGK--ISLLDKGIAL 305
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 44.2 bits (104), Expect = 4e-05
Identities = 32/115 (27%), Positives = 57/115 (49%), Gaps = 5/115 (4%)
Query: 61 LPSLNRKMDGPFLMPVVEKFK--DMGTVVMGKVESGEAKKGQS--LVLMPNRTPVIVDQL 116
+P R+ D PFL+ V + F GTV G+VE G K G++ +V + V +
Sbjct: 279 IPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGV 338
Query: 117 WSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTARVFDAQIVILE 171
+ + G+N+ + L+GI++ D+ G VL P + + F+A + +L+
Sbjct: 339 EMFQKILDEALAGDNVGLLLRGIQKADIQRGMVLAKPGSITPHTK-FEAIVYVLK 392
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 43.7 bits (104), Expect = 5e-05
Identities = 27/127 (21%), Positives = 52/127 (40%), Gaps = 12/127 (9%)
Query: 48 WWKGGAFIPFIDALPSLNRKMDGPFLMPV--V----EKFKDMGTVVMGKVESGEAKKGQS 101
W+ G + ++ + PF PV V F+ G + SG K G
Sbjct: 222 WYSGPTLLEVLETVDIQRVVDAQPFRFPVQYVNRPNLDFRGY----AGTLASGVVKVGDR 277
Query: 102 LVLMPNRTPVIVDQLWSDDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNPARTAR 161
+ ++P+ V ++ + D ++ GE I + L+ +E D+S G +L + + +
Sbjct: 278 VKVLPSGKESNVARIVTFDGDLEEAFAGEAITLVLE--DEIDISRGDLLVAADEALQAVQ 335
Query: 162 VFDAQIV 168
A +V
Sbjct: 336 HASADVV 342
>gnl|CDD|239666 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the
domain II of the large subunit of ATP sulfurylase
(ATPS): CysN or the N-terminal portion of NodQ, found
mainly in proteobacteria and homologous to the domain II
of EF-Tu. Escherichia coli ATPS consists of CysN and a
smaller subunit CysD and CysN. ATPS produces
adenosine-5'-phosphosulfate (APS) from ATP and sulfate,
coupled with GTP hydrolysis. In the subsequent reaction
APS is phosphorylated by an APS kinase (CysC), to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for
use in amino acid (aa) biosynthesis. The Rhizobiaceae
group (alpha-proteobacteria) appears to carry out the
same chemistry for the sufation of a nodulation factor.
In Rhizobium meliloti, a the hererodimeric complex
comprised of NodP and NodQ appears to possess both ATPS
and APS kinase activities. The N and C termini of NodQ
correspond to CysN and CysC, respectively. Other
eubacteria, Archaea, and eukaryotes use a different ATP
sulfurylase, which shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha.
Length = 81
Score = 37.9 bits (89), Expect = 5e-04
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 72 FLMPV--VEKFKDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWSDDEEVSSVGPG 129
F PV V + G + SG + G +V++P+ V + + D E+ G G
Sbjct: 1 FRFPVQYVIRPNADFRGYAGTIASGSIRVGDEVVVLPSGKTSRVKSIETFDGELDEAGAG 60
Query: 130 ENIKVKLKGIEEDDVSPGFVLCD 152
E++ + L+ +E DVS G V+
Sbjct: 61 ESVTLTLE--DEIDVSRGDVIVA 81
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 36.3 bits (85), Expect = 0.007
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 30 SGQMGQNLKEPVGPEICTWWKGGAFIPFIDALPS 63
SG G NL E E W+KG + +D+L
Sbjct: 186 SGFTGDNLIEK--SENMPWYKGPTLLEALDSLEP 217
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 36.5 bits (85), Expect = 0.011
Identities = 32/115 (27%), Positives = 50/115 (43%), Gaps = 19/115 (16%)
Query: 56 PFIDAL----PSLNRKMDGPFLMPVVEKFKD--MGTVVMGKVESGEAKKGQSLVLMPNRT 109
P DA+ P+ +D P M V D +G + +G+V G KKGQ + LM R
Sbjct: 181 PLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALM-KRD 239
Query: 110 PVIVDQLWS--------DDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNP 156
I + S + E+ G G+ + V G+E+ ++ G + DP P
Sbjct: 240 GTIENGRISKLLGFEGLERVEIDEAGAGDIVAV--AGLEDINI--GETIADPEVP 290
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 36.3 bits (85), Expect = 0.014
Identities = 30/100 (30%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 69 DGPFLMPVVEKFKDM-----GTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLWS----D 119
DGP + V FK M G + + +V SG KKG +L V +L+
Sbjct: 286 DGPLVALV---FKTMDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQ 342
Query: 120 DEEVSSVGPGENIKV-KLKGIEEDDVSPGFVLCDPNNPAR 158
EEV G+ + V KLK D LCD +P
Sbjct: 343 REEVDEAVAGDIVAVAKLKDAATGDT-----LCDKGDPIL 377
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 34.6 bits (80), Expect = 0.040
Identities = 36/137 (26%), Positives = 54/137 (39%), Gaps = 9/137 (6%)
Query: 60 ALPSLNRKMDGPFLMPVVEKF--KDMGTVVMGKVESGEAKKGQSLVLMPNRTPVIVDQLW 117
LP F + + F K G VV G SGE K G +L L P+ V L
Sbjct: 163 QLPEREHAAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMRVRGLH 222
Query: 118 SDDEEVSSVGPGENIKVKLKG-IEEDDVSPGFVLCDPNNPARTARVFDAQIVILEHKSII 176
+ ++ G+ I + + G E++ ++ G L P RV IV L+ + +
Sbjct: 223 AQNQPTEQAQAGQRIALNIAGDAEKEQINRGDWLLADAPPEPFTRV----IVELQTHTPL 278
Query: 177 CAGYSAVMHIHCVAEEV 193
+HIH A V
Sbjct: 279 TQWQP--LHIHHAASHV 293
>gnl|CDD|166698 PLN03059, PLN03059, beta-galactosidase; Provisional.
Length = 840
Score = 30.0 bits (67), Expect = 1.4
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 15/89 (16%)
Query: 20 RQEILLIISPSGQMGQNLKEPVGPEICTWWKGGAFIPFIDALPSLNRKMD-GPF---LMP 75
R +++ I G + +GP IC W G F ++ +P + + D GPF +
Sbjct: 97 RYDLVKFIKVVQAAGLYVHLRIGPYICAEWNFGGFPVWLKYVPGIEFRTDNGPFKAAMQK 156
Query: 76 VVEKFKDM-----------GTVVMGKVES 93
EK DM G +++ ++E+
Sbjct: 157 FTEKIVDMMKSEKLFEPQGGPIILSQIEN 185
>gnl|CDD|232999 TIGR00506, ribB, 3,4-dihydroxy-2-butanone 4-phosphate synthase.
Several members of the family are bifunctional,
involving both ribA and ribB function. In these cases,
ribA tends to be on the C-terminal end of the protein
and ribB tends to be on the N-terminal [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 199
Score = 29.3 bits (66), Expect = 1.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 216 FVKQDQIAIMRLEAAGVICL 235
F+ +QIA MR A G+IC+
Sbjct: 38 FITPEQIAFMRRHAGGLICV 57
>gnl|CDD|233289 TIGR01140, L_thr_O3P_dcar, L-threonine-O-3-phosphate decarboxylase.
This family contains pyridoxal phosphate-binding class
II aminotransferases (see pfam00222) closely related to,
yet distinct from, histidinol-phosphate aminotransferase
(HisC). It is found in cobalamin biosynthesis operons in
Salmonella typhimurium and Bacillus halodurans (each of
which also has HisC) and has been shown to have
L-threonine-O-3-phosphate decarboxylase activity in
Salmonella. Although the gene symbol cobD was assigned
in Salmonella, cobD in other contexts refers to a
different cobalamin biosynthesis enzyme, modeled by
pfam03186 and called cbiB in Salmonella [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 330
Score = 28.7 bits (65), Expect = 2.5
Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 149 VLCDPNNPARTARVFDAQ 166
V+C+PNNP T R+ +
Sbjct: 130 VVCNPNNP--TGRLIPPE 145
>gnl|CDD|173083 PRK14620, PRK14620, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 326
Score = 28.6 bits (64), Expect = 3.4
Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 163 FDAQIVILEHKSIICAGYSAVMHIHCVAEEVNVKALIC 200
F+ ++ E KS+I G+S V + +A+++N++ IC
Sbjct: 268 FNINQILSEGKSVI-EGFSTVKPLISLAKKLNIELPIC 304
>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily
represents domain II of elongation factor (EF) EF-2
found eukaryotes and archaea and, the C-terminal portion
of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. During the process of peptide
synthesis and tRNA site changes, the ribosome is moved
along the mRNA a distance equal to one codon with the
addition of each amino acid. This translocation step is
catalyzed by EF-2_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Yeast Snu114p is essential for cell viability and for
splicing in vivo. U5-116 kD binds GTP. Experiments
suggest that GTP binding and probably GTP hydrolysis is
important for the function of the U5-116 kD/Snu114p.
Length = 93
Score = 26.8 bits (60), Expect = 3.7
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 15/66 (22%)
Query: 89 GKVESGEAKKGQSL-VLMPNRTP--------VIVDQLW----SDDEEVSSVGPGENIKVK 135
G+V SG +KGQ + VL PN +P + +L+ E V V G NI V
Sbjct: 21 GRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAG-NI-VL 78
Query: 136 LKGIEE 141
+ G+++
Sbjct: 79 IVGLDQ 84
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 28.4 bits (64), Expect = 3.8
Identities = 23/109 (21%), Positives = 49/109 (44%), Gaps = 15/109 (13%)
Query: 58 IDALPSLNRKMDGPFLMPVVEKFKD--MGTVVMGKVESGEAKKGQSLVLMPNRTPVI--- 112
+D +P+ +D P M V + + +G + +G++ G K Q + L+
Sbjct: 191 LDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALI-KSDGTTENG 249
Query: 113 -VDQLWS----DDEEVSSVGPGENIKVKLKGIEEDDVSPGFVLCDPNNP 156
+ +L + E+ G+ + + G+E+ ++ G +CDP+NP
Sbjct: 250 RITKLLGFLGLERIEIEEAEAGDIVAI--AGLEDINI--GDTICDPDNP 294
>gnl|CDD|146030 pfam03197, FRD2, Bacteriophage FRD2 protein.
Length = 102
Score = 26.3 bits (58), Expect = 6.5
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 181 SAVMHIHCVAEEVNVKALICLIDK 204
S V IHC+ +E NV +I L+ K
Sbjct: 75 SGVTKIHCIVDENNVDEIIELLRK 98
>gnl|CDD|218931 pfam06189, 5-nucleotidase, 5'-nucleotidase. This family consists
of both eukaryotic and prokaryotic 5'-nucleotidase
sequences (EC:3.1.3.5).
Length = 263
Score = 27.5 bits (62), Expect = 6.7
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 35 QNLKEPVGPEICTWWKGGAFIPFIDALPSLNRKMDGPFLMPVV 77
++ EP+ P G AF P + L +LN + L+ VV
Sbjct: 5 EHEDEPLKP-------GVAF-PLVKKLLALNTLLPEEPLVEVV 39
>gnl|CDD|239757 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal
domain:eEF2_C_snRNP: This family includes C-terminal
portion of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. This domain is homologous to
domain II of the eukaryotic translational elongation
factor EF-2. Yeast Snu114p is essential for cell
viability and for splicing in vivo. U5-116 kD binds GTP.
Experiments suggest that GTP binding and probably GTP
hydrolysis is important for the function of the U5-116
kD/Snu114p. In complex with GTP, EF-2 promotes the
translocation step of translation. During translocation
the peptidyl-tRNA is moved from the A site to the P
site, the uncharged tRNA from the P site to the E-site
and, the mRNA is shifted one codon relative to the
ribosome.
Length = 94
Score = 26.0 bits (58), Expect = 8.7
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 15/68 (22%)
Query: 87 VMGKVESGEAKKGQSL-VLMPNRTP--------VIVDQLWSDDE----EVSSVGPGENIK 133
G++ SG KKGQ + VL N + + +LW EV+ G N
Sbjct: 19 AFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGGRYKIEVNEAPAG-NW- 76
Query: 134 VKLKGIEE 141
V +KGI+
Sbjct: 77 VLIKGIDS 84
>gnl|CDD|131362 TIGR02309, HpaB-1, 4-hydroxyphenylacetate 3-monooxygenase,
oxygenase component. This gene for this monooxygenase
is found within apparent operons for the degradation of
4-hydroxyphenylacetic acid in Deinococcus, Thermus and
Oceanobacillus. Phylogenetic trees support inclusion of
the Bacillus halodurans sequence above trusted although
the complete 4-hydroxyphenylacetic acid degradation
pathway may not exist in that organism. Generally, this
enzyme acts with the assistance of a small flavin
reductase domain protein (HpaC) to provide the cycle the
flavin reductant for the reaction. This family of
sequences is a member of a larger subfamily of
monooxygenases (pfam03241).
Length = 477
Score = 27.2 bits (60), Expect = 9.9
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 12 WQPKLWTVRQEILLIISPSGQMG----QNLKEPVGPEICTWWKGGA 53
P+L+ +EIL + SG + ++ K P+GP + + +G
Sbjct: 369 LYPRLYPRLREILEQLGASGLITLPSEKDFKGPLGPFLEKFLQGAN 414
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
0.321 0.138 0.420
Gapped
Lambda K H
0.267 0.0817 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,063,136
Number of extensions: 1244215
Number of successful extensions: 1055
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1008
Number of HSP's successfully gapped: 61
Length of query: 252
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 157
Effective length of database: 6,723,972
Effective search space: 1055663604
Effective search space used: 1055663604
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: 58 (26.0 bits)