RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023032
(288 letters)
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 233 bits (596), Expect = 4e-77
Identities = 85/208 (40%), Positives = 127/208 (61%), Gaps = 5/208 (2%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRK 113
L +L+ G++ GE L + A++H+ ++ + N R+GT +T TR EV GGG+K
Sbjct: 3 LKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKK 62
Query: 114 PYSQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENT 173
P+ QK TGRAR+GS R+P GGGVVFGPKPRD+S K+NKK +RLA+ +A++ A
Sbjct: 63 PWRQKGTGRARQGSIRSPQWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAREGRL 122
Query: 174 IVVEEFDGKFERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPR 233
+VV++ E PKTKE ++ GL K + EV EN+ S+RN+ + +L +
Sbjct: 123 VVVDDL--SLEAPKTKELAAKLKNLGLK---KVLIVTDEVDENLYLSARNLPNVDVLPAQ 177
Query: 234 TLNLFDILDAETLVLTPSTVDFLNGRYG 261
LN++D+L A+ +VLT + V L R
Sbjct: 178 GLNVYDLLRADKVVLTKAAVKKLEERLA 205
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast has
been shown to bind rRNA.
Length = 190
Score = 223 bits (571), Expect = 1e-73
Identities = 82/180 (45%), Positives = 124/180 (68%), Gaps = 3/180 (1%)
Query: 80 RAVVHRALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVV 139
++HRA++ + N+R+GTAST TR EV GGG+KP+ QK TGRAR GS R+PL GGGV
Sbjct: 14 PDLLHRAVVAQLANRRQGTASTKTRSEVSGGGKKPWRQKGTGRARAGSIRSPLWRGGGVA 73
Query: 140 FGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGKFERPKTKEFIEAMRRWG 199
FGPKPRD+S K+NKK +RLA+ +A+++ A +VV++F+ E PKTK+ ++ ++ G
Sbjct: 74 FGPKPRDYSYKLNKKVRRLALRSALSAKAREGKLVVVDDFE--LEIPKTKDAVKLLKNLG 131
Query: 200 LDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILDAETLVLTPSTVDFLNGR 259
L K K +V E EN+ S+RN+ + ++T LN++D+L A+ +V+T S ++ L R
Sbjct: 132 LKNK-KVLIVVDEKDENLYLSARNLPGVDVVTVDGLNVYDLLPADKVVITKSALEKLEER 190
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
bacterial/organelle. Members of this protein family are
ribosomal protein L4. This model recognizes bacterial
and most organellar forms, but excludes homologs from
the eukaryotic cytoplasm and from archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 188
Score = 215 bits (550), Expect = 1e-70
Identities = 80/178 (44%), Positives = 119/178 (66%), Gaps = 4/178 (2%)
Query: 81 AVVHRALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVVF 140
++H+ + + N+R+GT T TR EV GGG+KP+ QK TGRAR+GS R+PL GGGV F
Sbjct: 15 HLLHQVVKAQLANRRQGTHKTKTRSEVSGGGKKPWRQKGTGRARQGSIRSPLWRGGGVAF 74
Query: 141 GPKPRDWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGKFERPKTKEFIEAMRRWGL 200
GPKPRD+S K+NKK +RLA+ +A++ A +VV++FD E PKTK+ + ++ GL
Sbjct: 75 GPKPRDYSYKLNKKVRRLALRSALSEKAREGKLVVVDDFD--LEEPKTKDLAKILKNLGL 132
Query: 201 DPKQKATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILDAETLVLTPSTVDFLNG 258
D +K + EV EN+ S+RN+ +K+L LN++D+L A+ +VLT + V+ L
Sbjct: 133 D--KKVLIVTDEVDENLYLSARNLPNVKVLPANGLNVYDLLRADKVVLTEAAVEKLEE 188
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 213 bits (545), Expect = 2e-69
Identities = 86/208 (41%), Positives = 131/208 (62%), Gaps = 2/208 (0%)
Query: 55 PILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRKP 114
P++ TG++ ET + + ++HRAL+ N+R+GTAST TR EVRGGGRKP
Sbjct: 10 PVIDLTGKEKSETIKLKLNVLEKSGNYLLHRALVRQNNNQRQGTASTKTRSEVRGGGRKP 69
Query: 115 YSQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENTI 174
+ QK TGRAR GSNR+PL GGGV+FGPKP+ +S K+NKKE+RLA+ T + + N
Sbjct: 70 WKQKGTGRARAGSNRSPLWKGGGVIFGPKPKTYSNKLNKKERRLALRTLL--YNKSNNIT 127
Query: 175 VVEEFDGKFERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLTPRT 234
VVE F+ PKTK FI +++ ++ QK +V E +EN+ S+RN+ +++++ T
Sbjct: 128 VVENFESSITNPKTKAFINLLKKLNINLDQKILIIVPEKTENLYLSTRNLKNVELISADT 187
Query: 235 LNLFDILDAETLVLTPSTVDFLNGRYGV 262
LN+ +L A+ +++T + + Y
Sbjct: 188 LNIKSLLKAKQIIITKEALKIIEEVYND 215
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 182 bits (464), Expect = 4e-57
Identities = 87/213 (40%), Positives = 130/213 (61%), Gaps = 6/213 (2%)
Query: 54 LPILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRK 113
L + GE++GE L + P+ ++HRA++ + N+R+GT ST TRGEV GGG+K
Sbjct: 4 LKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKK 63
Query: 114 PYSQKKTGRARRGSNRTPLRPGGGVVFGPKP-RDWSIKINKKEKRLAISTAIASAAAAEN 172
P+ QK TGRAR+GS R+P GGGV GPKP RD+S K+NKKE+RLA+ +A+++ A A
Sbjct: 64 PWGQKGTGRARQGSIRSPQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGK 123
Query: 173 TIVVEEFDGKFE-RPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEKSSRNIGTLKMLT 231
+VV FE PKTKE +E +++ GLD ++ + E N + S+RN+ +K++
Sbjct: 124 LVVVRGH--VFEDAPKTKELVEFLKKLGLD-VKRLLIVKGERDGNGKLSARNLKNVKVVL 180
Query: 232 P-RTLNLFDILDAETLVLTPSTVDFLNGRYGVE 263
L + D+L A+ LV+T + R V
Sbjct: 181 VVGGLPVVDVLRADKLVITKLAPGKIEERLTVW 213
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 157 bits (397), Expect = 3e-46
Identities = 80/235 (34%), Positives = 125/235 (53%), Gaps = 9/235 (3%)
Query: 56 ILSFTGEKIGETYLDLKSAAPDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRKPY 115
+L + G+K+G L LK +T ++H+ ++ M R+GT T TR EVRGGG+KP+
Sbjct: 6 VLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGGKKPW 65
Query: 116 SQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIV 175
QK TGRAR+GS R P GGG V GP+PR+++ + KK ++ A+ A++ A IV
Sbjct: 66 RQKGTGRARQGSIRAPQWRGGGTVHGPRPREYNQRTPKKMRQAALRGALSDRARDNRLIV 125
Query: 176 VEEF-DGKFERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEK-SSRNIGTLKMLTPR 233
VE DG + P TK +A+ + Q+A +V E S+ VE+ S RN+ + +L
Sbjct: 126 VESLQDG--DPPSTKAVAQAL---SVMEDQRALLVVAERSDAVERLSVRNLARVHVLGAD 180
Query: 234 TLNLFDILDAETLVLTPSTVDFLNGRYGVEFEGDGDEEEEESEAREAGEESDAAE 288
LN +D+L+ + +V T S ++ G G A +++ E
Sbjct: 181 QLNTYDVLNVDWVVFTQSALEAFVGAKSR--WGSAAAAAAPVPATNVADQAPYGE 233
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 113 bits (284), Expect = 1e-29
Identities = 60/174 (34%), Positives = 109/174 (62%), Gaps = 6/174 (3%)
Query: 87 LITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVVFGPKP-R 145
++++ ++R+GT TR EV G G+KP+ QK TGRAR GS R+P+ GGG FGP P R
Sbjct: 125 ILSERASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSPIFVGGGRAFGPTPER 184
Query: 146 DWSIKINKKEKRLAISTAIASAAAAENTIVVEEFDGKFERPKTKEFIEAMRRWGLDPKQK 205
++ +K+NKK + A +A+ + A ++V++F K E+ TK+ I+ + + ++ +
Sbjct: 185 NYKLKVNKKVRFNAFVSAL-TLLANSKAVLVDDF--KLEKISTKDLIKKLTKLKINNLKH 241
Query: 206 ATFLVMEVSENVEKSSRNIGTLKMLTPRTLNLFDILDAETLVLTPSTVDFLNGR 259
L++ EN+ KS+RN+ + ++ P +L++ ++ A+ LVL+ +++ L GR
Sbjct: 242 --ILIVSNDENIFKSARNLQNVIVVKPTSLSVELLIAADVLVLSKESIENLEGR 293
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 49.5 bits (119), Expect = 6e-07
Identities = 43/123 (34%), Positives = 55/123 (44%), Gaps = 33/123 (26%)
Query: 111 GRKPYSQKKT---------GRAR----RGSNRTPLRP---GGGVVFGPKP-RDWSIKINK 153
GR P + K+T G AR +G +R P GG PK +D KINK
Sbjct: 47 GRDPLAGKRTSAESWGSGRGIARVPRLKGGSRAAFVPQAVGGRRAHPPKVEKDLHEKINK 106
Query: 154 KEKRLAISTAIASAAAAENTIVVE---EFDGKFERP-----------KTKEFIEAMRRWG 199
KE+RLAI +AIA+ A E +V F+G E P KTKE E + + G
Sbjct: 107 KERRLAIRSAIAATANPE--LVKARGHVFEGVPELPLVVVDDFESLKKTKEVRELLEKLG 164
Query: 200 LDP 202
L
Sbjct: 165 LYD 167
>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P. One of the
primary rRNA binding proteins, this protein initially
binds near the 5'-end of the 23S rRNA. It is important
during the early stages of 50S assembly. It makes
multiple contacts with different domains of the 23S rRNA
in the assembled 50S subunit and ribosome.
Length = 251
Score = 45.7 bits (109), Expect = 1e-05
Identities = 40/121 (33%), Positives = 52/121 (42%), Gaps = 34/121 (28%)
Query: 111 GRKPYSQKKT---------GRAR----RGSNRTPLRP---GGGVVFGPKP-RDWSIKINK 153
G PY+ K+T G AR +G +R P GG PK +D KINK
Sbjct: 47 GADPYAGKRTSAESWGSGRGIARVPRIKGGSRAARVPQAVGGRRAHPPKVEKDLHEKINK 106
Query: 154 KEKRLAISTAIASAAAAENTIVVEEFDGKFERP--------------KTKEFIEAMRRWG 199
KE+RLAI +AIA+ A E +V+ FE KTKE E + G
Sbjct: 107 KERRLAIRSAIAATADPE---LVKARGHVFEGDELPIVVVDDFESLKKTKEVRELLEALG 163
Query: 200 L 200
+
Sbjct: 164 V 164
>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 34.3 bits (79), Expect = 0.067
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 18/81 (22%)
Query: 136 GGVVFGPKP--RDWSIKINKKEKRLAISTAIASAA--------------AAENTIVVEEF 179
GG +F P R W K+N +KR A+++A+A++ E +VV +
Sbjct: 97 GGRMFAPTKTWRRWHRKVNLNQKRHAVASALAASGVPALVMARGHRISNVPEVPLVVSDS 156
Query: 180 DGKFERPKTKEFIEAMRRWGL 200
+E KTKE + ++ G
Sbjct: 157 VESYE--KTKEAVAFLKALGA 175
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 34.0 bits (78), Expect = 0.086
Identities = 30/111 (27%), Positives = 45/111 (40%), Gaps = 30/111 (27%)
Query: 76 PDTARAVVHRALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPG 135
PD V H + +N R+ A + + G + TGRA +R P PG
Sbjct: 38 PDIVNFV-HTNI---SKNSRQPYAVS-----KKAGHQTSAESWGTGRA---VSRIPRVPG 85
Query: 136 GGV----------------VFGPKP--RDWSIKINKKEKRLAISTAIASAA 168
GG +F P R W K+N +KR A+ +A+A++A
Sbjct: 86 GGTHRAGQGAFGNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASA 136
>gnl|CDD|218733 pfam05755, REF, Rubber elongation factor protein (REF). This
family consists of the highly related rubber elongation
factor (REF), small rubber particle protein (SRPP) and
stress-related protein (SRP) sequences. REF and SRPP are
released from the rubber particle membrane into the
cytosol during osmotic lysis of the sedimentable
organelles (lutoids). The exact function of this family
is unknown.
Length = 216
Score = 31.4 bits (71), Expect = 0.36
Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 17/118 (14%)
Query: 53 PLPILSFTGEKIGETYLDLKSAAPDTARAVVHRA--LITDMQNKRRGTASTLTRGEVRGG 110
PL +L F K+ ++ +L P + +A + R AS + R V
Sbjct: 67 PLELLKFVDRKVDDSVTELDRHVPPLVKQASAQAYSVAQKAPEVARAVASEVRRTGVVET 126
Query: 111 GR---------------KPYSQKKTGRARRGSNRTPLRPGGGVVFGPKPRDWSIKINK 153
+ +P +++ A R N+ PL P V P WS K N
Sbjct: 127 AKGIAKSVYSKYLYTNYEPVAEQYAVSAWRSLNQLPLFPQVAQVVVPTAAYWSEKYND 184
>gnl|CDD|227270 COG4934, COG4934, Predicted protease [Posttranslational
modification, protein turnover, chaperones].
Length = 1174
Score = 32.0 bits (73), Expect = 0.37
Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 7 SLSFFSSTIFLTSSSNKVPKPIQLAKPNSLINLPP---KPLIVSSQLASP-LPILSFTGE 62
++SF S +L + PN I P + V L S +PIL+ E
Sbjct: 643 TISFIYSPSYLAPTFLGNSYSYDYFLPNIGIMRPAVGVNMIGVYDNLVSLSVPILNVNPE 702
Query: 63 KIGETYL 69
L
Sbjct: 703 GFAYPGL 709
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 29.9 bits (67), Expect = 1.3
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 254 DFLNGRYGVEFEGDGDEEEEESEAREAGEESDAAE 288
DF YG E + D + + E G++ D +
Sbjct: 263 DFKGVNYGYESDDDEGSSSNDYDEEEDGDDDDNED 297
>gnl|CDD|219398 pfam07394, DUF1501, Protein of unknown function (DUF1501). This
family contains a number of hypothetical bacterial
proteins of unknown function approximately 400 residues
long.
Length = 393
Score = 30.0 bits (68), Expect = 1.5
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 75 APDTARAVVHRALITDMQNKRRGTA-STLTRGEVRGG--GRKPYSQKKTGR 122
A + +A+ AL+ D+ K+RG TL V GG GR P GR
Sbjct: 271 AKELDQALA--ALLKDL--KQRGLLDDTLV---VWGGEFGRTPRINGNGGR 314
>gnl|CDD|177904 PLN02263, PLN02263, serine decarboxylase.
Length = 470
Score = 29.0 bits (65), Expect = 3.6
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 183 FERPKTKEFIEAMRRWGLDPKQKATFLVMEVSENVEK 219
FERPK +EF+ RRW L + +V+ S +EK
Sbjct: 396 FERPKDEEFV---RRWQLACQGNIAHVVVMPSVTIEK 429
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 28.1 bits (63), Expect = 3.6
Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 6/95 (6%)
Query: 200 LDPKQKATFLVMEV-SENVEKSSRN--IGTLKMLTPRTLNL--FDILDAETLVL-TPSTV 253
L P+ K F V+EV + N E I LK ++L F++ T L + S
Sbjct: 39 LGPEAKDEFNVVEVEAMNYEGKKVKVPIAVLKPSVLPMVSLGGFELTPPVTFRLKSGSGP 98
Query: 254 DFLNGRYGVEFEGDGDEEEEESEAREAGEESDAAE 288
++G++ V E D +++EE E E EE D +
Sbjct: 99 VHISGQHLVASEEDESDDDEEDEEEEDDEEDDDED 133
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 28.8 bits (65), Expect = 3.8
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 263 EFEGDGDEEEEESEAREAGEESDAAE 288
E + D D EEEE + + EE D +
Sbjct: 335 EEDDDDDLEEEEEDVDLSDEEEDEED 360
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 28.7 bits (64), Expect = 4.9
Identities = 19/62 (30%), Positives = 25/62 (40%)
Query: 85 RALITDMQNKRRGTASTLTRGEVRGGGRKPYSQKKTGRARRGSNRTPLRPGGGVVFGPKP 144
R L M + G A T GE RGGGR +++ G R G G F +
Sbjct: 549 RILNKPMNMQLLGDAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGER 608
Query: 145 RD 146
R+
Sbjct: 609 RE 610
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 28.2 bits (63), Expect = 5.8
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 261 GVEFEGDGDEEEEESEAREAGEESDAAE 288
+ + DEEE E+ AR AG +SD E
Sbjct: 6 NTQANEEEDEEELEAVARSAGSDSDDDE 33
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 27.7 bits (61), Expect = 6.2
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 263 EFEGDGDEEEEESEAREAGEESDAAE 288
E GDGD EEE E + EE + +
Sbjct: 52 EENGDGDSSEEEGEEETSNEEENNED 77
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 26.7 bits (58), Expect = 6.3
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 252 TVDFLNGRYGVEFEGDGDEEEEESEAREAGEESDAAE 288
T+ FL G + + D DEEE++ + E ++ D E
Sbjct: 2 TLHFLEG--EEDSDSDSDEEEDDDDEDEEDDDEDDDE 36
>gnl|CDD|211664 TIGR01512, ATPase-IB2_Cd, heavy
metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase.
This model describes the P-type ATPase primarily
responsible for translocating cadmium ions (and other
closely-related divalent heavy metals such as cobalt,
mercury, lead and zinc) across biological membranes.
These transporters are found in prokaryotes and plants.
Experimentally characterized members of the seed
alignment include: SP|P37617 from E. coli, SP|Q10866
from Mycobacterium tuberculosis and SP|Q59998 from
Synechocystis PCC6803. The cadmium P-type ATPases have
been characterized as Type IB based on a phylogenetic
analysis which combines the copper-translocating ATPases
with the cadmium-translocating species. This model and
that describing the copper-ATPases (TIGR01511) are well
separated, and thus we further type the copper-ATPases
as IB1 and the cadmium-ATPases as IB2. Several sequences
which have not been characterized experimentally fall
just below trusted cutoff for both of these models
(SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from
Sulfolobus solfataricus, OMNI|NTL01CJ01098 from
Campylobacter jejuni, OMNI|NTL01HS01687 from
Halobacterium sp., GP|6899169 from Ureaplasma
urealyticum and OMNI|HP1503 from Helicobacter pylori)
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 536
Score = 28.1 bits (63), Expect = 6.8
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 9/57 (15%)
Query: 155 EKRLAISTAIASAAAAENTIVVEEFDGKFE---------RPKTKEFIEAMRRWGLDP 202
R + A +A TIV DG + RP E I ++ G++
Sbjct: 325 NPRSLEAAVGARPESAGKTIVHVARDGTYLGYILLSDEPRPDAAEAIAELKALGIEK 381
>gnl|CDD|226364 COG3845, COG3845, ABC-type uncharacterized transport systems,
ATPase components [General function prediction only].
Length = 501
Score = 27.9 bits (63), Expect = 6.9
Identities = 33/93 (35%), Positives = 42/93 (45%), Gaps = 18/93 (19%)
Query: 169 AAENTIVVEE--FDGKFERPKTKEFI-EAMRRWGL--DPKQKATFLVMEVSENVEKSSRN 223
AEN I+ E G +R + + I E R+GL DP K V ++S V + R
Sbjct: 96 VAENIILGLEPSKGGLIDRRQARARIKELSERYGLPVDPDAK----VADLS--VGEQQR- 148
Query: 224 IGTLKML--TPRTLNLFDILDAETLVLTPSTVD 254
+ LK L R L ILD T VLTP D
Sbjct: 149 VEILKALYRGARLL----ILDEPTAVLTPQEAD 177
>gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.
Coenzyme A acylating aldehyde dehydrogenase (ACDH), an
NAD+ and CoA-dependent acetaldehyde dehydrogenase,
acetylating (EC=1.2.1.10), converts acetaldehyde into
acetyl-CoA. This CD is limited to such monofunctional
enzymes as the Ethanolamine utilization protein, EutE,
in Salmonella typhimurium. Mutations in eutE abolish
the ability to utilize ethanolamine as a carbon source.
Length = 429
Score = 28.0 bits (63), Expect = 7.1
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 135 GGGVVFGPKPRDWSIKINKKEKRLAISTAIASAAAAENTIV-VEE 178
G VVF P P + K++ L I+ AIA A +N +V VEE
Sbjct: 125 GNAVVFNPHPG--AKKVSAYAVEL-INKAIAEAGGPDNLVVTVEE 166
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3
subunit 7 (eIF-3). This family is made up of eukaryotic
translation initiation factor 3 subunit 7 (eIF-3
zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is
a multi-subunit complex that is required for binding of
mRNA to 40 S ribosomal subunits, stabilisation of
ternary complex binding to 40 S subunits, and
dissociation of 40 and 60 S subunits. These functions
and the complex nature of eIF3 suggest multiple
interactions with many components of the translational
machinery. The gene coding for the protein has been
implicated in cancer in mammals.
Length = 517
Score = 28.0 bits (63), Expect = 7.1
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 89 TDMQNKRRGTASTLTRGEVRGGGRKPYSQK-KTGRARRGSNRTPLRPGGGVVFGPKPRDW 147
+ K+ T RG+ G R S++ K G R+ R G + R+
Sbjct: 96 RKRRGKQTRTQR---RGQGPQGKRGMTSRRAKRGGQRKQKRFQTGRGGRRGARHRRLREA 152
Query: 148 SIKIN 152
S++I
Sbjct: 153 SVEIR 157
>gnl|CDD|188097 TIGR00931, antiport_nhaC, Na+/H+ antiporter NhaC. A single
member of the NhaC family, a protein from Bacillus
firmus, has been functionally characterized.It is
involved in pH homeostasis and sodium extrusion.
Members of the NhaC family are found in both
Gram-negative bacteria and Gram-positive bacteria.
Intriguingly, archaeal homolog ArcD (just outside
boundaries of family) has been identified as an
arginine/ornithine antiporter [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 454
Score = 27.5 bits (61), Expect = 9.3
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 36 LINLPPKPLIVSSQLASPLPILSFTGEKIGETYLDLKSA 74
+++LPP +V S L I + G +G Y DL+SA
Sbjct: 25 VLDLPPHIPLVVSLL-----IAAVLGRYLGVGYNDLESA 58
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.312 0.130 0.359
Gapped
Lambda K H
0.267 0.0572 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,670,697
Number of extensions: 1419502
Number of successful extensions: 1525
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1488
Number of HSP's successfully gapped: 47
Length of query: 288
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 192
Effective length of database: 6,679,618
Effective search space: 1282486656
Effective search space used: 1282486656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.5 bits)