RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15197
(902 letters)
>gnl|CDD|163712 cd08156, catalase_clade_3, Clade 3 of the heme-binding enzyme
catalase. Catalase is a ubiquitous enzyme found in both
prokaryotes and eukaryotes, which is involved in the
protection of cells from the toxic effects of peroxides.
It catalyzes the conversion of hydrogen peroxide to
water and molecular oxygen. Catalases also utilize
hydrogen peroxide to oxidize various substrates such as
alcohol or phenols. Clade 3 catalases are the most
abundant subfamily and are found in all three kingdoms
of life; they have a relatively small subunit size of 43
to 75 kDa, and bind a protoheme IX (heme b) group buried
deep inside the structure. Clade 3 catalases also bind
NADPH as a second redox-active cofactor. They form
tetramers, and in eukaryotic cells, catalases are
located in peroxisomes.
Length = 429
Score = 731 bits (1890), Expect = 0.0
Identities = 239/390 (61%), Positives = 294/390 (75%), Gaps = 4/390 (1%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
VTHDIT TKA IFSE+GK+TPV RFSTV GERGSADT RDPRGFALKFYTE+GNWDLV
Sbjct: 20 VTHDITKYTKAKIFSEVGKKTPVFVRFSTVAGERGSADTERDPRGFALKFYTEEGNWDLV 79
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRGIP 632
GNNTP+FF+RDP +F FIH+QKRNP T+L+D D FWDF SL PE+ HQV ILFSDRGIP
Sbjct: 80 GNNTPVFFIRDPIKFPDFIHTQKRNPQTNLKDPDMFWDFWSLSPESLHQVTILFSDRGIP 139
Query: 633 DGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLY 692
DG+RHM+GYGSHTF LVN E + KFHF+TDQGIKN++ + A +LA DPDY+ RDL+
Sbjct: 140 DGYRHMNGYGSHTFSLVNAKGERFWVKFHFKTDQGIKNLTNEEAAELAGEDPDYAQRDLF 199
Query: 693 DNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGNYY 752
+ I +G+FPSWT Y+QVM E+A+ YR+NPFD+TK+WP D+PL+ VG + L++NP NY+
Sbjct: 200 EAIERGDFPSWTLYVQVMPEEDAEKYRFNPFDLTKVWPHKDYPLIEVGKLELNRNPENYF 259
Query: 753 AEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVANY 812
AE+EQ AF+P+NL+PGI +PDKMLQGRL SY D H +RLG N++Q+PVN P V NY
Sbjct: 260 AEVEQAAFSPSNLVPGIGFSPDKMLQGRLFSYADAHRYRLGVNYHQLPVNRPK-CPVNNY 318
Query: 813 QRDAPMAID-NQNGAPNYYPNSFKGPEPTPRGAWSTYNATGDVKRYKT-EDEDNFSQPRI 870
QRD M +D N GAPNY PNSF GP P A +GD RY +D+D+++Q
Sbjct: 319 QRDGAMRVDGNGGGAPNYEPNSFGGPPEDPEYAEPPLPVSGDADRYNYRDDDDDYTQAGD 378
Query: 871 LWSNVLDDAARDRMTTNIASVLKLAAPFIQ 900
L+ V + R+R+ NIA LK A FIQ
Sbjct: 379 LYRLV-SEDERERLVENIAGHLKGAPEFIQ 407
Score = 50.2 bits (121), Expect = 3e-06
Identities = 17/20 (85%), Positives = 17/20 (85%)
Query: 185 RNPERVVHAKGGGAFGYFEV 204
R PERVVHAKG GAFG FEV
Sbjct: 1 RIPERVVHAKGAGAFGTFEV 20
Score = 47.9 bits (115), Expect = 2e-05
Identities = 16/19 (84%), Positives = 16/19 (84%)
Query: 134 RNPERVVHAKGGGAFGYFE 152
R PERVVHAKG GAFG FE
Sbjct: 1 RIPERVVHAKGAGAFGTFE 19
>gnl|CDD|215003 smart01060, Catalase, Catalases are antioxidant enzymes that
catalyse the conversion of hydrogen peroxide to water
and molecular oxygen, serving to protect cells from its
toxic effects. Hydrogen peroxide is produced as a
consequence of oxidative cellular metabolism and can be
converted to the highly reactive hydroxyl radical via
transition metals, this radical being able to damage a
wide variety of molecules within a cell, leading to
oxidative stress and cell death. Catalases act to
neutralise hydrogen peroxide toxicity, and are produced
by all aerobic organisms ranging from bacteria to man.
Most catalases are mono-functional, haem-containing
enzymes, although there are also bifunctional
haem-containing peroxidase/catalases that are closely
related to plant peroxidases, and non-haem,
manganese-containing catalases that are found in
bacteria.
Length = 373
Score = 620 bits (1601), Expect = 0.0
Identities = 201/318 (63%), Positives = 249/318 (78%), Gaps = 2/318 (0%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
VT DI+ TKAA F ++GK+TPV RFSTV GERGSADT RDPRGFA+KFYTE+GNWDLV
Sbjct: 57 VTEDISDYTKAAFFQKVGKKTPVFVRFSTVAGERGSADTVRDPRGFAVKFYTEEGNWDLV 116
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRGIP 632
GNNTP+FF+RDP +F FIH+QKR+P T+L D D FWDF SL PE+ HQV L SDRGIP
Sbjct: 117 GNNTPVFFIRDPIKFPDFIHAQKRDPRTNLPDHDMFWDFWSLNPESLHQVTWLMSDRGIP 176
Query: 633 DGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLY 692
+RHM+G+G HTFKLVN + E Y KFHF+ DQGIKN++ + A KLA DPDY RDLY
Sbjct: 177 ASYRHMNGFGVHTFKLVNAEGERFYVKFHFKPDQGIKNLTWEEAAKLAGKDPDYHRRDLY 236
Query: 693 DNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGNYY 752
+ I +G++P WT Y+QVM E+A+ +R++PFD+TK+WP D+PL+ VG M L++NP NY+
Sbjct: 237 EAIERGDYPEWTLYVQVMPEEDAEKFRFDPFDLTKVWPHKDYPLIEVGKMTLNRNPDNYF 296
Query: 753 AEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVANY 812
AE+EQ AF+P+NL+PGIE +PDKMLQGRL SY DT +RLG N++Q+PVN P R V NY
Sbjct: 297 AEVEQAAFSPSNLVPGIEFSPDKMLQGRLFSYPDTQRYRLGPNYHQLPVNRP-RCPVHNY 355
Query: 813 QRDAPMAID-NQNGAPNY 829
QRD M +D NQ G PNY
Sbjct: 356 QRDGAMRVDGNQGGDPNY 373
Score = 88.3 bits (220), Expect = 1e-18
Identities = 32/56 (57%), Positives = 36/56 (64%)
Query: 97 AGNPVDSETIIKTIGPHGPVPLEDTYYLDKLFHFAGERNPERVVHAKGGGAFGYFE 152
G PV T GP GPV L+D + ++KL HF ER PERVVHAKG GA GYFE
Sbjct: 1 QGAPVADNQNSLTAGPRGPVLLQDFHLIEKLAHFDRERIPERVVHAKGSGAHGYFE 56
Score = 85.2 bits (212), Expect = 2e-17
Identities = 30/45 (66%), Positives = 34/45 (75%)
Query: 160 TIGPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEV 204
T GP GPV L+D + ++KL HF ER PERVVHAKG GA GYFEV
Sbjct: 13 TAGPRGPVLLQDFHLIEKLAHFDRERIPERVVHAKGSGAHGYFEV 57
>gnl|CDD|223824 COG0753, KatE, Catalase [Inorganic ion transport and metabolism].
Length = 496
Score = 575 bits (1483), Expect = 0.0
Identities = 214/393 (54%), Positives = 270/393 (68%), Gaps = 7/393 (1%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
VT DI+ TKA +F E+GK+TPV RFSTV GERGSADT RD RGFALKFYTE+GNWDLV
Sbjct: 76 VTEDISKYTKAKLFQEVGKKTPVFVRFSTVAGERGSADTVRDVRGFALKFYTEEGNWDLV 135
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRGIP 632
GNNTP+FF+RD +F FIH+QK +P T+LRD D FWDF SL PE+ HQV L SDRGIP
Sbjct: 136 GNNTPVFFIRDAIKFPDFIHAQKPDPRTNLRDADTFWDFWSLNPESLHQVTWLMSDRGIP 195
Query: 633 DGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLY 692
+RHM G+G HTFK VN + V+ KFHF+ QGIKN++ A KLA DPDY RDLY
Sbjct: 196 ASYRHMEGFGVHTFKFVNAKGKRVWVKFHFKPKQGIKNLTWDEAAKLAGKDPDYHQRDLY 255
Query: 693 DNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGNYY 752
+ I G+FP W Y+QVM E+A+ + ++P D+TK+WP+ D+PL+ VG MVL++NP N++
Sbjct: 256 EAIENGDFPEWDLYVQVMPEEDAEKFDFDPLDLTKLWPEEDYPLIEVGTMVLNRNPDNFF 315
Query: 753 AEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVANY 812
AE+EQ AF P NL+PGI+ +PD +LQGRL SY DT +RLG N++QIPVN P + V N
Sbjct: 316 AEVEQAAFAPGNLVPGIDFSPDPLLQGRLFSYGDTQRYRLGPNYHQIPVNRP-KCPVHNN 374
Query: 813 QRDAPMAIDNQNGAPNYYPNSF-KGPEPTPRGAWSTYNAT--GDVKRYKTE-DEDNFSQP 868
QRD M + G NY PNSF PE + + GD +R + D+D FSQP
Sbjct: 375 QRDGQMRMGINTGPANYEPNSFGDNPEAPEQPGFVEPPERVEGDKQRRRAISDDDYFSQP 434
Query: 869 RILWSNVLDDAARDRMTTNIASVL-KLAAPFIQ 900
R L+ L DA + + NIA L K+ P I+
Sbjct: 435 RALY-RSLSDAEKQHLVDNIAFELSKVTDPEIK 466
Score = 84.7 bits (210), Expect = 5e-17
Identities = 38/74 (51%), Positives = 43/74 (58%)
Query: 86 SSCEIPVDTTSAGNPVDSETIIKTIGPHGPVPLEDTYYLDKLFHFAGERNPERVVHAKGG 145
+ E TT+ G PV T GP GP L+D + L+KL HF ER PERVVHAKG
Sbjct: 9 AKDEETTLTTNQGAPVADNQNSLTAGPRGPTLLQDFHLLEKLAHFDRERIPERVVHAKGS 68
Query: 146 GAFGYFEDRETIIK 159
GA GYFE E I K
Sbjct: 69 GAHGYFEVTEDISK 82
Score = 74.7 bits (184), Expect = 8e-14
Identities = 30/45 (66%), Positives = 33/45 (73%)
Query: 160 TIGPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEV 204
T GP GP L+D + L+KL HF ER PERVVHAKG GA GYFEV
Sbjct: 32 TAGPRGPTLLQDFHLLEKLAHFDRERIPERVVHAKGSGAHGYFEV 76
>gnl|CDD|215783 pfam00199, Catalase, Catalase.
Length = 383
Score = 551 bits (1423), Expect = 0.0
Identities = 194/326 (59%), Positives = 239/326 (73%), Gaps = 2/326 (0%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
VT D + LTKAA FS +GK+TPV RFSTV GE GSADT RDPRGFALKFYTE+GNWDLV
Sbjct: 60 VTGDASDLTKAAFFSAVGKKTPVFVRFSTVGGEPGSADTARDPRGFALKFYTEEGNWDLV 119
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRGIP 632
GNNTP+FF+RDP +F FIH+QK +P T+L D FWDF++L PE+ HQV LFSDRG P
Sbjct: 120 GNNTPVFFIRDPIKFPDFIHAQKPDPATNLPDPTMFWDFLALHPESLHQVTWLFSDRGTP 179
Query: 633 DGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLY 692
FRHM+GYG HTFK VN D + Y KFHF+ DQG+KN++ + A KLA DPD+ RDLY
Sbjct: 180 ASFRHMNGYGVHTFKFVNADGKRTYVKFHFKPDQGVKNLTAEEAAKLAGEDPDFLTRDLY 239
Query: 693 DNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGNYY 752
+ I +G P WT Y+QVM +A+ +R+NPFD TK+WP +PL+ VG + L++NP NY+
Sbjct: 240 EAIERGGPPKWTLYVQVMDPGDAEDFRFNPFDATKVWPHDRYPLIEVGTLTLNRNPDNYF 299
Query: 753 AEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVANY 812
AE+EQ AF+P+NL+PGIEP+ D MLQ RL +Y D+ RLG N+ Q+PVN P R V N
Sbjct: 300 AEVEQAAFDPSNLVPGIEPSDDPMLQARLFAYADSQRRRLGPNYQQLPVNRP-RCPVHNQ 358
Query: 813 QRDAPMAIDNQNGAPNYYPNSFKGPE 838
RD M N G PNY PNSF GP+
Sbjct: 359 -RDGAMRFGNYGGEPNYEPNSFGGPQ 383
Score = 87.7 bits (218), Expect = 2e-18
Identities = 33/59 (55%), Positives = 39/59 (66%)
Query: 94 TTSAGNPVDSETIIKTIGPHGPVPLEDTYYLDKLFHFAGERNPERVVHAKGGGAFGYFE 152
TT+ G PV T GP GP+ L+D + ++KL HF ER PERVVHAKG GAFG FE
Sbjct: 1 TTANGAPVADNQNSLTAGPRGPLLLQDFHLIEKLAHFDRERIPERVVHAKGAGAFGTFE 59
Score = 80.4 bits (199), Expect = 7e-16
Identities = 29/45 (64%), Positives = 34/45 (75%)
Query: 160 TIGPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEV 204
T GP GP+ L+D + ++KL HF ER PERVVHAKG GAFG FEV
Sbjct: 16 TAGPRGPLLLQDFHLIEKLAHFDRERIPERVVHAKGAGAFGTFEV 60
>gnl|CDD|163713 cd08157, catalase_fungal, Fungal catalases similar to yeast
catalases A and T. Catalase is a ubiquitous enzyme
found in both prokaryotes and eukaryotes, which is
involved in the protection of cells from the toxic
effects of peroxides. It catalyzes the conversion of
hydrogen peroxide to water and molecular oxygen.
Catalases also utilize hydrogen peroxide to oxidize
various substrates such as alcohol or phenols. This
family of fungal catalases has a relatively small
subunit size, and binds a protoheme IX (heme b) group
buried deep inside the structure. Fungal catalases also
bind NADPH as a second redox-active cofactor. They form
tetramers; in eukaryotic cells, catalases are typically
located in peroxisomes. Saccharomyces cerevisiae
catalase T is found in the cytoplasm, though.
Length = 451
Score = 547 bits (1412), Expect = 0.0
Identities = 205/398 (51%), Positives = 272/398 (68%), Gaps = 11/398 (2%)
Query: 511 YPVTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWD 570
+ VT DI+ +T A + +GK+TP RFSTV GE+GSADT RDPRGFA+KFYTE+GNWD
Sbjct: 34 FEVTDDISDITSADMLQGVGKKTPCLVRFSTVGGEKGSADTVRDPRGFAVKFYTEEGNWD 93
Query: 571 LVGNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRG 630
V NNTP+FF+RDP +F HFIHSQKR+P T+L+D FWD++S PE+ HQVMILFSDRG
Sbjct: 94 WVFNNTPVFFIRDPIKFPHFIHSQKRDPQTNLKDSTMFWDYLSQNPESIHQVMILFSDRG 153
Query: 631 IPDGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRD 690
P +R M+GY HT+K VN D Y +FH ++DQG K ++ + A +LA ++PDY+ +D
Sbjct: 154 TPASYRSMNGYSGHTYKWVNPDGSFKYVQFHLKSDQGPKFLTGEEAARLAGSNPDYATKD 213
Query: 691 LYDNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGN 750
L++ I +G++PSWT Y+QVMT E+A+ R+N FD+TK+WP DFPL PVG + L++NP N
Sbjct: 214 LFEAIERGDYPSWTVYVQVMTPEQAEKLRFNIFDLTKVWPHKDFPLRPVGKLTLNENPKN 273
Query: 751 YYAEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVA 810
Y+AEIEQ AF+P++++PGIEP+ D +LQ RL SY D H HRLG N+ Q+PVN P V
Sbjct: 274 YFAEIEQAAFSPSHMVPGIEPSADPVLQARLFSYPDAHRHRLGPNYQQLPVNRPKTSPVY 333
Query: 811 N-YQRDAPMAIDNQNGA-PNY----YPNSFKGPEPTPRGAWSTYNATGDVKRYKTE--DE 862
N YQRD PM+++ G PNY P ++ G N G+V + TE DE
Sbjct: 334 NPYQRDGPMSVNGNYGGDPNYVSSILPPTYFKKRVDADG--HHENWVGEVVAFLTEITDE 391
Query: 863 DNFSQPRILWSNVLDDAARDRMTTNIASVLKLAAPFIQ 900
D F QPR LW V ++R N+A L A P I+
Sbjct: 392 D-FVQPRALWEVVGKPGQQERFVKNVAGHLSGAPPEIR 428
Score = 63.9 bits (156), Expect = 2e-10
Identities = 23/36 (63%), Positives = 27/36 (75%)
Query: 169 LEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEV 204
L+D + +D L HF ER PERVVHAKG GA+G FEV
Sbjct: 1 LQDFHLIDTLAHFDRERIPERVVHAKGAGAYGEFEV 36
Score = 61.2 bits (149), Expect = 1e-09
Identities = 22/35 (62%), Positives = 26/35 (74%)
Query: 118 LEDTYYLDKLFHFAGERNPERVVHAKGGGAFGYFE 152
L+D + +D L HF ER PERVVHAKG GA+G FE
Sbjct: 1 LQDFHLIDTLAHFDRERIPERVVHAKGAGAYGEFE 35
>gnl|CDD|163705 cd00328, catalase, Catalase heme-binding enzyme. Catalase is a
ubiquitous enzyme found in both prokaryotes and
eukaryotes, which is involved in the protection of cells
from the toxic effects of peroxides. It catalyzes the
conversion of hydrogen peroxide to water and molecular
oxygen. Catalases also utilize hydrogen peroxide to
oxidize various substrates such as alcohol or phenols.
Most catalases exist as tetramers of 65KD subunits
containing a protoheme IX group buried deep inside the
structure. In eukaryotic cells, catalases are located in
peroxisomes.
Length = 433
Score = 511 bits (1317), Expect = e-174
Identities = 199/395 (50%), Positives = 264/395 (66%), Gaps = 10/395 (2%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
D + ++ AA FS IGK+TPV RFSTV G GSADT RDP GFA KFYTE+GN+DLV
Sbjct: 20 AYGDWSDISAAAFFSAIGKKTPVFVRFSTVVGGAGSADTVRDPHGFATKFYTEEGNFDLV 79
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRGIP 632
GNNTPIFF+RD +F FIH+QK NP T L D D FWDF+SL PE+ HQV LFSDRGIP
Sbjct: 80 GNNTPIFFIRDAIKFPDFIHAQKPNPQTALPDADRFWDFLSLRPESLHQVSFLFSDRGIP 139
Query: 633 DGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLY 692
+RHM+GYGSHTFKLVN + + Y KFH++TDQGI N+ + A +LA DPDY +DL+
Sbjct: 140 AAYRHMNGYGSHTFKLVNANGKVHYVKFHWKTDQGIANLVWEEAARLAGEDPDYHRQDLF 199
Query: 693 DNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGNYY 752
+ I G++PSW YIQVMTF +A+ + +NP D TK+WP+ PL+ VG +VL++NP N++
Sbjct: 200 EAIEAGDYPSWELYIQVMTFNDAEKFPFNPLDPTKVWPEELVPLIVVGKLVLNRNPLNFF 259
Query: 753 AEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVANY 812
AE+EQ AF+P +++PG+E + D +LQGRL SY DT ++RLG NF Q+PVN PY V N
Sbjct: 260 AEVEQAAFDPGHIVPGVEFSEDPLLQGRLFSYADTQLYRLGPNFQQLPVNRPY-APVHNN 318
Query: 813 QRDAPMAIDNQNGAPNYYPNSFKGPEPTP------RGAWSTYNATGDVKRYKTEDEDNFS 866
QRD +++ G PNY PN+ P RG +S + + G + T ++DNF+
Sbjct: 319 QRDGAGNMNDNTGVPNYEPNAKDVRYPAQGAPKFDRGHFSHWKS-GVNREASTTNDDNFT 377
Query: 867 QPRILWSNVLDDAARDRMTTNIA-SVLKLAAPFIQ 900
Q R+ + L + R+ + +P IQ
Sbjct: 378 QARLFY-RSLTPGQQKRLVDAFRFELADAVSPQIQ 411
Score = 42.4 bits (100), Expect = 9e-04
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 185 RNPERVVHAKGGGAFGYFEVRK 206
R PERVVHA+G GAFGYF
Sbjct: 1 RIPERVVHARGAGAFGYFTAYG 22
Score = 41.7 bits (98), Expect = 0.002
Identities = 15/24 (62%), Positives = 16/24 (66%)
Query: 134 RNPERVVHAKGGGAFGYFEDRETI 157
R PERVVHA+G GAFGYF
Sbjct: 1 RIPERVVHARGAGAFGYFTAYGDW 24
>gnl|CDD|215328 PLN02609, PLN02609, catalase.
Length = 492
Score = 499 bits (1287), Expect = e-169
Identities = 163/394 (41%), Positives = 236/394 (59%), Gaps = 8/394 (2%)
Query: 511 YPVTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWD 570
+ VTHDI++LT A G QTPV RFSTV ERGS +T RDPRGFA+KFYT +GN+D
Sbjct: 75 FEVTHDISNLTCADFLRAPGVQTPVIVRFSTVIHERGSPETLRDPRGFAVKFYTREGNFD 134
Query: 571 LVGNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRG 630
+VGNN P+FF+RD +F +H+ K NP TH+++ DF+S PE+ H LF DRG
Sbjct: 135 MVGNNFPVFFIRDGMKFPDMVHALKPNPKTHIQEPWRILDFLSHHPESLHMFTFLFDDRG 194
Query: 631 IPDGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRD 690
IP +RHM G+G HT+KL+NK + Y KFH++ G+KN+ + A ++ ++ ++ +D
Sbjct: 195 IPQDYRHMEGFGVHTYKLINKAGKAHYVKFHWKPTCGVKNLLDEEAVRVGGSNHSHATQD 254
Query: 691 LYDNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGN 750
LYD+IA GN+P W +IQ M E+ + ++P DVTK WP+ PL PVG +VL++N N
Sbjct: 255 LYDSIAAGNYPEWKLFIQTMDPEDEDKFDFDPLDVTKTWPEDILPLQPVGRLVLNRNIDN 314
Query: 751 YYAEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVA 810
++AE EQLAF P ++PGI + DK+LQ R+ +Y DT HRLG N+ Q+PVN P +
Sbjct: 315 FFAENEQLAFCPAIVVPGIYYSDDKLLQTRIFAYADTQRHRLGPNYLQLPVNAP-KCAHH 373
Query: 811 NYQRDAPMAIDNQNGAPNYYPNSF---KGPEPTPRGAWSTYNATGDVKRYKTEDEDNFSQ 867
N + M +++ NY+P+ F + E P +G ++ K E E+NF Q
Sbjct: 374 NNHHEGFMNFMHRDEEVNYFPSRFDPVRHAERVPI---PHPPLSGRREKCKIEKENNFKQ 430
Query: 868 PRILWSNVLDDAARDRMTTNIASVLKLAAPFIQI 901
P + + ++R L +I
Sbjct: 431 PGERYRS-WSPDRQERFIKRWVDALSDPRVTHEI 463
Score = 74.4 bits (183), Expect = 9e-14
Identities = 31/67 (46%), Positives = 43/67 (64%)
Query: 86 SSCEIPVDTTSAGNPVDSETIIKTIGPHGPVPLEDTYYLDKLFHFAGERNPERVVHAKGG 145
S+ P TT++G PV + T+G GP+ LED + ++KL +F ER PERVVHA+G
Sbjct: 10 SAYNSPFFTTNSGAPVWNNNSSLTVGSRGPILLEDYHLVEKLANFDRERIPERVVHARGA 69
Query: 146 GAFGYFE 152
A G+FE
Sbjct: 70 SAKGFFE 76
Score = 68.2 bits (167), Expect = 7e-12
Identities = 25/45 (55%), Positives = 33/45 (73%)
Query: 160 TIGPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEV 204
T+G GP+ LED + ++KL +F ER PERVVHA+G A G+FEV
Sbjct: 33 TVGSRGPILLEDYHLVEKLANFDRERIPERVVHARGASAKGFFEV 77
>gnl|CDD|163710 cd08154, catalase_clade_1, Clade 1 of the heme-binding enzyme
catalase. Catalase is a ubiquitous enzyme found in both
prokaryotes and eukaryotes, which is involved in the
protection of cells from the toxic effects of peroxides.
It catalyzes the conversion of hydrogen peroxide to
water and molecular oxygen. Catalases also utilize
hydrogen peroxide to oxidize various substrates such as
alcohol or phenols. Clade 1 catalases are found in
bacteria, algae, and plants; they have a relatively
small subunit size of 55 to 69 kDa, and bind a protoheme
IX (heme b) group buried deep inside the structure. They
appear to form tetramers. In eukaryotic cells, catalases
are located in peroxisomes.
Length = 469
Score = 491 bits (1265), Expect = e-166
Identities = 167/381 (43%), Positives = 243/381 (63%), Gaps = 2/381 (0%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
DI+ T+A+ E GK+TPV RFSTV +GS +T RDPRGFA+KFYTE+GNWDLV
Sbjct: 62 AYGDISDYTRASFLQEPGKKTPVFVRFSTVIHGKGSPETLRDPRGFAVKFYTEEGNWDLV 121
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRGIP 632
GNN P+FF+RD +F IH+ K +PVT+++D + +DF S +PE+TH + L+SD G P
Sbjct: 122 GNNLPVFFIRDAIKFPDMIHALKPSPVTNIQDPNRIFDFFSHVPESTHMLTFLYSDWGTP 181
Query: 633 DGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLY 692
+RHM G G HT+K VN + + VY K+H++ QG+KN++ + A ++ + +++ +DLY
Sbjct: 182 ASYRHMDGSGVHTYKWVNAEGKVVYVKYHWKPKQGVKNLTAEEAAEVQGKNFNHATQDLY 241
Query: 693 DNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGNYY 752
D IA GN+P W Y+Q+M ++ ++P D TKIWP+ FPL PVG M L+KNP N++
Sbjct: 242 DAIAAGNYPEWELYVQIMDPKDLDKLDFDPLDDTKIWPEDQFPLKPVGKMTLNKNPDNFF 301
Query: 753 AEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLGANFNQIPVNCPYRVRVANY 812
AE+EQ+AF+P NL+PGIEP+ DKMLQGRL SY DT +RLG N+ Q+P+N P + V N
Sbjct: 302 AEVEQVAFSPGNLVPGIEPSDDKMLQGRLFSYSDTQRYRLGPNYLQLPINAP-KAAVHNN 360
Query: 813 QRDAPMAIDNQNGAPNYYPNSFKGPEPTPRGAWSTYNATGDVKRYKTEDEDNFSQPRILW 872
QRD M + NY P+ G P+ +S +G ++ +NF Q +
Sbjct: 361 QRDGQMNYGHDTSDVNYEPSRLDGLPEAPKYPYSQPPLSGTTQQAPIAKTNNFKQAGERY 420
Query: 873 SNVLDDAARDRMTTNIASVLK 893
+ + ++ + N+ L
Sbjct: 421 RS-FSEEEQENLIKNLVVDLS 440
Score = 78.5 bits (194), Expect = 4e-15
Identities = 34/59 (57%), Positives = 41/59 (69%)
Query: 94 TTSAGNPVDSETIIKTIGPHGPVPLEDTYYLDKLFHFAGERNPERVVHAKGGGAFGYFE 152
TT+ G PV +T+GP GPV LED + ++KL HF ER PERVVHA+G GA GYFE
Sbjct: 3 TTNQGAPVGDNQNSQTVGPRGPVLLEDYHLIEKLAHFDRERIPERVVHARGAGAHGYFE 61
Score = 72.7 bits (179), Expect = 3e-13
Identities = 29/46 (63%), Positives = 35/46 (76%)
Query: 159 KTIGPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEV 204
+T+GP GPV LED + ++KL HF ER PERVVHA+G GA GYFE
Sbjct: 17 QTVGPRGPVLLEDYHLIEKLAHFDRERIPERVVHARGAGAHGYFEA 62
>gnl|CDD|163711 cd08155, catalase_clade_2, Clade 2 of the heme-binding enzyme
catalase. Catalase is a ubiquitous enzyme found in both
prokaryotes and eukaryotes, which is involved in the
protection of cells from the toxic effects of peroxides.
It catalyzes the conversion of hydrogen peroxide to
water and molecular oxygen. Catalases also utilize
hydrogen peroxide to oxidize various substrates such as
alcohol or phenols. Clade 2 catalases are mostly found
in bacteria and fungi; they have a large subunit size of
75 to 84 kDa, and bind a heme d group buried deep inside
the structure. They appear to form tetramers. In
eukaryotic cells, catalases are located in peroxisomes.
Length = 443
Score = 389 bits (1001), Expect = e-127
Identities = 160/376 (42%), Positives = 224/376 (59%), Gaps = 21/376 (5%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
V ++ TKA + GK+TPV RFSTV G RGSADT RD RGFA+KFYTE+GN+DLV
Sbjct: 23 VYESLSQYTKAKFLQDPGKKTPVFVRFSTVAGSRGSADTVRDVRGFAVKFYTEEGNYDLV 82
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNP--------VTHLRDWDAFWDFISLLPETTHQVMI 624
GNN P+FF++D +F IH+ K P H D FWDF+SL PE+ H VM
Sbjct: 83 GNNIPVFFIQDAIKFPDLIHAVKPEPHNEMPQAQSAH----DTFWDFVSLQPESAHMVMW 138
Query: 625 LFSDRGIPDGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDP 684
SDR IP +R M G+G HTF+LVN + + KFH++ G+ ++ A K+A DP
Sbjct: 139 AMSDRAIPRSYRMMEGFGVHTFRLVNAQGKSTFVKFHWKPVLGVHSLVWDEAQKIAGKDP 198
Query: 685 DYSIRDLYDNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVL 744
D+ RDL++ I G++P W +Q++ E+ + ++ D TK+ P+ P+ VG MVL
Sbjct: 199 DFHRRDLWEAIESGDYPEWELGVQLIDEEDEFKFDFDILDPTKLIPEELVPVQRVGKMVL 258
Query: 745 DKNPGNYYAEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRLG-ANFNQIPVNC 803
++NP N++AE EQ+AF P N++PGI+ + D +LQGRL SY+DT + RLG NF+++P+N
Sbjct: 259 NRNPDNFFAETEQVAFCPANVVPGIDFSNDPLLQGRLFSYLDTQLSRLGGPNFHELPINR 318
Query: 804 PYRVRVANYQRDAPMAIDNQNGAPNYYPNSFKG----PEPTPRGAWSTY--NATGDVKRY 857
P V N QRD M + G NY+PNS G + Y G R
Sbjct: 319 P-VCPVHNNQRDGHMRMTINKGRVNYFPNSLGAGPPRAASPAEGGFVHYPEKVEGPKIRI 377
Query: 858 KTED-EDNFSQPRILW 872
++E D++SQ R+ W
Sbjct: 378 RSESFADHYSQARLFW 393
Score = 44.7 bits (106), Expect = 2e-04
Identities = 16/23 (69%), Positives = 19/23 (82%)
Query: 184 ERNPERVVHAKGGGAFGYFEVRK 206
ER PERVVHA+G GA GYF+V +
Sbjct: 3 ERIPERVVHARGSGAHGYFQVYE 25
Score = 43.1 bits (102), Expect = 5e-04
Identities = 15/20 (75%), Positives = 17/20 (85%)
Query: 133 ERNPERVVHAKGGGAFGYFE 152
ER PERVVHA+G GA GYF+
Sbjct: 3 ERIPERVVHARGSGAHGYFQ 22
>gnl|CDD|236886 PRK11249, katE, hydroperoxidase II; Provisional.
Length = 752
Score = 366 bits (941), Expect = e-114
Identities = 167/383 (43%), Positives = 231/383 (60%), Gaps = 33/383 (8%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGNWDLV 572
++ +TKAA + GK TPV RFSTV G RGSADT RD RGFA KFYTE+GN+DLV
Sbjct: 137 PYKSLSDITKAAFLQDPGKITPVFVRFSTVQGPRGSADTVRDIRGFATKFYTEEGNFDLV 196
Query: 573 GNNTPIFFVRDPFRFIHFIHSQKRNP--------VTHLRDWDAFWDFISLLPETTHQVMI 624
GNNTP+FF++D +F F+H+ K P H D FWD++SL PET H VM
Sbjct: 197 GNNTPVFFIQDAIKFPDFVHAVKPEPHNEIPQGQSAH----DTFWDYVSLQPETLHNVMW 252
Query: 625 LFSDRGIPDGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDP 684
SDRGIP +R M G+G HTF+L+N + + + +FH++ G ++ A KL DP
Sbjct: 253 AMSDRGIPRSYRTMEGFGIHTFRLINAEGKATFVRFHWKPVAGKASLVWDEAQKLTGRDP 312
Query: 685 DYSIRDLYDNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVL 744
D+ RDL++ I G++P + +Q++ E+ + ++ D TK+ P+ P+ VG MVL
Sbjct: 313 DFHRRDLWEAIEAGDYPEYELGVQLIPEEDEFKFDFDLLDPTKLIPEELVPVQRVGKMVL 372
Query: 745 DKNPGNYYAEIEQLAFNPNNLIPGIEPTPDKMLQGRLHSYIDTHIHRL-GANFNQIPVN- 802
++NP N++AE EQ+AF+P +++PGI+ T D +LQGRL SY DT I RL G NF++IP+N
Sbjct: 373 NRNPDNFFAETEQVAFHPGHIVPGIDFTNDPLLQGRLFSYTDTQISRLGGPNFHEIPINR 432
Query: 803 --CPYRVRVANYQRDAP--MAIDNQNGAPNYYPNSFKG--PEPTP----RGAWSTYNATG 852
CPY N+QRD M ID G NY PNS G P TP RG + +Y
Sbjct: 433 PTCPY----HNFQRDGMHRMTID--TGPANYEPNSINGNWPRETPPAPKRGGFESYQERV 486
Query: 853 DVKRYKTEDE---DNFSQPRILW 872
+ + + D +SQPR+ W
Sbjct: 487 EGNKVRERSPSFGDYYSQPRLFW 509
Score = 60.1 bits (146), Expect = 4e-09
Identities = 27/64 (42%), Positives = 35/64 (54%)
Query: 162 GPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKGGGAFGYFEVRKLPAGVVKIEFACLVM 221
G GP LED +K+ HF ER PER+VHA+G A GYF+ K + + K F
Sbjct: 95 GSRGPSLLEDFILREKITHFDHERIPERIVHARGSAAHGYFQPYKSLSDITKAAFLQDPG 154
Query: 222 RIVP 225
+I P
Sbjct: 155 KITP 158
Score = 57.0 bits (138), Expect = 4e-08
Identities = 22/42 (52%), Positives = 27/42 (64%)
Query: 111 GPHGPVPLEDTYYLDKLFHFAGERNPERVVHAKGGGAFGYFE 152
G GP LED +K+ HF ER PER+VHA+G A GYF+
Sbjct: 95 GSRGPSLLEDFILREKITHFDHERIPERIVHARGSAAHGYFQ 136
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 336 bits (864), Expect = e-107
Identities = 132/286 (46%), Positives = 181/286 (63%), Gaps = 4/286 (1%)
Query: 234 NRGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
RG+T+DV S+FET T++DAPGH+DF+ NMITGA+QADVA+LVVDA GEFE GF
Sbjct: 68 ERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAGF 127
Query: 294 ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIE 353
GGQTREHA L R+LG+ QL V +NK+D VSW ++RF+EIV+++ LK G+ D+
Sbjct: 128 GVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPKDVP 187
Query: 354 YVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIYKSTG 413
++P SG G+NLT S+ WY GP LL+ +D + P RPL KPLR+ + D+Y +G
Sbjct: 188 FIPISGFKGDNLTKKSEN---MPWYKGPTLLEALDQLEPPERPLDKPLRLPIQDVYSISG 244
Query: 414 SGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQQ 473
G GRVE+GVI G+KV P V VK++ + +S A GDNV + ++
Sbjct: 245 IGTVPVGRVESGVIKPGQKVTFMPAGVVGEVKSIEMHHEEISQAEPGDNVGFNVRGVEKN 304
Query: 474 NVSVGFLLSELSHPCPVSSKFEARIVVFNITTPITIGY-PVTHDIT 518
++ G ++ +P VS +F A+I+V IT GY PV H T
Sbjct: 305 DIRRGDVIGHSDNPPTVSPEFTAQIIVLWHPGIITSGYTPVLHAHT 350
Score = 98.9 bits (247), Expect = 9e-22
Identities = 38/66 (57%), Positives = 49/66 (74%)
Query: 20 QAGGKGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWIL 79
A K L+LV IGHVDAGKSTL+G LLY +G + R + K E E+K+LGK+SF +AW+L
Sbjct: 1 MASEKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVL 60
Query: 80 DETGEE 85
D+T EE
Sbjct: 61 DKTKEE 66
>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 = 280 bits (719), Expect = 1e-88
Identities = 88/161 (54%), Positives = 118/161 (73%), Gaps = 5/161 (3%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RG+T+DVG ++FET+ T++DAPGH+DF+ NMITGA+QADVA+LVV A +GEFE GFE
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFE 120
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVS--WSQDRFQEIVTKLGAFLKQAGFRDSDI 352
GGQTREHALL R+LGV QL V +NK+D V+ WSQ+R+ EI K+ FLK+ G+ D+
Sbjct: 121 KGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDV 180
Query: 353 EYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTP 393
++P SG TG+NL S+ WY GP LL+ +D+ + P
Sbjct: 181 PFIPISGFTGDNLIEKSE---NMPWYKGPTLLEALDSLEPP 218
Score = 111 bits (279), Expect = 1e-27
Identities = 38/58 (65%), Positives = 47/58 (81%)
Query: 28 HLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWILDETGEE 85
+LVVIGHVDAGKSTL GHLLY +G V R I K+E E+K++GK+SF YAW+LD+ EE
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEE 58
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 278 bits (714), Expect = 4e-85
Identities = 112/282 (39%), Positives = 168/282 (59%), Gaps = 9/282 (3%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RG+T+D+ +FET Y T++D PGH+DF+ NMITGA+QAD A+LVV A G
Sbjct: 68 RGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAG---GVM 124
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEY 354
QTREH L R+LG+NQL V INK+D V++ + R++E+ ++ LK G++ DI +
Sbjct: 125 --PQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPF 182
Query: 355 VPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIYKSTGS 414
+P S G+N+ S+ WY+GP LL+ +DN K P +P KPLR+ + D+Y +G
Sbjct: 183 IPVSAFEGDNVVKKSEN---MPWYNGPTLLEALDNLKPPEKPTDKPLRIPIQDVYSISGV 239
Query: 415 GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQQN 474
G GRVETGV+ G+KV+ P V VK++ + + A GDN+ + +++
Sbjct: 240 GTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQAEPGDNIGFNVRGVGKKD 299
Query: 475 VSVGFLLSELSHPCPVSSKFEARIVVFNITTPITIGY-PVTH 515
+ G + +P V+ +F A+IVV + IT+GY PV H
Sbjct: 300 IKRGDVCGHPDNPPTVAEEFTAQIVVLQHPSAITVGYTPVFH 341
Score = 85.0 bits (211), Expect = 3e-17
Identities = 31/62 (50%), Positives = 41/62 (66%)
Query: 24 KGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWILDETG 83
K L+L VIGHVD GKSTL+G LLY G + I + E+K+ GK+SF +AW++D
Sbjct: 4 KPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLK 63
Query: 84 EE 85
EE
Sbjct: 64 EE 65
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 262 bits (671), Expect = 9e-79
Identities = 122/283 (43%), Positives = 173/283 (61%), Gaps = 7/283 (2%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+D+ +FET Y T++DAPGH+DFI NMITG +QADVA+LVV +T GEFE G
Sbjct: 69 RGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGIS 128
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLD--TVSWSQDRFQEIVTKLGAFLKQAGFRDSDI 352
GQTREHALL +LGV Q+ V INK+D TV++SQ+R+ EI ++ A+LK+ G+ +
Sbjct: 129 KDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKV 188
Query: 353 EYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIYKST 412
++P SG G+N+ S WY GP LL+ +D + P RP+ KPLR+ + D+YK
Sbjct: 189 PFIPISGWQGDNMIEKS---DNMPWYKGPTLLEALDTLEPPKRPVDKPLRLPLQDVYKIG 245
Query: 413 GSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQ 472
G G GRVETG++ G V P T VK+V + ++ A GDNV + N
Sbjct: 246 GIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSV 305
Query: 473 QNVSVGFLLSEL-SHPCPVSSKFEARIVVFNITTPITIGY-PV 513
+++ G++ S+ + P + F A+++V N I GY PV
Sbjct: 306 KDIKRGYVASDSKNDPAKECADFTAQVIVLNHPGQIKNGYTPV 348
Score = 86.3 bits (214), Expect = 1e-17
Identities = 37/73 (50%), Positives = 47/73 (64%), Gaps = 2/73 (2%)
Query: 23 GKGRLH--LVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWILD 80
GK + H LVVIGHVD+GKST GHL+Y G + R I K E E+ ++GK SF YAW+LD
Sbjct: 2 GKEKTHINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLD 61
Query: 81 ETGEESSCEIPVD 93
+ E I +D
Sbjct: 62 KLKAERERGITID 74
>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 = 261 bits (668), Expect = 1e-78
Identities = 111/282 (39%), Positives = 167/282 (59%), Gaps = 8/282 (2%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RG+T+DV +FET +T++D PGH+DFI NMITGA+QAD A+LVV GEFE
Sbjct: 69 RGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQ-- 126
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEY 354
QTREHA L R+LG+NQL V INK+D+V++ ++ F+ I ++ +K+ G+ + +
Sbjct: 127 --PQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPF 184
Query: 355 VPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIYKSTGS 414
+P S G+N+ S+ T WY G LL+ +D + P +P KPLR+ + D+Y TG
Sbjct: 185 IPISAWNGDNVIKKSEN---TPWYKGKTLLEALDALEPPEKPTDKPLRIPIQDVYSITGV 241
Query: 415 GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQQN 474
G GRVETGV+ G+KV+ +P VK++ + + A GDN+ + +++
Sbjct: 242 GTVPVGRVETGVLKPGDKVVFEPAGVSGEVKSIEMHHEQIEQAEPGDNIGFNVRGVSKKD 301
Query: 475 VSVGFLLSELSHPCPVSSKFEARIVVFNITTPITIGY-PVTH 515
+ G + +P V+ +F A+IVV IT+GY PV H
Sbjct: 302 IRRGDVCGHPDNPPKVAKEFTAQIVVLQHPGAITVGYTPVFH 343
Score = 73.0 bits (179), Expect = 2e-13
Identities = 30/70 (42%), Positives = 44/70 (62%)
Query: 24 KGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWILDETG 83
K +++ IGHVD GKST +GHLLY G + + I K E E+++ GK SF +AW++D
Sbjct: 5 KEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLK 64
Query: 84 EESSCEIPVD 93
EE + +D
Sbjct: 65 EERERGVTID 74
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 223 bits (570), Expect = 2e-64
Identities = 122/307 (39%), Positives = 173/307 (56%), Gaps = 6/307 (1%)
Query: 226 LEGIASALNRGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDAT 285
L+ + + RGIT+D+ +FET Y T++DAPGH+DFI NMITG +QAD A+L++D+T
Sbjct: 60 LDKLKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDST 119
Query: 286 RGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLD--TVSWSQDRFQEIVTKLGAFLK 343
G FE G GQTREHALL +LGV Q+ NK+D T +S+ R+ EIV ++ ++LK
Sbjct: 120 TGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLK 179
Query: 344 QAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRM 403
+ G+ I +VP SG G+N+ S WY GP LL+ +D P RP KPLR+
Sbjct: 180 KVGYNPDKIPFVPISGFEGDNMIERS---TNLDWYKGPTLLEALDQINEPKRPSDKPLRL 236
Query: 404 SVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNV 463
+ D+YK G G GRVETGVI G V P T VK+V + S+ A GDNV
Sbjct: 237 PLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMHHESLQEALPGDNV 296
Query: 464 SVTLLNYDQQNVSVGFLLSELSH-PCPVSSKFEARIVVFNITTPITIGYPVTHDITHLTK 522
+ N +++ G++ S P ++ F +++++ N I GY D
Sbjct: 297 GFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHI 356
Query: 523 AAIFSEI 529
A F+EI
Sbjct: 357 AVKFAEI 363
Score = 71.7 bits (175), Expect = 6e-13
Identities = 34/73 (46%), Positives = 49/73 (67%), Gaps = 2/73 (2%)
Query: 23 GKGRLHL--VVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWILD 80
GK ++H+ VVIGHVD+GKST GHL+Y +G + R I + E E+ ++ K+SF YAW+LD
Sbjct: 2 GKEKVHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLD 61
Query: 81 ETGEESSCEIPVD 93
+ E I +D
Sbjct: 62 KLKAERERGITID 74
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 191 bits (487), Expect = 4e-53
Identities = 92/290 (31%), Positives = 153/290 (52%), Gaps = 22/290 (7%)
Query: 213 KIEFACLVMRIVPLEGIASALNRGITMDVGQSQFET-KTKYITLLDAPGHKDFIPNMITG 271
KI+ A LV +G+ + +GIT+DV F T K K+I + D PGH+ + NM TG
Sbjct: 54 KIDLALLV------DGLEAEREQGITIDVAYRYFSTEKRKFI-IADTPGHEQYTRNMATG 106
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF 331
A+ AD+A+L+VDA +G E QTR H+ + LG+ + V +NK+D V +S++ F
Sbjct: 107 ASTADLAILLVDARKGVLE-------QTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVF 159
Query: 332 QEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFK 391
+ IV AF Q G + D+ ++P S L G+N+ + S WY GP LL++++ +
Sbjct: 160 EAIVADYLAFAAQLGLK--DVRFIPISALLGDNVVSKS---ENMPWYKGPTLLEILETVE 214
Query: 392 TPSRPLTKPLRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDE 451
K R V + + AG + +G + G++V+V P + + VK + +
Sbjct: 215 IADDRSAKAFRFPVQYVNRPNLDFRGYAGTIASGSVKVGDEVVVLPSGKTSRVKRIVTFD 274
Query: 452 MSVSAAYAGDNVSVTLLNYDQQNVSVGFLLSELSHPCPVSSKFEARIVVF 501
++ A AG+ V++ L D+ ++S G L+ P V+ F+A +V
Sbjct: 275 GELAQASAGEAVTLVL--ADEIDISRGDLIVAADAPPAVADAFDADVVWM 322
Score = 40.0 bits (94), Expect = 0.006
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 24 KGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQ--SFMYAWILD 80
K L + G VD GKSTL+G LLY + ++ E +SK+ G Q A ++D
Sbjct: 4 KSLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVD 62
>gnl|CDD|163706 cd08150, catalase_like, Catalase-like heme-binding proteins and
protein domains. Catalase is a ubiquitous enzyme found
in both prokaryotes and eukaryotes involved in the
protection of cells from the toxic effects of peroxides.
It catalyses the conversion of hydrogen peroxide to
water and molecular oxygen. Several other related
protein families share the catalase fold and bind to
heme, but do not necessarily have catalase activity.
Length = 283
Score = 178 bits (454), Expect = 2e-50
Identities = 71/284 (25%), Positives = 114/284 (40%), Gaps = 22/284 (7%)
Query: 513 VTHDITHLTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGN--WD 570
V D+ + +F+E GK P RFS G DT D RGFA+KF D
Sbjct: 18 VLADLKERLRVGLFAE-GKVYPAYIRFSNG---AGIDDTKPDIRGFAIKFTGVADAGTLD 73
Query: 571 LVGNNTPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFSDRG 630
V NNTP+FF+R+ + F+ R+ D ++ PE ++ +
Sbjct: 74 FVLNNTPVFFIRNTSDYEDFVAEFARSA-RGEPPLDFIAWYVEKRPEDLPNLL--GARSQ 130
Query: 631 IPDGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRD 690
+PD + + TF +N + + GI ++ +L A PDY +
Sbjct: 131 VPDSYAAARYFSQVTFAFINGAGKYRVVRSKDNPVDGIPSLEDH---ELEARPPDYLREE 187
Query: 691 LYDNIAKGNFPSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFPLLPVGHMVLDKNPGN 750
L + + +G + F IQ+ +A T + T +WP ++ P+ V + +
Sbjct: 188 LTERLQRG-PVVYDFRIQLNDDTDATTI----DNPTILWP-TEHPVEAVAKITIPPPTFT 241
Query: 751 YYAEIEQLAFNPNNLIPGIEPTPDK--MLQGRLHSYIDTHIHRL 792
A E AFNP G+ T D +L+ R Y + R
Sbjct: 242 --AAQEAFAFNPFTPWHGLLETNDLGPILEVRRRVYTSSQGLRH 283
Score = 30.6 bits (69), Expect = 3.7
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 187 PERVVHAKGGGAFGYFEV 204
R H +G AFG FEV
Sbjct: 1 GLRGQHFQGTCAFGTFEV 18
Score = 30.2 bits (68), Expect = 5.1
Identities = 14/63 (22%), Positives = 19/63 (30%), Gaps = 14/63 (22%)
Query: 136 PERVVHAKGGGAFGYFEDRETIIKTIGPHGPVPLEDTYYLDKLFHFSGERNPERVVHAKG 195
R H +G AFG FE + LF G+ P + + G
Sbjct: 1 GLRGQHFQGTCAFGTFE-------------VLADLKERLRVGLF-AEGKVYPAYIRFSNG 46
Query: 196 GGA 198
G
Sbjct: 47 AGI 49
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 173 bits (442), Expect = 1e-45
Identities = 95/292 (32%), Positives = 157/292 (53%), Gaps = 26/292 (8%)
Query: 214 IEFACLVMRIVPLEGIASALNRGITMDVGQSQFET-KTKYITLLDAPGHKDFIPNMITGA 272
I+ A LV +G+A+ +GIT+DV F T K K+I + D PGH+ + NM+TGA
Sbjct: 73 IDLALLV------DGLAAEREQGITIDVAYRYFATPKRKFI-VADTPGHEQYTRNMVTGA 125
Query: 273 TQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQ 332
+ AD+A+++VDA +G QTR H+ + LG+ + + +NK+D V + Q+ F
Sbjct: 126 STADLAIILVDARKGVLT-------QTRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFD 178
Query: 333 EIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKT 392
EIV AF + G D+ ++P S L G+N+ T S A WY GP LL+ ++ +
Sbjct: 179 EIVADYRAFAAKLGL--HDVTFIPISALKGDNVVTRS---ARMPWYEGPSLLEHLETVEI 233
Query: 393 PSRPLTKPLRMSVSDIYKSTGS--GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVD 450
S K R V + + G+ AG V +GV+ G++V+V P + + VK +
Sbjct: 234 ASDRNLKDFRFPVQYVNRPNLDFRGF--AGTVASGVVRPGDEVVVLPSGKTSRVKRIVTP 291
Query: 451 EMSVSAAYAGDNVSVTLLNYDQQNVSVGFLLSELSHPCPVSSKFEARIVVFN 502
+ + A+AG V++TL D+ ++S G +L+ + V+ +F+A +V
Sbjct: 292 DGDLDEAFAGQAVTLTL--ADEIDISRGDMLARADNRPEVADQFDATVVWMA 341
Score = 36.8 bits (86), Expect = 0.053
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 13 IEEYTREQAGGKGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQ 71
I Y + K L + G VD GKSTL+G LLY + ++ E +SKK+G Q
Sbjct: 12 ILAYLAQHER-KSLLRFITCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQ 69
>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 = 165 bits (420), Expect = 2e-44
Identities = 94/290 (32%), Positives = 154/290 (53%), Gaps = 26/290 (8%)
Query: 213 KIEFACLVMRIVPLEGIASALNRGITMDVGQSQFET-KTKYITLLDAPGHKDFIPNMITG 271
+I+ A LV +G+ + +GIT+DV F T K K+I + D PGH+ + NM TG
Sbjct: 48 EIDLALLV------DGLQAEREQGITIDVAYRYFSTDKRKFI-VADTPGHEQYTRNMATG 100
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF 331
A+ AD+A+L+VDA +G E QTR H+ + LG+ + + +NK+D V + ++ F
Sbjct: 101 ASTADLAVLLVDARKGVLE-------QTRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVF 153
Query: 332 QEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFK 391
+ I AF +Q GFR D+ ++P S L G+N+ + S WYSGP LL++++ +
Sbjct: 154 ENIKKDYLAFAEQLGFR--DVTFIPLSALKGDNVVSRS---ESMPWYSGPTLLEILETVE 208
Query: 392 TPSRPLTKPLRMSVSDIYKSTGS--GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYV 449
PLR V + + GY AG + +G + G++V+V P + V +
Sbjct: 209 VERDAQDLPLRFPVQYVNRPNLDFRGY--AGTIASGSVHVGDEVVVLPSGRSSRVARIVT 266
Query: 450 DEMSVSAAYAGDNVSVTLLNYDQQNVSVGFLLSELSHPCPVSSKFEARIV 499
+ + A AG V++TL D+ ++S G LL+ V+ +F A +V
Sbjct: 267 FDGDLEQARAGQAVTLTL--DDEIDISRGDLLAAADSAPEVADQFAATLV 314
Score = 36.6 bits (85), Expect = 0.050
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 27 LHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQ 71
L + G VD GKSTL+G LL+ ++ ++ E +SKK G Q
Sbjct: 1 LRFLTCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQ 45
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 157 bits (400), Expect = 6e-44
Identities = 65/183 (35%), Positives = 101/183 (55%), Gaps = 20/183 (10%)
Query: 213 KIEFACLVMRIVPLEGIASALNRGITMDVGQSQFET-KTKYITLLDAPGHKDFIPNMITG 271
K++ A LV +G+ + +GIT+DV F T K K+I + D PGH+ + NM+TG
Sbjct: 46 KLDLALLV------DGLQAEREQGITIDVAYRYFSTPKRKFI-IADTPGHEQYTRNMVTG 98
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF 331
A+ AD+A+L+VDA +G E QTR H+ + LG+ + V +NK+D V + ++ F
Sbjct: 99 ASTADLAILLVDARKGVLE-------QTRRHSYIASLLGIRHVVVAVNKMDLVDYDEEVF 151
Query: 332 QEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFK 391
+EI AF G DI ++P S L G+N+ + S WY GP LL+ ++ +
Sbjct: 152 EEIKADYLAFAASLGIE--DITFIPISALEGDNVVSRS---ENMPWYKGPTLLEHLETVE 206
Query: 392 TPS 394
S
Sbjct: 207 IAS 209
Score = 38.7 bits (91), Expect = 0.005
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 29 LVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQ--SFMYAWILD 80
+ G VD GKSTL+G LLY + ++ E SK G Q A ++D
Sbjct: 2 FITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALER-SKSSGTQGEKLDLALLVD 54
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 165 bits (420), Expect = 9e-44
Identities = 88/290 (30%), Positives = 146/290 (50%), Gaps = 25/290 (8%)
Query: 213 KIEFACLVMRIVPLEGIASALNRGITMDVGQSQFET-KTKYITLLDAPGHKDFIPNMITG 271
K++ A LV +G+ + +GIT+DV F T K K+I + D PGH+ + NM TG
Sbjct: 75 KLDLALLV------DGLQAEREQGITIDVAYRYFSTEKRKFI-IADTPGHEQYTRNMATG 127
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF 331
A+ D+A+L++DA +G + QTR H+ + LG+ L V +NK+D V +S++ F
Sbjct: 128 ASTCDLAILLIDARKGVLD-------QTRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVF 180
Query: 332 QEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFK 391
+ I F +Q + DI +VP S L G+N+ + S WYSGP LL+V++
Sbjct: 181 ERIREDYLTFAEQLP-GNLDIRFVPLSALEGDNVVSQS---ESMPWYSGPTLLEVLETVD 236
Query: 392 TPSRPLTKPLRMSVSDIYKSTGS--GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYV 449
+P R V + + GY G + +GV+ G++V V P + + V +
Sbjct: 237 IQRVVDAQPFRFPVQYVNRPNLDFRGYA--GTLASGVVKVGDRVKVLPSGKESNVARIVT 294
Query: 450 DEMSVSAAYAGDNVSVTLLNYDQQNVSVGFLLSELSHPCPVSSKFEARIV 499
+ + A+AG+ +++ L D+ ++S G LL A +V
Sbjct: 295 FDGDLEEAFAGEAITLVL--EDEIDISRGDLLVAADEALQAVQHASADVV 342
Score = 33.7 bits (78), Expect = 0.39
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 11/64 (17%)
Query: 13 IEEYTREQAGGKGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKH-----ETESKK 67
+E Y Q K L + G VD GKSTL+G LL+ ++I++ +SK+
Sbjct: 15 VEAYLHAQQH-KSLLRFLTCGSVDDGKSTLIGRLLH-----DTKQIYEDQLASLHNDSKR 68
Query: 68 LGKQ 71
G Q
Sbjct: 69 HGTQ 72
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 140 bits (355), Expect = 3e-38
Identities = 60/157 (38%), Positives = 82/157 (52%), Gaps = 26/157 (16%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+ + FETK + I ++D PGH DF MI GA+QAD A+LVVDA G
Sbjct: 50 RGITIKIAAVSFETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGV------ 103
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKL-GAFLKQAGFRDSDIE 353
QTREH LL ++LGV + V INK+D V +E+V ++ L++ GF +
Sbjct: 104 -MPQTREHLLLAKTLGVPII-VFINKIDRV--DDAELEEVVEEISRELLEKYGFGGETVP 159
Query: 354 YVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNF 390
VP S LTGE + LL+ +D +
Sbjct: 160 VVPGSALTGEGIDE---------------LLEALDLY 181
Score = 51.3 bits (124), Expect = 3e-07
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 15/57 (26%)
Query: 29 LVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMYAWILDETGEE 85
+ +IGHVD GK+TL LLY+ G + K+S A +LD+ EE
Sbjct: 6 IGIIGHVDHGKTTLTDALLYVTGAI---------------SKESAKGARVLDKLKEE 47
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 139 bits (353), Expect = 9e-36
Identities = 90/288 (31%), Positives = 136/288 (47%), Gaps = 30/288 (10%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT++ ++ET ++ +D PGH D++ NMITGA Q D A+LVV AT G
Sbjct: 59 RGITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP---- 114
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEY 354
QTREH LL R +GV + V +NK+D V ++ + + ++ L + GF D
Sbjct: 115 ---QTREHILLARQVGVPYIVVFLNKVDMVD-DEELLELVEMEVRELLSEYGF-PGDDTP 169
Query: 355 VPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDN-FKTPSRPLTKPLRMSVSDIYKSTG 413
+ + L+D +D+ TP R + KP M V D++ +G
Sbjct: 170 IIRGSALKALEGDAKWEAKIEE------LMDAVDSYIPTPERDIDKPFLMPVEDVFSISG 223
Query: 414 SGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEM---SVSAAYAGDNVSVTLLNY 470
G + GRVE G++ GE+V + T V EM + AGDNV V L
Sbjct: 224 RGTVVTGRVERGILKVGEEV-EIVGIKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGV 282
Query: 471 DQQNVSVGFLLSELSHPCPVS--SKFEARIVVFNI-----TTPITIGY 511
+++V G +L++ P + +KFEA + V + TP GY
Sbjct: 283 KREDVERGQVLAK---PGSIKPHTKFEAEVYVLSKEEGGRHTPFFHGY 327
Score = 30.0 bits (68), Expect = 6.4
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 22 GGKGRLHLVVIGHVDAGKSTL 42
K +++ IGHVD GK+TL
Sbjct: 8 RTKPHVNVGTIGHVDHGKTTL 28
>gnl|CDD|163709 cd08153, srpA_like, Catalase-like heme-binding proteins similar to
the uncharacterized srpA. Catalase is a ubiquitous
enzyme found in both prokaryotes and eukaryotes involved
in the protection of cells from the toxic effects of
peroxides. It catalyses the conversion of hydrogen
peroxide to water and molecular oxygen. Several other
related protein families share the catalase fold and
bind to heme, but do not necessarily have catalase
activity. This family contains uncharacterized proteins
similar to the Synechococcus elongatus PCC 7942
periplasmic protein srpA, of mostly bacterial origin.
The plasmid-encoded srpA is regulated by sulfate, but
does not seem to function in its uptake or metabolism.
Length = 295
Score = 132 bits (334), Expect = 4e-34
Identities = 75/267 (28%), Positives = 116/267 (43%), Gaps = 26/267 (9%)
Query: 520 LTKAAIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYTEDGN-WDLVGNNTPI 578
L++A +FS G PV RFS G + D +PRG ALKF DG W +V N+ P+
Sbjct: 37 LSRAPLFS--GGSVPVTGRFSLGGGNPKAPDDAANPRGMALKFRLPDGEQWRMVMNSFPV 94
Query: 579 FFVRDPFRFIHFIHSQKRNP-VTHLRDWDAFWDFISLLPETTHQVMILFSDRGIPDGFRH 637
F VR P F+ + + P T D F++ PE + + + P F +
Sbjct: 95 FPVRTPEEFLALL--KAIAPDATGKPDPAKLKAFLAAHPEAAAFLAWIKT-APPPASFAN 151
Query: 638 MHGYGSHTFKLVNKDNEPVYCKFHFRTDQGIKNISPQTATKLAATDPDYSIRDLYDNIAK 697
YG + F N + + ++ F + G+K +S + A KL PD+ +L +A+
Sbjct: 152 TTYYGVNAFYFTNANGKRQPVRWRFVPEDGVKYLSDEEAAKL---GPDFLFDELAQRLAQ 208
Query: 698 GNFPSWTFYIQVMTFEEAKTYRWNPFDV----TKIWPQSDFPLLPVGHMVLDKNPGNYYA 753
G W +Q+ P D TK WP +D + G + + K +
Sbjct: 209 GPV-RWDLVLQLA----------EPGDPTDDPTKPWP-ADRKEVDAGTLTITKVAPDQGG 256
Query: 754 EIEQLAFNPNNLIPGIEPTPDKMLQGR 780
+ F+P L GIEP+ D +L R
Sbjct: 257 ACRDINFDPLVLPDGIEPSDDPLLAAR 283
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 135 bits (341), Expect = 5e-34
Identities = 93/298 (31%), Positives = 141/298 (47%), Gaps = 38/298 (12%)
Query: 234 NRGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
RGIT++ ++ET+ ++ +D PGH D++ NMITGA Q D A+LVV A G
Sbjct: 58 ARGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP--- 114
Query: 294 ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTK-LGAFLKQAGFRDSDI 352
QT+EH LL + +GV + V +NK D V + E+V + L + F DI
Sbjct: 115 ----QTKEHILLAKQVGVPNIVVFLNKEDQV--DDEELLELVELEVRELLSKYDFPGDDI 168
Query: 353 EYVPCSGLTG-ENLT-TPSQVPALTSW----YSGPCLLDVIDNF-KTPSRPLTKPLRMSV 405
V S L E LT P W Y+ L+D +D++ TP R KP M++
Sbjct: 169 PIVSGSALLALEALTENPKIKRGENKWVDKIYN---LMDAVDSYIPTPERDTDKPFLMAI 225
Query: 406 SDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEM---SVSAAYAGDN 462
D++ TG G GR+E G + G+ V + E T + EM ++ AGDN
Sbjct: 226 EDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKTTTVTGL-EMFQKTLDEGLAGDN 284
Query: 463 VSVTLLNYDQQNVSVGFLLSE----LSHPCPVSSKFEARIVVFNI-----TTPITIGY 511
V + L ++++ G +L++ H +KFEA++ + TP GY
Sbjct: 285 VGILLRGIQKEDIERGMVLAKPGTITPH-----TKFEAQVYILTKEEGGRHTPFFPGY 337
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 130 bits (330), Expect = 1e-32
Identities = 94/273 (34%), Positives = 134/273 (49%), Gaps = 27/273 (9%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT++ ++ET+ ++ +D PGH D++ NMITGA Q D A+LVV AT G
Sbjct: 59 RGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP---- 114
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIV-TKLGAFLKQAGFRDSDIE 353
QTREH LL R +GV L V +NK+D V + E+V ++ L + F DI
Sbjct: 115 ---QTREHILLARQVGVPYLVVFLNKVDLV--DDEELLELVEMEVRELLSEYDFPGDDIP 169
Query: 354 YVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVSDIYKST 412
+ S L P A+ L+D +D + TP R KP M V D++ T
Sbjct: 170 VIRGSALKALE-GDPKWEDAIME------LMDAVDEYIPTPERDTDKPFLMPVEDVFTIT 222
Query: 413 GSGYCIAGRVETGVILAGEKVMVQPQNEV--TTVKAVYVDEM---SVSAAYAGDNVSVTL 467
G G + GRVE G + G++V + E T V V EM + AGDNV V L
Sbjct: 223 GRGTVVTGRVERGTVKVGDEVEIVGIKETQKTVVTGV---EMFRKLLDEGQAGDNVGVLL 279
Query: 468 LNYDQQNVSVGFLLSELSHPCPVSSKFEARIVV 500
D+ V G +L++ P +KF+A + +
Sbjct: 280 RGVDRDEVERGQVLAKPGSIKP-HTKFKAEVYI 311
>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 = 128 bits (323), Expect = 7e-32
Identities = 88/271 (32%), Positives = 133/271 (49%), Gaps = 23/271 (8%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT++ ++ET+ ++ +D PGH D++ NMITGA Q D A+LVV AT G
Sbjct: 59 RGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMP---- 114
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVT-KLGAFLKQAGFRDSDIE 353
QTREH LL R +GV + V +NK D V + E+V ++ L + F D
Sbjct: 115 ---QTREHILLARQVGVPYIVVFLNKCDMVD--DEELLELVEMEVRELLSEYDFPGDDTP 169
Query: 354 YVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVSDIYKST 412
+ S L + L L+D +D + TP R KP M + D++ T
Sbjct: 170 IIRGSALKALEGDAEWEAKILE-------LMDAVDEYIPTPERETDKPFLMPIEDVFSIT 222
Query: 413 GSGYCIAGRVETGVILAGEKVM---VQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLN 469
G G + GRVE G++ GE+V ++ + TTV V + + AGDNV + L
Sbjct: 223 GRGTVVTGRVERGIVKVGEEVEIVGLKDTRK-TTVTGVEMFRKELDEGRAGDNVGLLLRG 281
Query: 470 YDQQNVSVGFLLSELSHPCPVSSKFEARIVV 500
++ + G +L++ P +KFEA + V
Sbjct: 282 IKREEIERGMVLAKPGSIKP-HTKFEAEVYV 311
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 128 bits (323), Expect = 2e-31
Identities = 90/280 (32%), Positives = 129/280 (46%), Gaps = 33/280 (11%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+ ++ET ++ +D PGH D++ NMITGA Q D +LVV A G
Sbjct: 108 RGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMP---- 163
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVT----KLGAFLKQAGFRDS 350
QT+EH LL R +GV L V +NK+D V + E+V +L +F K F
Sbjct: 164 ---QTKEHILLARQVGVPSLVVFLNKVDVV--DDEELLELVEMELRELLSFYK---FPGD 215
Query: 351 DIEYVPCSGLT---GENLTTPSQVPALTSWYSGPCLLDVIDNFKT-PSRPLTKPLRMSVS 406
+I + S L+ G N A+ L+D +D + P R L KP M +
Sbjct: 216 EIPIIRGSALSALQGTNDEIGKN--AILK------LMDAVDEYIPEPVRVLDKPFLMPIE 267
Query: 407 DIYKSTGSGYCIAGRVETGVILAGEKV----MVQPQNEVTTVKAVYVDEMSVSAAYAGDN 462
D++ G G GRVE G I GE+V + TTV V + + + AGDN
Sbjct: 268 DVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMFKKILDQGQAGDN 327
Query: 463 VSVTLLNYDQQNVSVGFLLSELSHPCPVSSKFEARIVVFN 502
V + L +++V G ++ + KFEA I V
Sbjct: 328 VGLLLRGLKREDVQRGQVICKPG-SIKTYKKFEAEIYVLT 366
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 124 bits (313), Expect = 2e-30
Identities = 92/280 (32%), Positives = 135/280 (48%), Gaps = 39/280 (13%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT++ ++ET+ ++ +D PGH D++ NMITGA Q D A+LVV A G
Sbjct: 59 RGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP---- 114
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIV-TKLGAFLKQAGFRDSDIE 353
QTREH LL R +GV + V +NK D V + E+V ++ L + F D
Sbjct: 115 ---QTREHILLARQVGVPYIVVFLNKCDMV--DDEELLELVEMEVRELLSKYDFPGDDTP 169
Query: 354 YVPCSGLTG-ENLTTPSQVPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVSDIYKS 411
+ S L E + L+D +D++ TP R + KP M + D++
Sbjct: 170 IIRGSALKALEGDDDEEWEKKILE------LMDAVDSYIPTPERAIDKPFLMPIEDVFSI 223
Query: 412 TGSGYCIAGRVETGVILAGEKV----MVQPQNEVTTVKAVYVDEM---SVSAAYAGDNVS 464
+G G + GRVE G+I GE+V + Q TTV V EM + AGDNV
Sbjct: 224 SGRGTVVTGRVERGIIKVGEEVEIVGIRDTQK--TTVTGV---EMFRKLLDEGQAGDNVG 278
Query: 465 VTLLNYDQQNVSVGFLLSELSHPCPVS----SKFEARIVV 500
L +++V G +L++ P S +KFEA + V
Sbjct: 279 ALLRGIKREDVERGQVLAK-----PGSITPHTKFEAEVYV 313
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 123 bits (310), Expect = 5e-30
Identities = 90/280 (32%), Positives = 135/280 (48%), Gaps = 39/280 (13%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT++ ++ET ++ +D PGH D++ NMITGA Q D A+LVV A G
Sbjct: 59 RGITINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP---- 114
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIV-TKLGAFLKQAGFRDSDIE 353
QTREH LL R +GV + V +NK D V + E+V ++ L + F D
Sbjct: 115 ---QTREHILLARQVGVPYIVVFLNKCDMV--DDEELLELVEMEVRELLSKYDFPGDDTP 169
Query: 354 YVPCSGLTG-ENLTTPSQVPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVSDIYKS 411
+ S L E + L+D +D++ P R + KP M + D++
Sbjct: 170 IIRGSALKALEGDDDEEWEAKILE------LMDAVDSYIPEPERAIDKPFLMPIEDVFSI 223
Query: 412 TGSGYCIAGRVETGVILAGEKV----MVQPQNEVTTVKAVYVDEM---SVSAAYAGDNVS 464
+G G + GRVE G++ G++V + + Q TTV V EM + AGDNV
Sbjct: 224 SGRGTVVTGRVERGIVKVGDEVEIVGIKETQK--TTVTGV---EMFRKLLDEGQAGDNVG 278
Query: 465 VTLLNYDQQNVSVGFLLSELSHPCPVS----SKFEARIVV 500
V L +++V G +L++ P S +KFEA + V
Sbjct: 279 VLLRGTKREDVERGQVLAK-----PGSIKPHTKFEAEVYV 313
>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 = 122 bits (307), Expect = 8e-29
Identities = 75/280 (26%), Positives = 122/280 (43%), Gaps = 31/280 (11%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RG+T+D+G + F + +D PGH+ FI N I G D ALLVVDA G
Sbjct: 34 RGMTIDLGFAYFPLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEG------- 86
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEY 354
QT EH ++ LG+ VVI K D V +++ + + L F + +
Sbjct: 87 VMTQTGEHLAVLDLLGIPHTIVVITKADRV--NEEEIKRTEMFMKQILNSYIF-LKNAKI 143
Query: 355 VPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIYKSTGS 414
S TG+ + L LL+ +D + + KPLRM++ +K G+
Sbjct: 144 FKTSAKTGQGIG------ELKKELKN--LLESLDI-----KRIQKPLRMAIDRAFKVKGA 190
Query: 415 GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQQN 474
G + G +G + G+ + + P N VKA+ V AYAG +++ L++ + ++
Sbjct: 191 GTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQAQNQDVEIAYAGQRIALNLMDVEPES 250
Query: 475 VSVGFLLSELSHPCPVSSKFEARIVVFNIT-TPITIGYPV 513
+ G L+ + R+VV I P+ P
Sbjct: 251 LKRGLLILT-------PEDPKLRVVVKFIAEVPLLELQPY 283
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 120 bits (303), Expect = 8e-29
Identities = 87/276 (31%), Positives = 133/276 (48%), Gaps = 21/276 (7%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT++ ++ET+ ++ +D PGH D++ NMITGA Q D A+LVV G
Sbjct: 128 RGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMP---- 183
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEY 354
QT+EH LL + +GV + V +NK D V ++ + + ++ L F DI
Sbjct: 184 ---QTKEHILLAKQVGVPNMVVFLNKQDQVD-DEELLELVELEVRELLSSYEFPGDDIPI 239
Query: 355 VPCSGLTG-ENLTT-PSQVPALTSW----YSGPCLLDVIDNF-KTPSRPLTKPLRMSVSD 407
+ S L E L P+ W Y L+D +D++ P R P ++V D
Sbjct: 240 ISGSALLALEALMENPNIKRGDNKWVDKIYE---LMDAVDSYIPIPQRQTDLPFLLAVED 296
Query: 408 IYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEV--TTVKAVYVDEMSVSAAYAGDNVSV 465
++ TG G GRVE G + GE V + E TTV V + + + A AGDNV +
Sbjct: 297 VFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGVEMFQKILDEALAGDNVGL 356
Query: 466 TLLNYDQQNVSVGFLLSELSHPCPVSSKFEARIVVF 501
L + ++ G +L++ P +KFEA + V
Sbjct: 357 LLRGIQKADIQRGMVLAKPGSITP-HTKFEAIVYVL 391
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 107 bits (270), Expect = 9e-27
Identities = 50/132 (37%), Positives = 70/132 (53%), Gaps = 13/132 (9%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+ G +FE + I +D PGH+DF + G QAD ALLVVDA G
Sbjct: 46 RGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGV------ 99
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFR---DSD 351
QTREH + + G+ + V +NK+D V ++ F E++ ++ LK GF D
Sbjct: 100 -EPQTREHLNIALAGGLPII-VAVNKIDRV--GEEDFDEVLREIKELLKLIGFTFLKGKD 155
Query: 352 IEYVPCSGLTGE 363
+ +P S LTGE
Sbjct: 156 VPIIPISALTGE 167
Score = 43.8 bits (104), Expect = 1e-04
Identities = 19/44 (43%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREI--------HKHETESK 66
VIGHVD GK+TL G LLY G + R K E E
Sbjct: 4 VIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERG 47
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 114 bits (286), Expect = 1e-26
Identities = 72/282 (25%), Positives = 124/282 (43%), Gaps = 34/282 (12%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+D+G + + + +D PGH DFI N++ G D ALLVV A G
Sbjct: 34 RGITIDLGFYYRKLEDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEG------- 86
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEY 354
QT EH L++ LG+ +V+ K D V + R ++ + ++ A L A + +
Sbjct: 87 LMAQTGEHLLILDLLGIKNGIIVLTKADRV--DEARIEQKIKQILADLSLA-----NAKI 139
Query: 355 VPCSGLTGENLTTPSQVPALTSWYSGPCLL--DVIDNFKTPSRPLTKPLRMSVSDIYKST 412
S TG G L ++ID + R KP R+++ +
Sbjct: 140 FKTSAKTGR----------------GIEELKNELIDLLEEIERDEQKPFRIAIDRAFTVK 183
Query: 413 GSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQ 472
G G + G V +G + G+K+ + P N+ V+++ ++ V A AG V + L ++
Sbjct: 184 GVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRSIQAHDVDVEEAKAGQRVGLALKGVEK 243
Query: 473 QNVSVGFLLSELSHPCPVSSKFEARIVVFN-ITTPITIGYPV 513
+ + G L + P V+++ + + + G PV
Sbjct: 244 EEIERGDWLLK-PEPLEVTTRLIVELEIDPLFKKTLKQGQPV 284
>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 = 101 bits (253), Expect = 1e-25
Identities = 33/83 (39%), Positives = 52/83 (62%), Gaps = 1/83 (1%)
Query: 400 PLRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYA 459
P R+ +SD YK G G ++G+VE+G I G+ ++V P E VK++YVD+ V A A
Sbjct: 1 PFRLPISDKYKDQG-GTVVSGKVESGSIQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVA 59
Query: 460 GDNVSVTLLNYDQQNVSVGFLLS 482
G+NV + L D++++S G +L
Sbjct: 60 GENVRLKLKGIDEEDISPGDVLC 82
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 92.3 bits (230), Expect = 2e-21
Identities = 45/132 (34%), Positives = 67/132 (50%), Gaps = 12/132 (9%)
Query: 235 RGITMDVGQSQFETKT-KYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
RGIT+D+G + + K + +D PGH+ F+ NM+ GA D LLVV A G
Sbjct: 33 RGITIDLGFAYLDLPDGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMP--- 89
Query: 294 ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIE 353
QTREH ++ LG+ + VV+ K D V +DR + + ++ L D+ I
Sbjct: 90 ----QTREHLEILELLGIKKGLVVLTKADLV--DEDRLELVEEEILELLAGTFLADAPI- 142
Query: 354 YVPCSGLTGENL 365
P S +TGE +
Sbjct: 143 -FPVSSVTGEGI 153
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. 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.
Length = 195
Score = 91.9 bits (229), Expect = 4e-21
Identities = 57/159 (35%), Positives = 77/159 (48%), Gaps = 17/159 (10%)
Query: 234 NRGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
RGIT++ ++ET ++ +D PGH D+I NMITGA Q D A+LVV AT G
Sbjct: 48 ARGITINTAHVEYETANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMP--- 104
Query: 294 ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTK-LGAFLKQAGFRDSDI 352
QTREH LL R +GV + V +NK D V + E+V + L + GF D
Sbjct: 105 ----QTREHLLLARQVGVPYIVVFLNKADMV--DDEELLELVEMEVRELLSKYGFDGDDT 158
Query: 353 EYVPCSGLTG-ENLTTPSQVPALTSWYSGPCLLDVIDNF 390
V S L E V + LLD +D++
Sbjct: 159 PIVRGSALKALEGDDPNKWVDKILE------LLDALDSY 191
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 86.8 bits (215), Expect = 1e-17
Identities = 84/302 (27%), Positives = 140/302 (46%), Gaps = 31/302 (10%)
Query: 247 ETKTKYITLLDAPGHKDFIPNMITG--ATQADVALLVVDATRGEFETGFESGGQTREHAL 304
+ K ++ +D GH+ ++ I G + D LLVV A G + T+EH
Sbjct: 197 KRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAADDGVTKM-------TKEHLG 249
Query: 305 LVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAG---FRDSDIEYVPCSGLT 361
+ ++ + + VV+ K+D V DRFQ +V ++ A LK+ G D + V +
Sbjct: 250 IALAMELPVI-VVVTKIDMVP--DDRFQGVVEEISALLKRVGRIPLIVKDTDDVVLAAKA 306
Query: 362 GENLTTPSQVPAL-TSWYSGPCLLDVIDNF--KTPSRPLT---KPLRMSVSDIYKSTGSG 415
+ VP TS +G L D++D F P R P M + IY TG G
Sbjct: 307 MK--AGRGVVPIFYTSSVTGEGL-DLLDEFFLLLPKRRRWDDEGPFLMYIDKIYSVTGVG 363
Query: 416 YCIAGRVETGVILAGEKVMVQPQNE----VTTVKAVYVDEMSVSAAYAGDNVSVTLLNYD 471
++G V++G++ G+ V++ P + VK++ + V +A AG + + L +
Sbjct: 364 TVVSGSVKSGILHVGDTVLLGPFKDGKFREVVVKSIEMHHYRVDSAKAGSIIGIALKGVE 423
Query: 472 QQNVSVGFLLSELSHPCPVSSKFEARIVVFNITTPITIGY-PVTHDITHLTKAAIFSEIG 530
++ + G +LS + P V +F+A ++V T I GY PV H T + +A F EI
Sbjct: 424 KEELERGMVLSAGADPKAV-REFDAEVLVLRHPTTIRAGYEPVFHYET-IREAVYFEEID 481
Query: 531 KQ 532
K
Sbjct: 482 KG 483
Score = 37.4 bits (87), Expect = 0.036
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 10/56 (17%)
Query: 18 REQAGGKGRLHLVVIGHVDAGKSTLMGHLLYLMGRV--------SAREIHKHETES 65
R+ + + V GHVD GKSTL+G L + GR+ S ++ KHE E
Sbjct: 109 RKTEEAPEHVLVGVAGHVDHGKSTLVGVL--VTGRLDDGDGATRSYLDVQKHEVER 162
>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 = 74.5 bits (184), Expect = 2e-16
Identities = 29/85 (34%), Positives = 43/85 (50%)
Query: 399 KPLRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAY 458
KPLR+ + D+YK G G GRVETGV+ G V P VK+V + + A
Sbjct: 3 KPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMHHEPLEEAL 62
Query: 459 AGDNVSVTLLNYDQQNVSVGFLLSE 483
GDNV + N ++++ G + +
Sbjct: 63 PGDNVGFNVKNVSKKDIKRGDVAGD 87
>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 = 73.0 bits (180), Expect = 7e-16
Identities = 28/83 (33%), Positives = 50/83 (60%), Gaps = 2/83 (2%)
Query: 400 PLRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYA 459
PLR+ + D YK G+ + G+VE+G I G+K++V P V ++Y +++ V A
Sbjct: 1 PLRLPIIDKYKDMGT--VVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARP 58
Query: 460 GDNVSVTLLNYDQQNVSVGFLLS 482
G+NV + L +++++S GF+L
Sbjct: 59 GENVRLRLKGIEEEDISPGFVLC 81
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 71.6 bits (176), Expect = 3e-14
Identities = 49/145 (33%), Positives = 71/145 (48%), Gaps = 26/145 (17%)
Query: 235 RGITMDVGQSQFETKTKY--------------ITLLDAPGHKDFIPNMITGATQADVALL 280
RGIT+D+G S FE ITL+D PGH I +I GA D+ LL
Sbjct: 38 RGITLDLGFSSFEVDKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLL 97
Query: 281 VVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQ--DRFQEIVTKL 338
VVDA +G +T QT E L++ L L VV+NK+D + + + +++ +L
Sbjct: 98 VVDAKKG-IQT------QTAEC-LVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKRL 149
Query: 339 GAFLKQAGFRDSDIEYVPCSGLTGE 363
L++ +DS I +P S GE
Sbjct: 150 QKTLEKTRLKDSPI--IPVSAKPGE 172
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 69.7 bits (171), Expect = 2e-12
Identities = 61/236 (25%), Positives = 101/236 (42%), Gaps = 50/236 (21%)
Query: 253 ITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVN 312
++ +DAPGH+ + M++GA D ALLV+ A + QTREH + + +G+
Sbjct: 82 VSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQP------QTREHLMALEIIGIK 135
Query: 313 QLGVVINKLDTVSWSQ--DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQ 370
+ +V NK+D VS + + ++EI F+K ++ I +P S L N+
Sbjct: 136 NIVIVQNKIDLVSKEKALENYEEIK----EFVKGTIAENAPI--IPVSALHNANIDA--- 186
Query: 371 VPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVS---DIYKSTGS-----GYCIAGR 421
LL+ I+ F TP R L KP M V+ D+ K G I G
Sbjct: 187 ------------LLEAIEKFIPTPERDLDKPPLMYVARSFDVNKPGTPPEKLKGGVIGGS 234
Query: 422 VETGVILAGEKVMVQP------------QNEVTTVKAVYVDEMSVSAAYAGDNVSV 465
+ G + G+++ ++P + T + ++ V A G V V
Sbjct: 235 LIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTEITSLRAGGYKVEEARPGGLVGV 290
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 64.8 bits (159), Expect = 4e-12
Identities = 44/137 (32%), Positives = 65/137 (47%), Gaps = 18/137 (13%)
Query: 235 RGITMDVGQSQFETKTKY--ITLLDAPGHKDFIPNMIT-GATQADVALLVVDATRGEFET 291
GIT +G Q K IT +D PGH+ F NM GA+ D+A+LVV A
Sbjct: 31 GGITQHIGAYQVPIDVKIPGITFIDTPGHEAFT-NMRARGASVTDIAILVVAAD-----D 84
Query: 292 GFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQ---DRFQEIVTKLGAFLKQAGFR 348
G QT E ++ V + V INK+D ++ +R + +++LG ++ G
Sbjct: 85 GVMP--QTIEAINHAKAANV-PIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWG-- 139
Query: 349 DSDIEYVPCSGLTGENL 365
D+ VP S TGE +
Sbjct: 140 -GDVSIVPISAKTGEGI 155
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 66.4 bits (163), Expect = 2e-11
Identities = 62/241 (25%), Positives = 102/241 (42%), Gaps = 53/241 (21%)
Query: 253 ITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVN 312
++ +DAPGH+ + M++GA D A+LV+ A + QT+EH + + +G+
Sbjct: 87 VSFVDAPGHETLMATMLSGAALMDGAILVIAANEPCPQP------QTKEHLMALDIIGIK 140
Query: 313 QLGVVINKLDTVSWSQ--DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQ 370
+ +V NK+D VS + + +++I F+K G + +P S L N+
Sbjct: 141 NIVIVQNKIDLVSKERALENYEQIK----EFVK--GTVAENAPIIPVSALHKVNIDA--- 191
Query: 371 VPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVS---DIYKSTGS-----------G 415
L++ I+ TP R L KP RM V+ D+ K G+ G
Sbjct: 192 ------------LIEAIEEEIPTPERDLDKPPRMYVARSFDVNKP-GTPPEKLKGGVIGG 238
Query: 416 YCIAGRVETG---VILAGEKVMVQPQNE----VTTVKAVYVDEMSVSAAYAGDNVSV-TL 467
I G ++ G I G KV + + T + ++ V A G V V T
Sbjct: 239 SLIQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKIVSLRAGGEKVEEARPGGLVGVGTK 298
Query: 468 L 468
L
Sbjct: 299 L 299
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 65.4 bits (160), Expect = 5e-11
Identities = 60/238 (25%), Positives = 102/238 (42%), Gaps = 54/238 (22%)
Query: 253 ITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFES--GGQTREHALLVRSLG 310
++ +DAPGH+ + M++GA D ALLV+ A E QTREH + + +G
Sbjct: 88 VSFVDAPGHETLMATMLSGAALMDGALLVIAAN--------EPCPQPQTREHLMALEIIG 139
Query: 311 VNQLGVVINKLDTVSWSQ--DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTP 368
+ + +V NK+D VS + + +++I F+K ++ I +P S N+
Sbjct: 140 IKNIIIVQNKIDLVSRERALENYEQIK----EFVKGTVAENAPI--IPISAQHKANI--- 190
Query: 369 SQVPALTSWYSGPCLLDVIDNF-KTPSRPLTKPLRMSVS---DIYK-----STGSGYCIA 419
L++ I+ + TP R L KP RM V+ D+ K G I
Sbjct: 191 ------------DALIEAIEKYIPTPERDLDKPPRMYVARSFDVNKPGTPPEELKGGVIG 238
Query: 420 GRVETGVILAGEKVMVQP------------QNEVTTVKAVYVDEMSVSAAYAGDNVSV 465
G + GV+ G+++ ++P + T + ++ V A G V V
Sbjct: 239 GSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQAGGEDVEEARPGGLVGV 296
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 65.8 bits (161), Expect = 6e-11
Identities = 63/292 (21%), Positives = 124/292 (42%), Gaps = 36/292 (12%)
Query: 235 RGITMDVGQSQF-ETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
RG+T+D+G + + + + + +D PGH+ F+ NM+ G D ALLVV G
Sbjct: 34 RGMTIDLGYAYWPQPDGRVLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVM---- 89
Query: 294 ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIE 353
QTREH +++ G L V + K D V + R E+ ++ A L++ GF ++ +
Sbjct: 90 ---AQTREHLAILQLTGNPMLTVALTKADRV--DEARIAEVRRQVKAVLREYGFAEAKL- 143
Query: 354 YVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIYKSTG 413
+ G + L + + R+++ + G
Sbjct: 144 -FVTAATEGRGIDA---------------LREHLLQLPEREHAAQHRFRLAIDRAFTVKG 187
Query: 414 SGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAGDNVSVTLL-NYDQ 472
+G + G +G + G+ + + N+ V+ ++ A AG +++ + + ++
Sbjct: 188 AGLVVTGTALSGEVKVGDTLWLTGVNKPMRVRGLHAQNQPTEQAQAGQRIALNIAGDAEK 247
Query: 473 QNVSVG-FLLSELSHPCPVSSKFEARIVVFNITTPITIGYPV--THDITHLT 521
+ ++ G +LL++ F IV TP+T P+ H +H+T
Sbjct: 248 EQINRGDWLLAD-----APPEPFTRVIVELQTHTPLTQWQPLHIHHAASHVT 294
>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 = 57.1 bits (139), Expect = 3e-10
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 401 LRMSVSDIYKSTGS--GYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAY 458
R V + + GY AG + +G I G++V+V P + + VK++ + + A
Sbjct: 1 FRFPVQYVIRPNADFRGY--AGTIASGSIRVGDEVVVLPSGKTSRVKSIETFDGELDEAG 58
Query: 459 AGDNVSVTLLNYDQQNVSVGFLL 481
AG++V++TL D+ +VS G ++
Sbjct: 59 AGESVTLTL--EDEIDVSRGDVI 79
>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 = 54.6 bits (132), Expect = 2e-09
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 401 LRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQ--NEVTTVKAVYVDEMSVSAAY 458
LR V ++K G G GRVE+G + G+KV V P VK++ + V A
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 459 AGDNVSVTLLNYDQQNVSVGFLLSE 483
AGD V + L + D ++ +G L++
Sbjct: 61 AGDIVGIVLKDKD--DIKIGDTLTD 83
>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 = 59.2 bits (144), Expect = 7e-09
Identities = 68/273 (24%), Positives = 111/273 (40%), Gaps = 50/273 (18%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDF------IPNMITGATQADVALLVVDATRGE 288
RGIT+ + I ++D PGH DF + M+ G LL+VDA+ G
Sbjct: 48 RGITILAKNTAIRYNGTKINIVDTPGHADFGGEVERVLGMVDGV------LLLVDASEGP 101
Query: 289 FETGFESGGQTR---EHALLVRSLGVNQLGVVINKLDT----VSWSQDRFQEIVTKLGAF 341
QTR + AL LG+ + VVINK+D D ++ +LGA
Sbjct: 102 MP-------QTRFVLKKAL---ELGLKPI-VVINKIDRPSARPDEVVDEVFDLFAELGAD 150
Query: 342 LKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPL 401
+Q F V SG G S S P ++ + P L +PL
Sbjct: 151 DEQLDF-----PIVYASGRAG----WASLDLDDPSDNMAPLFDAIVRHVPAPKGDLDEPL 201
Query: 402 RMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTT---VKAVYVDE----MSV 454
+M V+++ G GRV G + G++V + ++ + + E + +
Sbjct: 202 QMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMKRDGTIENGRISKLLGFEGLERVEI 261
Query: 455 SAAYAGDNVSVTLLNYDQQNVSVGFLLSELSHP 487
A AGD V+V L +++++G +++ P
Sbjct: 262 DEAGAGDIVAVAGL----EDINIGETIADPEVP 290
Score = 30.0 bits (68), Expect = 7.8
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREI 58
+I HVD GK+TL+ LL G A E
Sbjct: 6 IIAHVDHGKTTLVDALLKQSGTFRANEA 33
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 54.5 bits (132), Expect = 5e-08
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 17/109 (15%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+ + F+ + + ++D PGH DFI + + D A+LV+ A G
Sbjct: 48 RGITIFSAVASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEG------- 100
Query: 295 SGGQTREHALLVRSLGVNQLGV----VINKLDTVSWSQDR-FQEIVTKL 338
QTR +L R L +L + +NK+D ++ +QEI KL
Sbjct: 101 VQAQTR---ILFRLL--RKLNIPTIIFVNKIDRAGADLEKVYQEIKEKL 144
Score = 30.3 bits (69), Expect = 3.7
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 31 VIGHVDAGKSTLMGHLLY 48
++ HVDAGK+TL LLY
Sbjct: 4 ILAHVDAGKTTLTESLLY 21
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 56.1 bits (136), Expect = 6e-08
Identities = 63/252 (25%), Positives = 105/252 (41%), Gaps = 46/252 (18%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDF------IPNMITGATQADVALLVVDATRGE 288
RGIT+ + I ++D PGH DF + +M+ D LL+VDA+ G
Sbjct: 52 RGITILAKNTAVNYNGTRINIVDTPGHADFGGEVERVLSMV------DGVLLLVDASEGP 105
Query: 289 FETGFESGGQTR---EHALLVRSLGVNQLGVVINKLDTVS----WSQDRFQEIVTKLGAF 341
QTR + AL +LG+ + VVINK+D D ++ +LGA
Sbjct: 106 MP-------QTRFVLKKAL---ALGLKPI-VVINKIDRPDARPDEVVDEVFDLFVELGAT 154
Query: 342 LKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPL 401
+Q F V S G T S P + P ++D+ P L +PL
Sbjct: 155 DEQLDF-----PIVYASARNG----TASLDPEDEADDMAPLFETILDHVPAPKGDLDEPL 205
Query: 402 RMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTT---VKAVY----VDEMSV 454
+M V+ + ++ G GR+ G + ++V + + T + + ++ + +
Sbjct: 206 QMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSDGTTENGRITKLLGFLGLERIEI 265
Query: 455 SAAYAGDNVSVT 466
A AGD V++
Sbjct: 266 EEAEAGDIVAIA 277
Score = 29.5 bits (67), Expect = 8.7
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSARE 57
+I HVD GK+TL+ LL G RE
Sbjct: 10 IIAHVDHGKTTLVDALLKQSGTFRERE 36
>gnl|CDD|206728 cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family
includes GTPBP2. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 52.3 bits (126), Expect = 2e-07
Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 16/145 (11%)
Query: 236 GITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGAT--QADVALLVVDATRGEFETGF 293
++ E +K +T +D GH+ ++ + G T D A+LVV A G
Sbjct: 69 NHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAMLVVGANAGII---- 124
Query: 294 ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIE 353
G T+EH L +L V + VV+ K+D + QE + L LK G R +
Sbjct: 125 ---GMTKEHLGLALALKV-PVFVVVTKIDMT--PANVLQETLKDLKRLLKSPGVRKLPVP 178
Query: 354 YVPCSG---LTGENLTTPSQVPALT 375
V L+ NL++ VP
Sbjct: 179 -VKSKDDVVLSASNLSSGRVVPIFQ 202
Score = 41.9 bits (99), Expect = 7e-04
Identities = 22/43 (51%), Positives = 26/43 (60%), Gaps = 6/43 (13%)
Query: 29 LVVIGHVDAGKSTLMGHLLYLM---GRVSAREI---HKHETES 65
+ V+G+VDAGKSTL+G L GR AR HKHE ES
Sbjct: 2 VAVVGNVDAGKSTLLGVLTQGELDNGRGKARLNLFRHKHEVES 44
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 53.6 bits (129), Expect = 3e-07
Identities = 44/134 (32%), Positives = 63/134 (47%), Gaps = 18/134 (13%)
Query: 236 GITMDVGQSQFETKT-KYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
GIT +G E + K IT LD PGH+ F GA D+ +LVV A G
Sbjct: 119 GITQHIGAYHVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMP---- 174
Query: 295 SGGQTRE---HALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSD 351
QT E HA ++ V + V INK+D + DR ++ +++ G + G D
Sbjct: 175 ---QTIEAISHA---KAANV-PIIVAINKIDKPEANPDRVKQELSEYGLVPEDWG---GD 224
Query: 352 IEYVPCSGLTGENL 365
+VP S LTG+ +
Sbjct: 225 TIFVPVSALTGDGI 238
>gnl|CDD|219112 pfam06628, Catalase-rel, Catalase-related immune-responsive. This
family represents a small conserved region within
catalase enzymes (EC:1.11.1.6). All members also contain
the Catalase family, pfam00199 domain. Catalase
decomposes hydrogen peroxide into water and oxygen,
serving to protect cells from its toxic effects. This
domain carries the immune-responsive amphipathic
octa-peptide that is recognised by T cells.
Length = 68
Score = 47.4 bits (114), Expect = 5e-07
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 856 RYKTEDEDNFSQPRILWSNVLDDAARDRMTTNIA 889
R ++E D+FSQ + + + A + R+ NIA
Sbjct: 1 RARSEKFDHFSQAGLFY-RSMSPAEQQRLIDNIA 33
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 52.2 bits (126), Expect = 9e-07
Identities = 44/141 (31%), Positives = 63/141 (44%), Gaps = 30/141 (21%)
Query: 236 GITMDVGQSQFET---KTKYITLLDAPGHKDFIPNMIT-GATQADVALLVVDATRGEFET 291
GIT +G Q K IT +D PGH+ F M GA+ D+A+LVV A G
Sbjct: 37 GITQHIGAYQVPLDVIKIPGITFIDTPGHEAFT-AMRARGASVTDIAILVVAADDG-VMP 94
Query: 292 GFESGGQTRE---HALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFR 348
QT E HA ++ GV + V INK+D + ++ + L++ G
Sbjct: 95 ------QTIEAINHA---KAAGVPIV-VAINKIDKP---EANPDKVKQE----LQEYGLV 137
Query: 349 ----DSDIEYVPCSGLTGENL 365
D+ +VP S TGE +
Sbjct: 138 PEEWGGDVIFVPVSAKTGEGI 158
>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 = 46.8 bits (112), Expect = 2e-06
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 489 PVSSKFEARIVVFNITTPITIGYPVTHDITHLTKAAIFSEI 529
P S++FEARI+ FN+ PI G P L + A +++
Sbjct: 1 PSSTRFEARILTFNVDKPILPGTPFELFRHSLKEPATITKL 41
>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 = 45.3 bits (108), Expect = 3e-06
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 415 GYCIAGRVETGVILAGEKVMVQPQ--NEVTTVKAVYVDEMSVSAAYAGDNVSVTLLNYDQ 472
G GRVE+G + G+KV++ P + V ++ + + A AG N + L
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 473 QNVSVGFLLS 482
+++ G L+
Sbjct: 61 KDIKRGDTLT 70
>gnl|CDD|163707 cd08151, AOS, Allene oxide synthase. Allene oxide synthase
converts a fatty acid hydroperoxide to an allene oxide,
which is an unstable epoxide. In corals, the enzyme is
part of a eiconaosid synthesis pathway that is initiated
by a lipoxygenase, which generates the fatty acid
hydroperoxides in the first step. The structure of
allene oxide synthase closely resembles that of
catalase, but allene oxide synthase does not have
catalase activity.
Length = 328
Score = 49.7 bits (119), Expect = 4e-06
Identities = 55/269 (20%), Positives = 89/269 (33%), Gaps = 56/269 (20%)
Query: 524 AIFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFYT----EDGNWDLVGNN---- 575
A F+ GK+ PV R + + G D + D RG AL+F + G DLV N
Sbjct: 53 AFFTA-GKRFPVILRHANIVGGDD--DASLDGRGAALRFLNAGDDDAGPLDLVMNTGESF 109
Query: 576 --------TPIFFVRDPFRFIHFIHSQKRNPVTHLRDWDAFWDFISLLPETTHQVMILFS 627
PFR +K + A W +
Sbjct: 110 GFWTAASFADFAGAGLPFR-------EKAAKLRGPLARYAVWASL--------------- 147
Query: 628 DRGIPDGFRHMHGYGSHTFKLVNKDNEPVYCKFHFRT-DQGIKNISPQTATKLAATDPDY 686
R PD + +H Y ++ V D + Y +F D + + + P
Sbjct: 148 -RRAPDSYTDLHYYSQICYEFVALDGKSRYARFRLLPPDADTEWDLGEDVLETIFQRPRL 206
Query: 687 SIRDLYDNIAKGNF-----------PSWTFYIQVMTFEEAKTYRWNPFDVTKIWPQSDFP 735
+ L + ++ P + +Q+ E + D + W + + P
Sbjct: 207 YLPRLPGDTRPKDYLRNEFRQRLQSPGVRYRLQIQLREVSDDATAVALDCCRPWDEDEHP 266
Query: 736 LLPVGHMVLDKNPGNYYAEIEQLAFNPNN 764
L + + L N E+E+LAFNP N
Sbjct: 267 WLDLAVVRLGAPLPN--DELEKLAFNPGN 293
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 47.6 bits (114), Expect = 6e-06
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 253 ITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFES--GGQTREHALLVRSLG 310
++ +D PGH+ + M++GA D ALL++ A E QT EH + +G
Sbjct: 79 VSFVDCPGHEILMATMLSGAAVMDGALLLIAAN--------EPCPQPQTSEHLAALEIMG 130
Query: 311 VNQLGVVINKLDTVSWSQ--DRFQEI 334
+ + ++ NK+D V Q + +++I
Sbjct: 131 LKHIIILQNKIDLVKEEQALENYEQI 156
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 48.4 bits (116), Expect = 1e-05
Identities = 33/112 (29%), Positives = 49/112 (43%), Gaps = 18/112 (16%)
Query: 235 RGITMDVGQSQFETKTKY-ITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
RGIT+ + K Y I L+D PGH DF + D A++VVDA G
Sbjct: 59 RGITITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVE-----GV 113
Query: 294 ESGGQTREHALLVRSLGVNQLGV----VINKLDTVSWSQDR-FQEIVTKLGA 340
E QT + R ++ GV +NK+D + +++ +LGA
Sbjct: 114 EP--QT---ETVWRQA--DKYGVPRILFVNKMDRLGADFYLVVEQLKERLGA 158
Score = 34.9 bits (81), Expect = 0.20
Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAR-EIH 59
++ H+DAGK+TL +L+ G +S E+H
Sbjct: 15 IVAHIDAGKTTLTERILFYTGIISKIGEVH 44
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 48.2 bits (114), Expect = 2e-05
Identities = 71/280 (25%), Positives = 108/280 (38%), Gaps = 41/280 (14%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGIT+ + + I ++D PGH DF + + D LLVVDA G
Sbjct: 52 RGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMP---- 107
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLD----TVSWSQDRFQEIVTKLGAFLKQAGFRDS 350
QTR + G+ + VVINK+D W D+ ++ L A +Q
Sbjct: 108 ---QTRFVTKKAFAYGLKPI-VVINKVDRPGARPDWVVDQVFDLFVNLDATDEQL----- 158
Query: 351 DIEYVPCSGLTG-ENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVSDIY 409
D V S L G L +T Y ++D+ P L P +M +S +
Sbjct: 159 DFPIVYASALNGIAGLDHEDMAEDMTPLYQA-----IVDHVPAPDVDLDGPFQMQISQLD 213
Query: 410 KSTGSGYCIAGRVETGVILAGEKVMVQPQNEVT-------TVKAVYVDEMSVSAAYAGDN 462
++ G GR++ G + ++V + T + + ++ + A AGD
Sbjct: 214 YNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDI 273
Query: 463 VSVTLLNY--------DQQNVSVGFLLSELSHPCPVSSKF 494
V++T L D QNV L LS P S F
Sbjct: 274 VAITGLGELNISDTVCDTQNVEA---LPALSVDEPTVSMF 310
Score = 29.7 bits (66), Expect = 8.8
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 28 HLVVIGHVDAGKSTLMGHLLYLMGRVSAR-EIHKHETESKKLGKQ 71
++ +I HVD GK+TL+ LL G +R E + +S L K+
Sbjct: 7 NIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKE 51
>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 = 43.7 bits (104), Expect = 2e-05
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 4/83 (4%)
Query: 403 MSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEM---SVSAAYA 459
M + D++ G G + GR+E G I G++V + E + EM ++ A A
Sbjct: 3 MPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGI-EMFRKTLDEAEA 61
Query: 460 GDNVSVTLLNYDQQNVSVGFLLS 482
GDNV V L +++V G +L+
Sbjct: 62 GDNVGVLLRGVKREDVERGMVLA 84
>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 = 42.8 bits (102), Expect = 3e-05
Identities = 25/83 (30%), Positives = 43/83 (51%)
Query: 401 LRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYVDEMSVSAAYAG 460
R+ + ++ G G + G V +G + G+KV + P E T V+++ V V A AG
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAG 60
Query: 461 DNVSVTLLNYDQQNVSVGFLLSE 483
D V++ L D +++ G +LS
Sbjct: 61 DRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 44.4 bits (105), Expect = 4e-05
Identities = 28/126 (22%), Positives = 46/126 (36%), Gaps = 19/126 (15%)
Query: 245 QFETKTKYITLLDAPGHKDFIPNMITGAT-----QADVALLVVDATRGEFETGFESGGQT 299
+ + + L+D PG +F AD+ LLVVD+T E E
Sbjct: 41 ELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESE-----EDAK 95
Query: 300 REHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSG 359
+R G+ + +V NK+D + + V +L + A + S
Sbjct: 96 LLILRRLRKEGIPII-LVGNKIDLLE------EREVEELLRLEELAKI--LGVPVFEVSA 146
Query: 360 LTGENL 365
TGE +
Sbjct: 147 KTGEGV 152
Score = 30.5 bits (69), Expect = 1.9
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 30 VVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHET 63
VV+G GKS+L+ LL G V T
Sbjct: 1 VVVGRGGVGKSSLLNALLG--GEVGEVSDVPGTT 32
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 46.4 bits (110), Expect = 6e-05
Identities = 20/53 (37%), Positives = 29/53 (54%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRG 287
RGI++ QF + + LLD PGH+DF + T D L+V+DA +G
Sbjct: 64 RGISITTSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKG 116
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 46.1 bits (110), Expect = 7e-05
Identities = 34/108 (31%), Positives = 49/108 (45%), Gaps = 13/108 (12%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGI++ QF+ + LLD PGH+DF + T D A++V+DA +G E
Sbjct: 65 RGISVTSSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKG-IEP--- 120
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF---QEIVTKLG 339
QT + + R + INKLD +D EI +LG
Sbjct: 121 ---QTLKLFEVCRLRDIPIF-TFINKLDRE--GRDPLELLDEIEEELG 162
Score = 29.5 bits (67), Expect = 8.7
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 31 VIGHVDAGKST------LMGHLLYLMGRVSAREIHKHET 63
+I H DAGK+T L G + G V R+ KH
Sbjct: 17 IISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAK 55
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 44.5 bits (106), Expect = 1e-04
Identities = 25/104 (24%), Positives = 49/104 (47%), Gaps = 11/104 (10%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
R ++++ + E I L+D PG+ DF+ ++ D AL+VV+A +G E
Sbjct: 48 RKMSIETSVAPLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQ-----SGVE 102
Query: 295 SGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKL 338
G T + + + ++ + INK+D ++ F + + L
Sbjct: 103 VG--TEKVWEFLDDAKLPRI-IFINKMDR---ARADFDKTLAAL 140
Score = 32.2 bits (74), Expect = 1.1
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 29 LVVIGHVDAGKSTLMGHLLYLMGRVSAR 56
+ ++GH +GK+TL LLY G +
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRL 29
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 45.4 bits (108), Expect = 1e-04
Identities = 51/200 (25%), Positives = 85/200 (42%), Gaps = 42/200 (21%)
Query: 251 KYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFES--GGQTREHALLVRS 308
++++ +D PGH + M+ GA D ALL++ A ES QT EH V
Sbjct: 117 RHVSFVDCPGHDILMATMLNGAAVMDAALLLIAAN--------ESCPQPQTSEHLAAVEI 168
Query: 309 LGVNQLGVVINKLDTVSWS--QDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLT 366
+ + + ++ NK+D V + QD+++EI F+K ++ I +P S N+
Sbjct: 169 MKLKHIIILQNKIDLVKEAQAQDQYEEIR----NFVKGTIADNAPI--IPISAQLKYNID 222
Query: 367 TPSQVPALTSWYSGPCLLDVIDN-FKTPSRPLTKPLRMSVS---DIYK-----STGSGYC 417
+L+ I P R LT P RM V D+ K G
Sbjct: 223 ---------------VVLEYICTQIPIPKRDLTSPPRMIVIRSFDVNKPGEDIENLKGGV 267
Query: 418 IAGRVETGVILAGEKVMVQP 437
G + GV+ G+++ ++P
Sbjct: 268 AGGSILQGVLKVGDEIEIRP 287
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 44.1 bits (105), Expect = 1e-04
Identities = 23/53 (43%), Positives = 31/53 (58%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRG 287
RGI++ QFE K I LLD PGH+DF + T D A++V+DA +G
Sbjct: 55 RGISVTSSVMQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKG 107
Score = 30.3 bits (69), Expect = 3.7
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 31 VIGHVDAGKSTLMGHLLY------LMGRVSAREIHKHET 63
+I H DAGK+TL LL G V AR+ KH T
Sbjct: 7 IISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHAT 45
>gnl|CDD|163708 cd08152, y4iL_like, Catalase-like heme-binding proteins similar to
the uncharacterized y4iL. Catalase is a ubiquitous
enzyme found in both prokaryotes and eukaryotes involved
in the protection of cells from the toxic effects of
peroxides. It catalyses the conversion of hydrogen
peroxide to water and molecular oxygen. Several other
related protein families share the catalase fold and
bind to heme, but do not necessarily have catalase
activity. This family contains uncharacterized proteins
similar to Rhizobium sp. NGR234 y4iL, of mostly
bacterial origin.
Length = 305
Score = 44.2 bits (105), Expect = 2e-04
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 12/70 (17%)
Query: 525 IFSEIGKQTPVAARFSTVWGERGSADTNRDPRGFALKFY----------TEDGNWDLVGN 574
+F+E P RFS G+ D+ DPRG A+K + D V
Sbjct: 33 LFAE-PGTYPAVIRFSNAPGDILD-DSVPDPRGMAIKVLGVPGEKLLPEEDATTQDFVLV 90
Query: 575 NTPIFFVRDP 584
N P+FF RD
Sbjct: 91 NHPVFFARDA 100
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 44.2 bits (105), Expect = 3e-04
Identities = 71/290 (24%), Positives = 106/290 (36%), Gaps = 54/290 (18%)
Query: 235 RGITMDVGQSQFETKTK----Y-ITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEF 289
RGIT+ + K K Y + L+D PGH DF + + ALL+VDA +
Sbjct: 49 RGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQ--- 105
Query: 290 ETGFESGGQTREHALLVRSLGVNQLGV--VINKLDTVSWSQDRF-QEIVTKLGAFLKQAG 346
G E+ QT + L N L + VINK+D S +R +EI +G +A
Sbjct: 106 --GIEA--QTLANVYLALE---NDLEIIPVINKIDLPSADPERVKKEIEEVIGLDASEA- 157
Query: 347 FRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRM--- 403
+ S TG + + L ++ P PL+
Sbjct: 158 --------ILASAKTGIG------IEEI--------LEAIVKRVPPPKGDPDAPLKALIF 195
Query: 404 -SVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQN---EVTTVKAVYVDEMSVSAAYA 459
S D Y+ G RV G I G+K+ EV V A
Sbjct: 196 DSHYDNYR----GVVALVRVFEGTIKPGDKIRFMSTGKEYEVDEVGVFTPKLTKTDELSA 251
Query: 460 GDNVSVTLLNYDQQNVSVGFLLSELSHPC--PVSSKFEARIVVFNITTPI 507
G+ + D +V VG ++ + +P P+ E + +VF PI
Sbjct: 252 GEVGYIIAGIKDVSDVRVGDTITHVKNPAKEPLPGFKEVKPMVFAGLYPI 301
Score = 32.7 bits (75), Expect = 1.0
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREIH 59
+I H+D GKSTL LL G +S RE+
Sbjct: 8 IIAHIDHGKSTLADRLLEYTGAISEREMR 36
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 41.9 bits (99), Expect = 6e-04
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 14/89 (15%)
Query: 236 GITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFES 295
I++ + S+ K+ I ++D PGH +F+ + D +LVVD
Sbjct: 58 PISLVLEDSK--GKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVE--------- 106
Query: 296 GGQTREHALLVRSLGVNQLGV--VINKLD 322
G T L+R L + VINK+D
Sbjct: 107 -GLTSVTERLIRHAIQEGLPMVLVINKID 134
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 42.8 bits (102), Expect = 7e-04
Identities = 30/111 (27%), Positives = 48/111 (43%), Gaps = 15/111 (13%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFE 294
RGI++ + E K I L+D PGH DF + D A++VV A G E
Sbjct: 44 RGISITSAATTCEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAV-----GGVE 98
Query: 295 SGGQT--REHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLK 343
+T R+ GV ++ + +NK+D + F ++ +L L
Sbjct: 99 PQTETVWRQ----AEKYGVPRI-IFVNKMDR---AGADFFRVLAQLQEKLG 141
Score = 35.5 bits (83), Expect = 0.14
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 32 IGHVDAGKSTLMGHLLYLMGRVSAR-EIHKHET 63
+GH AGK+TL +L+ G + E+ T
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTT 33
>gnl|CDD|239665 cd03694, GTPBP_II, Domain II 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 = 38.7 bits (91), Expect = 0.001
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 403 MSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNE----VTTVKAVYVDEMSVSAAY 458
+ +IY G G + G V GVI G+ +++ P + TVK+++ + V
Sbjct: 3 FQIDEIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVR 62
Query: 459 AGDNVSVTLLNYD 471
AG + S+ L D
Sbjct: 63 AGQSASLALKKID 75
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 42.6 bits (100), Expect = 0.001
Identities = 33/117 (28%), Positives = 56/117 (47%), Gaps = 12/117 (10%)
Query: 235 RGITMDVGQ----SQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRG--- 287
RGIT++ ++E I L+D PGH DF ++ D A++VV A G
Sbjct: 66 RGITINAANVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMP 125
Query: 288 EFETGFESGGQTREHALLVRSLGVNQLGVVINKLD-TVSWSQDRFQEIVTKLGAFLK 343
+ ET + +L +N++ +IN+L T Q+RF +I+T++ +K
Sbjct: 126 QTETVLRQALKENVKPVLF----INKVDRLINELKLTPQELQERFIKIITEVNKLIK 178
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 39.9 bits (94), Expect = 0.001
Identities = 26/94 (27%), Positives = 39/94 (41%), Gaps = 17/94 (18%)
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF 331
A +AD+ LLVVD+ E + + LL G L +V+NK+D V S++
Sbjct: 74 ADRADLVLLVVDSDLTPVE-------EEAKLGLLRER-GKPVL-LVLNKIDLVPESEEEE 124
Query: 332 QEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 365
KL D+ + S L GE +
Sbjct: 125 LLRERKLELLP--------DLPVIAVSALPGEGI 150
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 40.8 bits (97), Expect = 0.002
Identities = 34/142 (23%), Positives = 54/142 (38%), Gaps = 38/142 (26%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPG-HKDFIPN------MITGATQA----DVALLVVD 283
RGI + +Q I +D PG HK P M A + D+ L VVD
Sbjct: 45 RGIVTE-DDAQ-------IIFVDTPGIHK---PKRALNRAMNKAAWSSLKDVDLVLFVVD 93
Query: 284 ATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLK 343
A G ++ + + +V+NK+D V ++ ++ +L +
Sbjct: 94 ADEK-------IGPGDEFILEKLKKVKTPVI-LVLNKIDLVK-DKEELLPLLEELSELMD 144
Query: 344 QAGFRDSDIEYVPCSGLTGENL 365
A E VP S L G+N+
Sbjct: 145 FA-------EIVPISALKGDNV 159
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 41.4 bits (98), Expect = 0.002
Identities = 49/145 (33%), Positives = 62/145 (42%), Gaps = 41/145 (28%)
Query: 236 GITMDVGQSQFETKTKYITLLDAPGHKDFIPNMIT-----GATQADVALLVVDATRGEFE 290
GIT +G Q ET IT LD PGH+ F T GA D+ +LVV A G
Sbjct: 281 GITQHIGAYQVETNGGKITFLDTPGHEAF-----TAMRARGAQVTDIVVLVVAADDGVMP 335
Query: 291 TGFESGGQTRE---HALLVRSLGVNQLGVVINKLDTVSWSQDR-FQE------IVTKLGA 340
QT E HA ++ GV + V INK+D + DR QE + + G
Sbjct: 336 -------QTIEAINHA---KAAGV-PIIVAINKIDKPGANPDRVKQELSEYGLVPEEWG- 383
Query: 341 FLKQAGFRDSDIEYVPCSGLTGENL 365
G D +VP S TGE +
Sbjct: 384 -----G----DTIFVPVSAKTGEGI 399
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 40.5 bits (96), Expect = 0.004
Identities = 24/55 (43%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 235 RGITMDVGQS--QFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRG 287
RGI+ V S QF + I LLD PGH+DF + T D AL+V+DA +G
Sbjct: 63 RGIS--VTSSVMQFPYRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKG 115
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 38.6 bits (91), Expect = 0.004
Identities = 36/143 (25%), Positives = 51/143 (35%), Gaps = 40/143 (27%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPG----HKDFIPNMITGATQ----ADVALLVVDATR 286
RGI D +Q I +D PG K M+ A D+ L VVDA+
Sbjct: 43 RGIYTD-DDAQ-------IIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASE 94
Query: 287 GEFETGFESGGQTREHALLVRSLGVNQLGV--VINKLDTVSWSQD--RFQEIVTKLGAFL 342
++ L ++ V V+NK+D V +D E + +L F
Sbjct: 95 WI----------GEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPLLEKLKELHPF- 143
Query: 343 KQAGFRDSDIEYVPCSGLTGENL 365
E P S L GEN+
Sbjct: 144 ---------AEIFPISALKGENV 157
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 39.1 bits (92), Expect = 0.005
Identities = 40/158 (25%), Positives = 55/158 (34%), Gaps = 41/158 (25%)
Query: 235 RGITMD--------VGQSQFETKTKY-ITLLDAPGHKDFIPNMITGATQADVALLVVDAT 285
RGIT+ + + Y I L+D+PGH DF + D AL+VVDA
Sbjct: 47 RGITIKSSAISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAV 106
Query: 286 RGEFETGFESGGQTR---EHALLVRSLGVNQLGVVINKLD--------TVSWSQDRFQEI 334
G QT AL R V +VINK+D + + R I
Sbjct: 107 EG-------VCVQTETVLRQALEERVKPV----LVINKIDRLILELKLSPEEAYQRLLRI 155
Query: 335 ---VTKLGAFLKQAGFRDSDIEYVP-------CSGLTG 362
V + F+ ++ P S L G
Sbjct: 156 VEDVNAIIETYAPEEFKQEKWKFSPQKGNVAFGSALDG 193
Score = 29.9 bits (68), Expect = 4.7
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFM 74
+I HVD GK+TL LL G +S K GK ++
Sbjct: 5 IIAHVDHGKTTLSDSLLASAGIIS----------EKLAGKARYL 38
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 40.2 bits (94), Expect = 0.005
Identities = 38/134 (28%), Positives = 62/134 (46%), Gaps = 15/134 (11%)
Query: 236 GITMDVG--QSQFETK--TKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEFET 291
GIT +G + +FE K + I LD PGH+ F GA D+A+L++ A G
Sbjct: 276 GITQKIGAYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDG---- 331
Query: 292 GFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSD 351
QT E +++ V + V INK+D + + +R ++ + K ++ G D
Sbjct: 332 ---VKPQTIEAINYIQAANVPII-VAINKIDKANANTERIKQQLAKYNLIPEKWG---GD 384
Query: 352 IEYVPCSGLTGENL 365
+P S G N+
Sbjct: 385 TPMIPISASQGTNI 398
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 39.9 bits (94), Expect = 0.007
Identities = 62/267 (23%), Positives = 102/267 (38%), Gaps = 48/267 (17%)
Query: 235 RGITMDVGQSQFETKTK-----YITLLDAPGHKDFIPNMITGATQADVALLVVDATRGEF 289
RGIT+ + K K + L+D PGH DF + + ALLVVDA++
Sbjct: 55 RGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQ--- 111
Query: 290 ETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRF-QEIVTKLGAFLKQAGFR 348
G E+ QT + L + ++ V+NK+D + +R QEI + G
Sbjct: 112 --GVEA--QTLANVYLALENNL-EIIPVLNKIDLPAADPERVKQEIEDII-------GID 159
Query: 349 DSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRM----S 404
SD V S TG + + L +++ P PL+ S
Sbjct: 160 ASDA--VLVSAKTGIG------IEDV--------LEAIVEKIPPPKGDPDAPLKALIFDS 203
Query: 405 VSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTTVKAVYV---DEMSVSAAYAGD 461
D Y G + R+ G + G+K+ + + V V + + V AG+
Sbjct: 204 WYDNYL----GVVVLVRIFDGTLKKGDKIRMMSTGKEYEVDEVGIFTPKMVKVDELKAGE 259
Query: 462 NVSVTLLNYDQQNVSVGFLLSELSHPC 488
+ D ++ VG ++ S+P
Sbjct: 260 VGYIIAGIKDVRDARVGDTITLASNPA 286
Score = 33.7 bits (78), Expect = 0.54
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREIHK 60
+I H+D GKSTL LL L G +S RE+
Sbjct: 14 IIAHIDHGKSTLADRLLELTGGLSEREMRA 43
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 39.4 bits (92), Expect = 0.010
Identities = 55/235 (23%), Positives = 93/235 (39%), Gaps = 52/235 (22%)
Query: 256 LDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLG 315
+D PGH+ F G AD+A+L+VD GF+ QT+E ++R
Sbjct: 74 IDTPGHEAFTNLRKRGGALADLAILIVDINE-----GFKP--QTQEALNILRMYKT-PFV 125
Query: 316 VVINKLDTV-SWS------------------QDRFQEIVTKLGAFLKQAGF------RDS 350
V NK+D + W Q V L L + GF R +
Sbjct: 126 VAANKIDRIPGWRSHEGRPFMESFSKQEIQVQQNLDTKVYNLVIKLHEEGFEAERFDRVT 185
Query: 351 D----IEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVIDNFKTPSRPLTKPLRMSVS 406
D + +P S +TGE +P L + +G + + K P R ++
Sbjct: 186 DFTKTVAIIPISAITGEG------IPELLTMLAGLAQQYLEEQLKL---EEEGPARGTIL 236
Query: 407 DIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNE--VTTVKAVY----VDEMSVS 455
++ + TG G I + G++ G+ + + ++ VT V+A+ ++EM S
Sbjct: 237 EVKEETGLGMTIDAVIYDGILRKGDTIAMAGSDDVIVTRVRALLKPRPLEEMRES 291
Score = 29.8 bits (67), Expect = 8.8
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 29 LVVIGHVDAGKSTLMGHLLYLMGRVSARE 57
+ V+GHVD GK+TL+ + V+ RE
Sbjct: 7 VSVLGHVDHGKTTLLDKI--RGSAVAKRE 33
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 37.6 bits (88), Expect = 0.012
Identities = 40/141 (28%), Positives = 56/141 (39%), Gaps = 35/141 (24%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDF------IPNMITGATQADVALLVVDATRGE 288
RGIT+ + K I ++D PGH DF + +M D LL+VDA+ G
Sbjct: 49 RGITILAKNTAITYKDTKINIIDTPGHADFGGEVERVLSM------VDGVLLLVDASEGP 102
Query: 289 FETGFESGGQTR---EHALLVRSLGVNQLGVVINKLD----TVSWSQDRFQEIVTKLGAF 341
QTR + AL G+ + VVINK+D D ++ +L A
Sbjct: 103 MP-------QTRFVLKKAL---EAGLKPI-VVINKIDRPDARPEEVVDEVFDLFLELNAT 151
Query: 342 LKQAGFRDSDIEYVPCSGLTG 362
+Q F V S G
Sbjct: 152 DEQLDFP-----IVYASAKNG 167
Score = 29.5 bits (67), Expect = 6.7
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 31 VIGHVDAGKSTLMGHLL 47
+I HVD GK+TL+ LL
Sbjct: 7 IIAHVDHGKTTLVDALL 23
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 38.4 bits (90), Expect = 0.016
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAR-EIHKHETES 65
++ H+DAGK+TL +L+ G++ E+ T +
Sbjct: 13 ILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVT 48
Score = 29.9 bits (68), Expect = 7.4
Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 18/75 (24%)
Query: 253 ITLLDAPGHKDFIPNMITGATQ-----ADVALLVVDATRGEFETGFESGGQTREHALLVR 307
I L+D PGH DF TG + D A++V DA TG + QT
Sbjct: 75 INLIDTPGHIDF-----TGEVERSLRVLDGAVVVFDAV-----TGVQP--QTETVWRQAD 122
Query: 308 SLGVNQLGVVINKLD 322
G+ +L + INK+D
Sbjct: 123 RYGIPRL-IFINKMD 136
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 36.3 bits (85), Expect = 0.027
Identities = 28/96 (29%), Positives = 40/96 (41%), Gaps = 22/96 (22%)
Query: 275 ADVALLVVDATRGEFETGFESGGQTREH--ALLVRSLGVNQLGVVINKLDTVSWSQDRFQ 332
ADV LLV+DA+ G E G E AL+ +V+NK D V + +
Sbjct: 85 ADVVLLVLDASEGITEQDLRIAGLILEEGKALI----------IVVNKWDLVEKDEKTMK 134
Query: 333 EIVTKLGAFLKQAGFRDSDIEYVPC---SGLTGENL 365
E +L L ++Y P S LTG+ +
Sbjct: 135 EFEKELRRKLPF-------LDYAPIVFISALTGQGV 163
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 37.1 bits (86), Expect = 0.045
Identities = 30/112 (26%), Positives = 49/112 (43%), Gaps = 20/112 (17%)
Query: 229 IASALNRGITMDVGQSQFETKTKYITLLDAPG---HKDFIPNM-----ITGATQADVALL 280
I S + +G T DV + FE I LLD G H DF+ + QAD+ +
Sbjct: 230 IVSDI-KGTTRDVVEGDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIY 288
Query: 281 VVDATRGEFETGFESGGQTREHALLVRSLGVNQ-LGVVINKLDTVSWSQDRF 331
V+DA++ T++ L++ + +V+NK+D S + F
Sbjct: 289 VLDASQPL----------TKDDFLIIDLNKSKKPFILVLNKIDLKINSLEFF 330
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 37.0 bits (87), Expect = 0.047
Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 28/98 (28%)
Query: 275 ADVALLVVDATRG--EFET---GF--ESGGQTREHALLVRSLGVNQLGVVINKLDTVSWS 327
ADV LLV+DAT G E + G E+G R+L V +V+NK D V
Sbjct: 256 ADVVLLVIDATEGITEQDLRIAGLALEAG----------RAL-V----IVVNKWDLV--D 298
Query: 328 QDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 365
+ +E +L L + + I ++ S LTG+ +
Sbjct: 299 EKTMEEFKKELRRRLPFLDY--APIVFI--SALTGQGV 332
Score = 29.2 bits (67), Expect = 10.0
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 8 DKLKKIEEYTREQAGGKGRLHLVVIGHVDAGKSTLMGHLL 47
D + + E+ + + +IG + GKS+L+ LL
Sbjct: 155 DAILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALL 194
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 36.0 bits (84), Expect = 0.061
Identities = 36/139 (25%), Positives = 52/139 (37%), Gaps = 32/139 (23%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPG-HK------DFIPNMITGATQ-ADVALLVVDATR 286
RGI +Q I +D PG HK + + A + D+ L VVDA
Sbjct: 46 RGIVTT-DNAQ-------IIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADE 97
Query: 287 GEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAG 346
G ++ + +V+NK+D V + KL AFLK+
Sbjct: 98 -------GWGPGDEFILEQLKKTKTPVI-LVVNKIDKVKPKTV-----LLKLIAFLKKLL 144
Query: 347 FRDSDIEYVPCSGLTGENL 365
E VP S L G+N+
Sbjct: 145 ---PFKEIVPISALKGDNV 160
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 35.2 bits (82), Expect = 0.065
Identities = 45/148 (30%), Positives = 62/148 (41%), Gaps = 47/148 (31%)
Query: 235 RGITMDVGQSQ-------FETKTKYI-TLLDAPGHKDFIPNMIT-------GATQADVAL 279
RGIT+ ++Q + +Y+ L+D PGH DF + A + AL
Sbjct: 46 RGITI---KAQAVRLFYKAKDGEEYLLNLIDTPGHVDF-----SYEVSRSLAACEG--AL 95
Query: 280 LVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGV--VINKLDTVSWSQDRF-QEIVT 336
LVVDAT+ G E+ QT + L N L + VINK+D + DR QEI
Sbjct: 96 LVVDATQ-----GVEA--QTLANFYLALE---NNLEIIPVINKIDLPAADPDRVKQEIED 145
Query: 337 KLGAFLKQAGFRDSDIEYVPCSGLTGEN 364
LG +A + S TG
Sbjct: 146 VLGLDASEA---------ILVSAKTGLG 164
Score = 34.8 bits (81), Expect = 0.10
Identities = 16/29 (55%), Positives = 19/29 (65%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREIH 59
+I H+D GKSTL LL L G VS RE+
Sbjct: 5 IIAHIDHGKSTLADRLLELTGTVSEREMK 33
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 36.8 bits (86), Expect = 0.066
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 235 RGITMDVGQ----SQFETKTKYITLLDAPGHKDFIPNMITGATQA-DVALLVVDATRG 287
RGIT+ ++E K I L+D PGH DF +T A +A D A++VVDA G
Sbjct: 67 RGITIKAANVSMVHEYEGKEYLINLIDTPGHVDF-GGDVTRAMRAVDGAIVVVDAVEG 123
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 35.6 bits (83), Expect = 0.10
Identities = 35/140 (25%), Positives = 48/140 (34%), Gaps = 35/140 (25%)
Query: 275 ADVALLVVDATRGEFETGFESGGQTREHAL-LVRSLGVNQLGVVINKLDTVSWSQDRFQE 333
ADV LLV+DAT G E G E +V +V+NK D V + +E
Sbjct: 261 ADVVLLVIDATEGISEQDLRIAGLIEEAGRGIV---------IVVNKWDLVEEDEATMEE 311
Query: 334 IVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVPALTSWYSGPCLLDVID----- 388
KL L F V S LTG+ L L + I
Sbjct: 312 FKKKLRRKLPFLDF----APIVFISALTGQGLDK---------------LFEAIKEIYEC 352
Query: 389 -NFKTPSRPLTKPLRMSVSD 407
+ + L + L +V+
Sbjct: 353 ATRRISTSLLNRVLEDAVAK 372
>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 = 32.5 bits (75), Expect = 0.17
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 490 VSSKFEARIVVFNITTPITIGY-PV----THDIT 518
+KF+A++ + N TPI GY PV T D+T
Sbjct: 4 PHTKFKAQVYILNHPTPIFNGYRPVFYCHTADVT 37
>gnl|CDD|240163 cd05140, Barstar_AU1054-like, Barstar_AU1054-like contains
uncharacterized sequences similar to the
uncharacterized, predicted RNAase inhibitor AU1054 found
in Burkholderia cenocepacia. This is a subfamily of the
Barstar family of RNAase inhibitors. Barstar is an
intracellular inhibitor of barnase, an extracellular
ribonuclease of Bacillus amyloliquefaciens. Barstar
binds tightly to the barnase active site and sterically
blocks it thus inhibiting its potentially lethal RNase
activity inside the cell. Barstar also binds and
inhibits a ribonuclease called RNase Sa (produced by
Streptomyces aureofaciens) which belongs to the same
enzyme family as does barnase.
Length = 86
Score = 31.6 bits (72), Expect = 0.27
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 603 RDWDAFWDFISLLPETTHQVMILFSD---RGIPDGFRHM 638
+WDAFWD I+ L + + R +P +
Sbjct: 30 CNWDAFWDAITGLVSMPPVLRFVGWSQFKRRLPRDAELL 68
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 34.3 bits (79), Expect = 0.35
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 253 ITLLDAPGHKDFIPNMITGATQ-ADVALLVVDATRG 287
I L+D+PGH DF + +T A + D AL+VVD G
Sbjct: 94 INLIDSPGHVDF-SSEVTAALRVTDGALVVVDCVEG 128
Score = 30.4 bits (69), Expect = 4.8
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSARE 57
VI HVD GKSTL L+ G +S++
Sbjct: 24 VIAHVDHGKSTLTDSLVCKAGIISSKN 50
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 86
Score = 31.3 bits (72), Expect = 0.43
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 11/85 (12%)
Query: 401 LRMSVSDIYKSTGSGYCIAGRVETGVILAGEKVMVQPQNEVTT---VKAVYV----DEMS 453
L+M V+ + G GR+ G + G++V V ++ + ++ +
Sbjct: 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVE 60
Query: 454 VSAAYAGDNVSVTLLNYDQQNVSVG 478
V A AGD V++ + ++++G
Sbjct: 61 VEEAEAGDIVAIAGIE----DITIG 81
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The
dynamin family of large mechanochemical GTPases
includes the classical dynamins and dynamin-like
proteins (DLPs) that are found throughout the Eukarya.
This family also includes bacterial DLPs. These
proteins catalyze membrane fission during
clathrin-mediated endocytosis. Dynamin consists of five
domains; an N-terminal G domain that binds and
hydrolyzes GTP, a middle domain (MD) involved in
self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific,
mediates uptake of synaptic vesicles in presynaptic
terminals; dynamin-2 is expressed ubiquitously and
similarly participates in membrane fission; mutations
in the MD, PH and GED domains of dynamin 2 have been
linked to human diseases such as Charcot-Marie-Tooth
peripheral neuropathy and rare forms of centronuclear
myopathy. Dynamin 3 participates in megakaryocyte
progenitor amplification, and is also involved in
cytoplasmic enlargement and the formation of the
demarcation membrane system. This family also includes
mitofusins (MFN1 and MFN2 in mammals) that are involved
in mitochondrial fusion. Dynamin oligomerizes into
helical structures around the neck of budding vesicles
in a GTP hydrolysis-dependent manner.
Length = 180
Score = 32.1 bits (74), Expect = 0.73
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 27 LHLVVIGHVDAGKSTLMGHLL 47
L V+G AGKSTL+ LL
Sbjct: 1 FLLAVVGEFSAGKSTLLNALL 21
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 32.7 bits (76), Expect = 0.90
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 32 IGHVDAGKSTLMGHLLYLMGRVSARE 57
I H+D GKSTL L+ L G +S RE
Sbjct: 13 IAHIDHGKSTLADRLIELTGTLSERE 38
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with
it. The ribosome may be prepared for these
rearrangements by the initial binding of EF-G as well.
The dissociation of EF-G leaves the ribosome ready to
accept the next aminoacyl-tRNA into the A site. This
group contains both eukaryotic and bacterial members.
Length = 270
Score = 32.1 bits (74), Expect = 1.0
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREIHK-HETESK 66
+I H+DAGK+T +LY GR IHK E
Sbjct: 4 IIAHIDAGKTTTTERILYYTGR-----IHKIGEVHGG 35
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this
model include Ras, RhoA, Rab11, translation elongation
factor G, translation initiation factor IF-2,
tetratcycline resistance protein TetM, CDC42, Era,
ADP-ribosylation factors, tdhF, and many others. In
some proteins the domain occurs more than once.This
model recognizes a large number of small GTP-binding
proteins and related domains in larger proteins. Note
that the alpha chains of heterotrimeric G proteins are
larger proteins in which the NKXD motif is separated
from the GxxxxGK[ST] motif (P-loop) by a long insert
and are not easily detected by this model [Unknown
function, General].
Length = 162
Score = 31.2 bits (71), Expect = 1.3
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 10/63 (15%)
Query: 29 LVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMY------AWILDET 82
+V++G + GKSTL+ LL ++ ++ +LD
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEY----KPGTTRNYVTTVIEEDGKTYKFNLLDTA 59
Query: 83 GEE 85
G+E
Sbjct: 60 GQE 62
Score = 30.0 bits (68), Expect = 3.0
Identities = 29/136 (21%), Positives = 45/136 (33%), Gaps = 18/136 (13%)
Query: 236 GITMDVGQSQFETKTKYIT--LLDAPGHKDFIPNMITGATQADVALLVVDATRGEFETGF 293
G T + + E K LLD G +D+ + +L V D
Sbjct: 34 GTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVI--LVLDV 91
Query: 294 ESG--GQTREHALLVRSLGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSD 351
E QT+E S GV + +V NK+D T + +
Sbjct: 92 EEILEKQTKEIIHHAES-GVPII-LVGNKIDLRDAKLK------THVAFLFAKLNGEP-- 141
Query: 352 IEYVPCSGLTGENLTT 367
+P S TG+N+ +
Sbjct: 142 --IIPLSAETGKNIDS 155
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 32.1 bits (74), Expect = 1.4
Identities = 38/137 (27%), Positives = 54/137 (39%), Gaps = 39/137 (28%)
Query: 257 DAPGHKDFIPNMIT-GATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLG 315
D PGH+ F N+ G AD+A+LVVD GF+ QT E +++ +
Sbjct: 77 DTPGHEAF-TNLRKRGGALADIAILVVDINE-----GFQP--QTIEAINILKRRKTPFV- 127
Query: 316 VVINKLDTVS-WS------------------QDRFQEIVTKLGAFLKQAGF------RDS 350
V NK+D + W Q +E + +L L + GF R
Sbjct: 128 VAANKIDRIPGWKSTEDAPFLESIEKQSQRVQQELEEKLYELIGQLSELGFSADRFDRVK 187
Query: 351 D----IEYVPCSGLTGE 363
D + VP S TGE
Sbjct: 188 DFTKTVAIVPVSAKTGE 204
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 32.1 bits (73), Expect = 1.7
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 15/63 (23%)
Query: 24 KGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFMY----AWIL 79
+G+L VV+G +GKSTL+ LL S EI +E + ++S Y AWI+
Sbjct: 685 RGKL-TVVLGATGSGKSTLLQSLL------SQFEI----SEGRVWAERSIAYVPQQAWIM 733
Query: 80 DET 82
+ T
Sbjct: 734 NAT 736
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 31.2 bits (71), Expect = 1.8
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 5/47 (10%)
Query: 249 KTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRG-EFETGFE 294
K + +T ++ P + I +MI A AD+ LL++D + G E ET FE
Sbjct: 81 KKRRLTFIECP---NDINSMIDVAKIADLVLLLIDGSYGFEMET-FE 123
>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 = 29.1 bits (66), Expect = 2.4
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 489 PVSSKFEARIVVFNITTPITIGY-PVTHDITHLTKAAIFSEIGK 531
+FEA I+V + T I+ GY H I + + A I K
Sbjct: 1 KACWEFEAEILVLHHPTTISPGYQATVH-IGSIRQTARIVSIDK 43
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 31.6 bits (72), Expect = 2.4
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 253 ITLLDAPGHKDFIPNMITGATQ-ADVALLVVDATRG 287
I L+D+PGH DF + +T A + D AL+VVD G
Sbjct: 100 INLIDSPGHVDF-SSEVTAALRITDGALVVVDCIEG 134
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 31.3 bits (71), Expect = 2.6
Identities = 18/53 (33%), Positives = 25/53 (47%)
Query: 235 RGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRG 287
RGIT+ + K I ++D PGH DF + D A+ V+DA G
Sbjct: 59 RGITITSAATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGG 111
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 31.4 bits (71), Expect = 2.6
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 256 LDAPGHKDFIPNMITGATQADVALLVVDATRG 287
+D PGH+ F G + AD+A+LVVD G
Sbjct: 531 IDTPGHEAFTSLRKRGGSLADLAVLVVDINEG 562
>gnl|CDD|224603 COG1689, COG1689, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 274
Score = 31.0 bits (70), Expect = 2.6
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 8/43 (18%)
Query: 115 PVPLEDTYYLDKLFHFAGERNPE-------RVVHA-KGGGAFG 149
PLE TY++ + E V G A+G
Sbjct: 120 ATPLEATYWMMSALNMVNYEYLEEMKEKVIEFVREFGIGDAYG 162
Score = 30.6 bits (69), Expect = 3.0
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 8/43 (18%)
Query: 166 PVPLEDTYYLDKLFHFSGERNPE-------RVVHA-KGGGAFG 200
PLE TY++ + E V G A+G
Sbjct: 120 ATPLEATYWMMSALNMVNYEYLEEMKEKVIEFVREFGIGDAYG 162
>gnl|CDD|181432 PRK08453, fliD, flagellar capping protein; Validated.
Length = 673
Score = 31.3 bits (71), Expect = 2.8
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 224 VPLEGIASALNRGITMDVGQ--SQFETK-----TKYITLLDAPGHKDFIPNMITGATQAD 276
VP++ I + D+ + ++F ++ TL KD+ ++ G T D
Sbjct: 93 VPIQDIKVDVQNLAQGDINELGAKFSSRDDVFSQVDTTLKFYTQGKDYAIDIKAGMTLGD 152
Query: 277 VALLVVDATRGE 288
VA + DAT GE
Sbjct: 153 VAQSITDATNGE 164
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 29.9 bits (68), Expect = 3.2
Identities = 23/101 (22%), Positives = 34/101 (33%), Gaps = 14/101 (13%)
Query: 29 LVVIGHVDAGKSTLMGHLL---YL---MGRVSAREIHKHETESKKLGKQSFMYAWILDET 82
+ V+G AGKS+++ LL L G + R + E + +
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDGLK 60
Query: 83 GEES------SCEIPVDT-TSAGNPVDSETIIKTI-GPHGP 115
E E D + G + SE II I P P
Sbjct: 61 KFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVP 101
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 30.1 bits (69), Expect = 3.2
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 9/50 (18%)
Query: 316 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 365
VV+NK+D + ++RF+++ L + P S LTGE L
Sbjct: 119 VVLNKIDLLDA-EERFEKLKELLKEL--------KGKKVFPISALTGEGL 159
>gnl|CDD|225438 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 30.3 bits (69), Expect = 4.0
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 31 VIGHVDAGKSTLMGHLLYLMGRVSAREI 58
+ G AGKSTL+ L+Y R + +I
Sbjct: 33 LTGPSGAGKSTLL-KLIYGEERPTRGKI 59
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 30.5 bits (70), Expect = 4.0
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 10/50 (20%)
Query: 316 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 365
VV+NK+D + ++ +E++ +L L P S LTGE L
Sbjct: 278 VVLNKIDLLD--EEELEELLKELKEAL--------GKPVFPISALTGEGL 317
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein
[General function prediction only].
Length = 398
Score = 30.4 bits (69), Expect = 4.2
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 8 DKLKKIEEYTREQAGGKGRLHLVVIGHVDAGKSTL 42
+++ E E AG G + +V+G VD+GKSTL
Sbjct: 57 EEIADTWESKSESAGKVGVV--MVVGPVDSGKSTL 89
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 29.9 bits (68), Expect = 4.3
Identities = 24/108 (22%), Positives = 39/108 (36%), Gaps = 20/108 (18%)
Query: 263 DFIPNMITGATQADVAL--LVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINK 320
+ ++ D AL VVD +F G L +G + +V NK
Sbjct: 21 EDFLEIL-STLLNDNALVVHVVDIF--DFPGSLIPG--------LAELIGAKPVILVGNK 69
Query: 321 LDTV--SWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLT 366
+D + +R ++ V K LK G + D+ V S G +
Sbjct: 70 IDLLPKDVKPNRLKQWVKKR---LKIGGLKIKDVILV--SAKKGWGVE 112
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 28.9 bits (65), Expect = 4.5
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 250 TKYITLLDAPGHKDFIPNMITGATQADVALLVVDATRGE 288
T + + D G ++ I AD LLV D T E
Sbjct: 47 TGLLNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRE 85
Score = 28.5 bits (64), Expect = 5.7
Identities = 12/41 (29%), Positives = 17/41 (41%)
Query: 28 HLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKL 68
+VVIG +GKS+L+ L+ EI L
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTL 41
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 29.7 bits (68), Expect = 4.7
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 24 KGRLHLVVIGHVDAGKSTLMGHLLYLMGRVSAREIHKHETESKKLGKQSFM--YAWILDE 81
KG L + ++G V +GKS+L L L+G E+ K G +++ WI +
Sbjct: 30 KGEL-VAIVGPVGSGKSSL---LSALLG-----ELEKLSGSVSVPGSIAYVSQEPWIQNG 80
Query: 82 T 82
T
Sbjct: 81 T 81
>gnl|CDD|237454 PRK13634, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 290
Score = 30.0 bits (68), Expect = 4.9
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 31 VIGHVDAGKSTLMGHL 46
+IGH +GKSTL+ HL
Sbjct: 38 IIGHTGSGKSTLLQHL 53
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 29.1 bits (66), Expect = 5.3
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 10/57 (17%)
Query: 249 KTKYITL----LDAPG----HKDFIPNMITGATQADVALLVVDAT--RGEFETGFES 295
KT+ I +D PG ++ F +I A ADV LV DAT F GF S
Sbjct: 30 KTQAIEFSDNMIDTPGEYLENRRFYSALIVTAADADVIALVQDATEPWSVFPPGFAS 86
>gnl|CDD|177739 PLN00128, PLN00128, Succinate dehydrogenase [ubiquinone]
flavoprotein subunit.
Length = 635
Score = 30.2 bits (68), Expect = 5.8
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 11/73 (15%)
Query: 724 DVTKIWPQSDFPLLPVGHMVLDKNPGNYYAEIEQLAF-NPNNLIPGIEPTPDKMLQGRLH 782
DVTK P+LP H + P NY+ E+ + +P+ ++PG+ M G
Sbjct: 384 DVTK----EPIPVLPTVHYNMGGIPTNYHGEVVTIKGDDPDAVVPGL------MAAGEAA 433
Query: 783 SYIDTHIHRLGAN 795
+RLGAN
Sbjct: 434 CASVHGANRLGAN 446
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 29.5 bits (67), Expect = 6.1
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 275 ADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLD 322
D+ ++VVD + T L LG+ ++ VV+NK+D
Sbjct: 156 VDLVIVVVDPSYKSLRT-------AERIKELAEELGIKRIFVVLNKVD 196
>gnl|CDD|179689 PRK03972, PRK03972, ribosomal biogenesis protein; Validated.
Length = 208
Score = 29.5 bits (66), Expect = 6.8
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 16/90 (17%)
Query: 501 FNITTPITIGYPVTHDITHLTKAAIFSEI--GKQTPVAARFSTVWGERGSADT----NRD 554
ITT +G + H+ A +F+E+ GK P + ++ + D R
Sbjct: 107 LVITTAKRVG------LDHMAFAQVFAELTGGKFVPRGGKSLQDIADKYNTDVLGVIERH 160
Query: 555 PRGFALKFYTEDGNWDL-VGNNTPIFFVRD 583
PRG A+ FY D + VG P+ FV+
Sbjct: 161 PRGMAVNFYRLDVTKERPVG---PLIFVKI 187
>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 = 28.1 bits (63), Expect = 6.9
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 3/44 (6%)
Query: 486 HPCPVSSKFEARIVVFNITTPITIGYPVTHDITHLTKAAIFSEI 529
KF A I V + P++ GY ++ +++
Sbjct: 1 QAVD---KFVAEIYVLDHPEPLSPGYKPVLNVGTAHVPGRIAKL 41
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 28.6 bits (65), Expect = 8.0
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 274 QADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGVVINKLDTVS 325
+AD+ LLVVDA+ G E ++ + VV+NK D +S
Sbjct: 82 EADLVLLVVDASE----------GLDEEDLEILELPAKKPVIVVLNKSDLLS 123
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 29.6 bits (67), Expect = 8.2
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 18/53 (33%)
Query: 556 RGFALKFYTEDGNWDLVGNNTPIF------------FVRDPFRFIHFIHSQKR 596
R A + Y + W+ NN F V DP RF HF+ + KR
Sbjct: 54 RALARELYGD--PWE---NNFTEFNVADFFDQGKKYLVEDP-RFAHFLGTDKR 100
>gnl|CDD|216783 pfam01915, Glyco_hydro_3_C, Glycosyl hydrolase family 3 C-terminal
domain. This domain is involved in catalysis and may be
involved in binding beta-glucan. This domain is found
associated with pfam00933.
Length = 221
Score = 29.2 bits (66), Expect = 8.6
Identities = 14/72 (19%), Positives = 22/72 (30%), Gaps = 12/72 (16%)
Query: 225 PLEGIASALNRGITMDVGQSQFETKTKYITLLDAPGHKDFIPNMITGATQADVALLVVDA 284
PL+GI + + I + A ADVA++ V +
Sbjct: 49 PLDGIRARAG------------NATVVVYGGSNLEDDDTGIAEAVAAAKDADVAIVFVGS 96
Query: 285 TRGEFETGFESG 296
GE +G
Sbjct: 97 DAGEGYINEVNG 108
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 29.4 bits (67), Expect = 8.8
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 23/96 (23%)
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVNQLGV--VINKLDTVSWSQD 329
+AD+ L VVDA+ + E Q ++ LG + V NK+D + +
Sbjct: 266 VREADLLLHVVDASDPDRE------EQIEAVEKVLEELGAEDIPQLLVYNKIDLL--DEP 317
Query: 330 RFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 365
R + + + E V S TGE L
Sbjct: 318 RIERL-------------EEGYPEAVFVSAKTGEGL 340
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 29.0 bits (66), Expect = 9.2
Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 24/97 (24%)
Query: 272 ATQADVALLVVDATRGEFETGFESGGQTREHALLVRSLGVN---QLGVVINKLDTVSWSQ 328
+AD+ L VVDA+ + E E+ +L + LG + + +V+NK+D
Sbjct: 118 VAEADLLLHVVDASDPDREEQIET-----VEEVL-KELGADDIPII-LVLNKID------ 164
Query: 329 DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 365
L + R + V S TGE L
Sbjct: 165 --------LLDDEELEERLRAGRPDAVFISAKTGEGL 193
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
0.319 0.137 0.418
Gapped
Lambda K H
0.267 0.0853 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 47,113,853
Number of extensions: 4713609
Number of successful extensions: 4333
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4180
Number of HSP's successfully gapped: 209
Length of query: 902
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 796
Effective length of database: 6,236,078
Effective search space: 4963918088
Effective search space used: 4963918088
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 (21.7 bits)
S2: 64 (28.2 bits)