RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017009
(379 letters)
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 474 bits (1222), Expect = e-168
Identities = 165/364 (45%), Positives = 249/364 (68%), Gaps = 3/364 (0%)
Query: 5 YNLRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVK 64
+ + ++ +++E IR + L++ L ELE +A D FW+++ AQ+ + L+ +K
Sbjct: 3 NEISERLKDLDEKLENIRGVLDVDALKERLEELEAEAEDPDFWNDQERAQKVTKELSSLK 62
Query: 65 DKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALDQFELTQLLSGP 124
K++ L + + ++DD +++L EE D D L EA + +K L K L EL +LLSG
Sbjct: 63 AKLDTLEELRQRLDDLEELLELAEEED--DEETLAEAEAELKALEKKLAALELERLLSGE 120
Query: 125 YDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIE 184
YD A+++I AGAGGT+AQDWA MLLRMY+RW E+ +K V++ S GEEAGIKSA +
Sbjct: 121 YDANNAILTIHAGAGGTEAQDWASMLLRMYLRWAERHGFKVEVLDYSEGEEAGIKSATFK 180
Query: 185 VEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEI 244
++G YAYGYL E G HR+VR SPF++ G R TSF+ EV P + +++++++I +DL I
Sbjct: 181 IKGPYAYGYLKSETGVHRLVRISPFDSAGRRHTSFASVEVYPEV-DDTIEIEINPKDLRI 239
Query: 245 SFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEE 304
R+ G GGQ+VNK ++AVRITHIPTG+ V+C ERSQ NK A+ LKAKL + E
Sbjct: 240 DTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELE 299
Query: 305 QRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFIKSY 364
+RA+E ++G+ + WG QIR+YV HPY++VKD+RTG+ET + +V+DG+L+ FI++Y
Sbjct: 300 KRAAEKDALKGEKKEIGWGSQIRSYVLHPYQMVKDLRTGYETGNTQAVLDGDLDGFIEAY 359
Query: 365 LKYK 368
L+++
Sbjct: 360 LRWR 363
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 369 bits (948), Expect = e-127
Identities = 156/366 (42%), Positives = 237/366 (64%), Gaps = 3/366 (0%)
Query: 3 DFYNLRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTD 62
+ + +E + R++ +R S ++ + L ELE + D +FW+++ AQ ++ +
Sbjct: 1 EINEVNNRIEDLTSRLDTVRGSLDPEKKKARLEELEKEMEDPNFWNDQERAQAVIKERSS 60
Query: 63 VKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALDQFELTQLLS 122
++ ++ L + K ++D +++L E D + +A +K L K L + EL +LS
Sbjct: 61 LEAVLDTLEELKNSLEDLSELLELAVEEDDEETFNELDAE--LKALEKKLAELELRTMLS 118
Query: 123 GPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAV 182
G YD A ++I AGAGGT+AQDWA ML RMY+RW E++ +K +++ S GEEAGIKS
Sbjct: 119 GEYDANNAYLTIQAGAGGTEAQDWASMLYRMYLRWAERRGFKVEIIDYSEGEEAGIKSVT 178
Query: 183 IEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDL 242
I ++G YAYGYL E+G HR+VR SPF+A G R TSF+ VMP + ++ +D++I EDL
Sbjct: 179 ILIKGPYAYGYLKSEQGVHRLVRISPFDANGRRHTSFASVFVMPEVDDD-IDIEIKPEDL 237
Query: 243 EISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIA 302
I RA G GGQ+VNK ++AVRITHIPTG+ V+C +RSQ NK A+ LKAKL +
Sbjct: 238 RIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELE 297
Query: 303 EEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFIK 362
E+ +E G+ + WG QIR+YV HPY +VKD+RTG+ET ++ +V+DG+++ FI+
Sbjct: 298 MEKEQAEKDAKEGEKSEIGWGSQIRSYVLHPYSMVKDLRTGYETGNVQAVLDGDIDQFIE 357
Query: 363 SYLKYK 368
+YLK+K
Sbjct: 358 AYLKWK 363
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 339 bits (870), Expect = e-115
Identities = 154/324 (47%), Positives = 219/324 (67%), Gaps = 4/324 (1%)
Query: 43 DSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAA 102
+ +FW++ EAQE +KDK++ + +++D + ++ E D +E
Sbjct: 3 EPNFWNDIKEAQEITSEEKYLKDKLDKYNHLRNRIEDIEVLCEMMSEEDDEMK---KEII 59
Query: 103 SIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQR 162
S +K + + +D+F++ LLSG YD+ A++++ +G GGTDAQDW +MLLRMY RW EK+
Sbjct: 60 SEVKNIKEEIDRFKIETLLSGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKG 119
Query: 163 YKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGA 222
YK +++ G+EAGIKS +++ G +AYGYL EKG HR+VR SPFNA G RQTSF+
Sbjct: 120 YKVEIIDLLEGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASV 179
Query: 223 EVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERS 282
EV+P L ++ D++I EDL+I RAGG GGQ+VNK E+AVRITHIPTG+ V+C ERS
Sbjct: 180 EVLPELTDDQ-DIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERS 238
Query: 283 QLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRT 342
Q +NK A+ LK+KL+ + E +I+ + G+ WG QIR+YVFHPY LVKD RT
Sbjct: 239 QHSNKETAMKMLKSKLVELKERAHKEKIEDLTGELKDMGWGSQIRSYVFHPYNLVKDHRT 298
Query: 343 GHETSDIVSVMDGELEPFIKSYLK 366
G ETS++ SVMDG+++ FI YLK
Sbjct: 299 GVETSNVDSVMDGDIDNFITQYLK 322
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 318 bits (818), Expect = e-109
Identities = 123/239 (51%), Positives = 166/239 (69%), Gaps = 1/239 (0%)
Query: 130 AVISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRY 189
A ++I AGAGGT+AQDWA MLLRMY RW E++ +K V++ S GEEAGIKSA ++++G
Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60
Query: 190 AYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRA 249
AYGYL E G HR+VR SPF++ G R TSF+ EV P L S++++IP++DL I RA
Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDI-SIEIEIPDDDLRIDTYRA 119
Query: 250 GGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASE 309
G GGQ+VNK ++AVR+TH+PTG+ V C ERSQ NK A LK KL ++A+E+R+ E
Sbjct: 120 SGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQE 179
Query: 310 IKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFIKSYLKYK 368
+ R WG QIR+YV PY+ KD+RTG E + V+DG+ + FIK+YLK+
Sbjct: 180 KNRERALKKLIGWGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYLKWD 238
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 284 bits (728), Expect = 5e-94
Identities = 137/332 (41%), Positives = 207/332 (62%), Gaps = 3/332 (0%)
Query: 39 MKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLL 98
KA D S W++ EAQ+ ++ + D IN + + ++D + ++ + EE D ++
Sbjct: 1 NKAEDPSLWNDAQEAQKLMRERQQLDDSINGINHLEQTLNDNIELIAMGEE--EGDKSIV 58
Query: 99 EEAASIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWG 158
E+A I++L +D+ ++ LLSG D + + AGAGGT++QDWA MLLRMY RW
Sbjct: 59 EDAEKTIRDLKDEIDRRQIDALLSGEADANDTYLEVHAGAGGTESQDWASMLLRMYTRWA 118
Query: 159 EKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTS 218
E+Q K V+E GEEAGIKSA I V+G AYG+L E G HR+VR SP+++ R TS
Sbjct: 119 ERQGRKVEVLEVHDGEEAGIKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTS 178
Query: 219 FSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCT 278
F+ V P++ +++++V + E D+ I R+ G GGQ+VN ++AVRITHIPTG+ V+C
Sbjct: 179 FASIWVYPVI-DDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQ 237
Query: 279 EERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVK 338
+ERSQ N+ KA S L+A+L ++R WG QIR+YV PY+LVK
Sbjct: 238 QERSQHKNRAKAWSMLRARLYEEELKKREEATNAAAASKTDIGWGHQIRSYVLQPYQLVK 297
Query: 339 DVRTGHETSDIVSVMDGELEPFIKSYLKYKYS 370
D+RTG E+++ V+DG+L F+++ L ++ S
Sbjct: 298 DLRTGVESTNPQDVLDGDLNEFMEAALAHRIS 329
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 272 bits (696), Expect = 2e-89
Identities = 145/327 (44%), Positives = 210/327 (64%), Gaps = 7/327 (2%)
Query: 44 SSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEM--DSTDAGLLEEA 101
+ FWD++ AQ + +KD + ++D+ +++T E+ + D L EE
Sbjct: 4 AGFWDDQQGAQAVINEANALKDMVGKFR----QLDETFENLEITHELLKEEYDEDLHEEL 59
Query: 102 ASIIKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYVRWGEKQ 161
S +K L + ++++EL LLS PYDK A++ + GAGGT++QDW MLLRMY RW EK+
Sbjct: 60 ESEVKGLIQEMNEYELQLLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAEKR 119
Query: 162 RYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLRQTSFSG 221
+K V+ G+EAGIKS + ++G AYGYL EKG HR+VR SPF++ G R TSF
Sbjct: 120 GFKVETVDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVS 179
Query: 222 AEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEER 281
EV+P +E +++++ EDL+I RA G GGQ+VN ++AVRITH PT V C ER
Sbjct: 180 CEVVPEFNDE-VEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSER 238
Query: 282 SQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYKLVKDVR 341
SQ+ N+ A+ LKAKL E++ +E+ +IRG+ + WG QIR+YVFHPY LVKD R
Sbjct: 239 SQIKNREHAMKMLKAKLYQKKLEEQQAELDEIRGEQKEIGWGSQIRSYVFHPYSLVKDHR 298
Query: 342 TGHETSDIVSVMDGELEPFIKSYLKYK 368
T E ++ +VMDGE++PFI +YL+ +
Sbjct: 299 TNTEVGNVQAVMDGEIDPFIDAYLRSR 325
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 228 bits (582), Expect = 2e-72
Identities = 122/283 (43%), Positives = 176/283 (62%), Gaps = 5/283 (1%)
Query: 99 EEAASIIKELNK---ALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQDWADMLLRMYV 155
+ A ++I +L+K +++ E ++ SG D A + I AGAGGT+AQDWA++LLRMY+
Sbjct: 33 DTALAVIADLDKYQAHVEKLEFQRMFSGQMDGANAFVDIQAGAGGTEAQDWAEILLRMYL 92
Query: 156 RWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTHRIVRQSPFNAKGLR 215
RW E + +KT ++E S GE AGIKSA + +EG YAYG+L E G HR+VR+SPF++ R
Sbjct: 93 RWAESRGWKTELMEVSGGEVAGIKSATVRIEGEYAYGWLKTEIGVHRLVRKSPFDSDNRR 152
Query: 216 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 275
TSF+ V P + ++++++ I DL R+ G GGQ+VNK E+AVRITHIPT V
Sbjct: 153 HTSFTSVFVSPEV-DDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVV 211
Query: 276 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 335
C RSQ N+ A+ L AKL + ++R +E + WG QIRNYV +
Sbjct: 212 ACQTGRSQHQNRDNAMKMLAAKLYELEVQKRNAEKDALEATKSDIGWGSQIRNYVLDQSR 271
Query: 336 LVKDVRTGHETSDIVSVMDGELEPFIKSYLKYKYSMSLSASDA 378
+KD+RTG E SD V+DG+L+ F+++ LK + DA
Sbjct: 272 -IKDLRTGIERSDTQKVLDGDLDEFVEASLKAGLAAGSKRLDA 313
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 206 bits (526), Expect = 2e-63
Identities = 110/345 (31%), Positives = 176/345 (51%), Gaps = 20/345 (5%)
Query: 27 LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKL 86
L+ LE+ ELE +D ++ ++ + +++ + ++K +D ++
Sbjct: 8 LEALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQED----LEE 63
Query: 87 TEEM--DSTDAGLLEEAASIIKELNKALDQFE--LTQLL--SGPYDKEGAVISITAGAGG 140
+EM + +D + E A +KEL + L++ E L LL P D + ++ I AG GG
Sbjct: 64 AKEMLEEESDPEMREMAKEELKELEERLEELEEELKILLLPKDPNDDKNVILEIRAGTGG 123
Query: 141 TDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGT 200
+A +A L RMY R+ E+Q +K ++ S GE G K + E+ G Y L E G
Sbjct: 124 DEAALFAGDLFRMYSRYAERQGWKVEILSASEGELGGYKEVIAEISGDGVYSKLKFESGV 183
Query: 201 HRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKV 260
HR+ R ++G TS + V+P E ++V+I +DL I R+ G GGQ+VN
Sbjct: 184 HRVQRVPATESQGRIHTSAATVAVLPEAEE--VEVEINPKDLRIDTFRSSGAGGQHVNTT 241
Query: 261 ETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-- 318
++AVRITH+PTG+ V C +ERSQ NK KA+ L+A+L ++ +E R V
Sbjct: 242 DSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAATRKSQVGS 301
Query: 319 --KAEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFI 361
++E +IR Y F P V D R + VM+G+L+ I
Sbjct: 302 GDRSE---RIRTYNF-PQGRVTDHRINLTLYKLDEVMEGDLDELI 342
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 205 bits (523), Expect = 5e-63
Identities = 106/343 (30%), Positives = 168/343 (48%), Gaps = 14/343 (4%)
Query: 27 LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKL 86
L+ L + ELE +D + E ++ + +++ + ++K +D
Sbjct: 9 LESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDA--- 65
Query: 87 TEEM--DSTDAGLLEEAASIIKELNKALDQFE--LTQLLS--GPYDKEGAVISITAGAGG 140
+EM + D + E A IKEL +++ E L LL P D + ++ I AG GG
Sbjct: 66 -KEMLAEEKDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIRAGTGG 124
Query: 141 TDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGT 200
+A +A L RMY R+ E + +K ++ S E G K + + G+ Y L E G
Sbjct: 125 DEAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKFESGV 184
Query: 201 HRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKV 260
HR+ R ++G TS + V+P EE +++I +DL I R+ G GGQ+VN
Sbjct: 185 HRVQRVPATESQGRIHTSAATVAVLPE-VEEVEEIEINPKDLRIDTFRSSGAGGQHVNTT 243
Query: 261 ETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-K 319
++AVRITH+PTG+ V C +ERSQ NK KA+ L+A+L ++ +E R V
Sbjct: 244 DSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKSQVGS 303
Query: 320 AEWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMD-GELEPFI 361
+ ++IR Y F P V D R + VM+ G+L+ I
Sbjct: 304 GDRSERIRTYNF-PQNRVTDHRINLTLYKLDEVMEGGKLDEII 345
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 196 bits (500), Expect = 1e-59
Identities = 103/343 (30%), Positives = 179/343 (52%), Gaps = 13/343 (3%)
Query: 27 LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKL 86
L+ L + ELE +D ++ + ++ + + +++ ++ +++ +D K
Sbjct: 9 LESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEEIVDCYREYQQAQEDI----KE 64
Query: 87 TEEM-DSTDAGLLEEAASIIKELNKALDQFE--LTQLL--SGPYDKEGAVISITAGAGGT 141
+E+ + +D + E A ++EL + +++ E L LL P D++ ++ I AG GG
Sbjct: 65 AKEILEESDPEMREMAKEELEELEEKIEELEEQLKVLLLPKDPNDEKNVILEIRAGTGGD 124
Query: 142 DAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGEKGTH 201
+A +A L RMY R+ E + +K ++ + E G K + E++G Y L E G H
Sbjct: 125 EAAIFAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVIAEIKGDGVYSRLKFESGVH 184
Query: 202 RIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVE 261
R+ R ++G TS + VMP L E ++V I DL I R+ G GGQ+VN +
Sbjct: 185 RVQRVPVTESQGRIHTSAATVAVMPELEE--VEVDINPADLRIDTFRSSGAGGQHVNTTD 242
Query: 262 TAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKA- 320
+AVRITH+PTG+ V C +ERSQ NK KA+ L+A+L +E++ + R V +
Sbjct: 243 SAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAAQASTRKSQVGSG 302
Query: 321 EWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFIKS 363
+ ++IR Y F P V D R + V++G+L+ I++
Sbjct: 303 DRSERIRTYNF-PQNRVTDHRINLTLYKLDEVLEGDLDELIEA 344
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 146 bits (372), Expect = 1e-43
Identities = 53/113 (46%), Positives = 73/113 (64%), Gaps = 2/113 (1%)
Query: 230 EESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIK 289
+E ++++IPE DL I R+ G GGQNVNK E+AVR+TH+PTG+ V+C EERSQ N+ K
Sbjct: 3 DEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREK 62
Query: 290 ALSRLKAKLLVIAEEQRASEIKQIRGDAVKA-EWGQQIRNYVFHPYKLVKDVR 341
AL RLKAKL +++ + K R V+ + ++IR Y P VKD R
Sbjct: 63 ALERLKAKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTY-NFPQGRVKDHR 114
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 134 bits (341), Expect = 5e-39
Identities = 53/113 (46%), Positives = 72/113 (63%), Gaps = 4/113 (3%)
Query: 89 EMDSTDAGLLEEAASIIKELNKALDQFE--LTQLL--SGPYDKEGAVISITAGAGGTDAQ 144
+ D L EEA ++EL K L++ E L LL PYD + A++ I AGAGGT+AQ
Sbjct: 3 LEEEDDPELREEAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQ 62
Query: 145 DWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGE 197
+A+ LLRMY R+ E++ +K V++ S GEE GIK A +E+EG AYGYL E
Sbjct: 63 LFAEDLLRMYQRYAERKGWKVEVIDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 132 bits (336), Expect = 2e-38
Identities = 44/118 (37%), Positives = 68/118 (57%), Gaps = 7/118 (5%)
Query: 85 KLTEEMDSTDAGLLEEAASIIKELN----KALDQFELTQLLSG-PYDKEGAVISITAGAG 139
+L EE + D + E A ++EL + L++ LL P D + A++ I AGAG
Sbjct: 1 ELLEEEE--DDEMRELAEEELEELEAELEEELEELLKLLLLPKDPNDDKNAILEIRAGAG 58
Query: 140 GTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAGIKSAVIEVEGRYAYGYLSGE 197
G +A +A LLRMY+R+ E++ +K V+++S GE GIK A +++ G AYG L E
Sbjct: 59 GDEAALFAGDLLRMYLRYAERKGWKVEVLDESEGELGGIKEATLKISGEGAYGKLKFE 116
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 95.9 bits (239), Expect = 2e-23
Identities = 58/204 (28%), Positives = 91/204 (44%), Gaps = 13/204 (6%)
Query: 132 ISITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAG-IKSAVIEVEGRYA 190
+ +++ G + L ++ +Q + V+E G ++SA++ ++G A
Sbjct: 4 LQLSSAQGPAECCLAVAKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSLDGDNA 63
Query: 191 YGYLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFS--R 248
GT + + SP+ R+ F G EE D EI F R
Sbjct: 64 EALAESWCGTIQWICPSPYRPHHGRKNWFVGIGRFSADEEEQSD--------EIRFETLR 115
Query: 249 AGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRAS 308
+ G GGQ+VNK ++AVR TH+ +G++V+ ERSQ ANK A + KL +EQ A+
Sbjct: 116 SSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQEQSAA 175
Query: 309 EIKQIRGDAVKAEWGQQIRNYVFH 332
Q R + E G R VF
Sbjct: 176 LKSQRRMFHHQIERGNPRR--VFT 197
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 95.2 bits (237), Expect = 4e-23
Identities = 56/195 (28%), Positives = 93/195 (47%), Gaps = 15/195 (7%)
Query: 134 ITAGAGGTDAQDWADMLLRMYVRWGEKQRYKTRVVEKSLGEEAG-IKSAVIEVEGRYAYG 192
+++ G + L R + + V+E+ GE G ++SA++ ++G A
Sbjct: 5 LSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSLDGEAAAA 64
Query: 193 YLSGEKGTHRIVRQSPFNAKGLRQTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGK 252
+GT + SP+ R+ F G + EE+ + +I E L R+ G
Sbjct: 65 LADRWEGTLLWICPSPYRPHHRRKNWFIGVQRFSA-SEEATEDEIRFETL-----RSSGP 118
Query: 253 GGQNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQ 312
GGQ+VNK E+AVR TH+ +G++V+ ERSQ ANK A L +L + +EQ A+ +
Sbjct: 119 GGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQAAALRAE 178
Query: 313 --------IRGDAVK 319
RG+ V+
Sbjct: 179 RRTAHHQIERGNPVR 193
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 67.9 bits (167), Expect = 7e-14
Identities = 35/89 (39%), Positives = 40/89 (44%), Gaps = 28/89 (31%)
Query: 234 DVQIPEEDLEISFSRAGGKGGQNVNKVETAV-------------------------RITH 268
+ IPE +LE F RA G GGQNVNKV TAV RIT
Sbjct: 7 RLVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRIT- 65
Query: 269 IPTGV-TVRCTEERSQLANKIKALSRLKA 296
GV ++ E RSQ N+ AL RL A
Sbjct: 66 -KDGVIVIKAQEFRSQERNREDALERLVA 93
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 33.8 bits (78), Expect = 0.13
Identities = 31/140 (22%), Positives = 60/140 (42%), Gaps = 27/140 (19%)
Query: 2 QDFYNLRKDVEAASDRVEEIRASAGLQQLEKELAEL-----EMKAADSSFWDN-RAEAQE 55
+D+ L K++E + ++R LE+EL +L E++ D + D + + ++
Sbjct: 158 EDYKLLMKELELLNSIKPKLRDR--KDALEEELRQLKQLEDELEDCDPTELDRAKEKLKK 215
Query: 56 TLQALTDVKDKINLLTDFKTKMDD-AVTIVKLTEEMDSTDAGLLEEAASI---------- 104
LQ ++ K+ L + + ++ + I LT + L E A
Sbjct: 216 LLQ---EIMIKVKKLEELEEELQELESKIEDLTNKKSE----LNTEIAEAEKKLEQCRGF 268
Query: 105 -IKELNKALDQFELTQLLSG 123
KE+ K +Q +L Q L+G
Sbjct: 269 TFKEIEKLKEQLKLLQSLTG 288
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 33.5 bits (77), Expect = 0.14
Identities = 30/136 (22%), Positives = 55/136 (40%), Gaps = 19/136 (13%)
Query: 2 QDFYNLRKDVEAASDRVEEIRASAGLQQLEKELAEL-----EMKAADSS-FWDNRAEAQE 55
+D L KD+ + ++R LQ L++E+A L E+ D R E +
Sbjct: 161 RDEELLNKDLNLINSIKPKLRKK--LQALKEEIASLRQLADELNLCDPLELEKARQELRS 218
Query: 56 TLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASII--------KE 107
+++ + ++ L ++ A+ LT + S + EA I KE
Sbjct: 219 LSVKISEKRKQLEELQQELQELTIAIE--ALTNKK-SELLEEIAEAEKIREECRGWSAKE 275
Query: 108 LNKALDQFELTQLLSG 123
++K + L Q L+G
Sbjct: 276 ISKLKAKVSLLQKLTG 291
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 32.8 bits (75), Expect = 0.39
Identities = 26/112 (23%), Positives = 49/112 (43%), Gaps = 7/112 (6%)
Query: 7 LRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDK 66
L +++E A V E A+A L + E L L A ++ + A + + +++ +
Sbjct: 813 LAEEIEEAEKEVSE--AAAALDEAEARLTALLRAARCTTIEELLAAVERSDTY-RELRKR 869
Query: 67 INLLTDFKTKMDDAVTIVKLTEEMDSTDA----GLLEEAASIIKELNKALDQ 114
I L + +++ L E + D LEE A I+EL + L++
Sbjct: 870 IAALERTLVRAGGGLSLEALVAEAAALDPDELPARLEELARDIEELEEELNE 921
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 31.6 bits (72), Expect = 0.78
Identities = 25/122 (20%), Positives = 56/122 (45%), Gaps = 18/122 (14%)
Query: 6 NLRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKD 65
L +++E + +EE A +++L+ EL EL + + E E + + +++
Sbjct: 250 RLEEELEELQEELEE--AEKEIEELKSELEELREELEELQ-----EELLELKEEIEELEG 302
Query: 66 KINLLTD-----FKTKMDDAVTIVKLTEEMDSTDA------GLLEEAASIIKELNKALDQ 114
+I+LL + + + +L E++++ LLEE ++ EL +A ++
Sbjct: 303 EISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEE 362
Query: 115 FE 116
E
Sbjct: 363 LE 364
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 30.7 bits (70), Expect = 1.4
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 5 YNLRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFW-DNRAEAQETLQALTD 62
Y L++++E +E LE E+ L+ + AD+ F+ + Q+ L L D
Sbjct: 564 YKLQRELEQLPQLLE---------DLEAEIEALQAQVADADFFSQPHEQTQKVLADLAD 613
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 62
Score = 27.5 bits (62), Expect = 1.9
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 9/43 (20%)
Query: 251 GKGGQNVNKV--ETAVRITHIPTG------VTVRCTEERSQLA 285
GK G N+ K+ ET V+I P +T+ +E + A
Sbjct: 16 GKKGSNIRKIMEETGVKI-RFPDPGSKSDTITITGPKENVEKA 57
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 30.1 bits (69), Expect = 2.2
Identities = 34/134 (25%), Positives = 53/134 (39%), Gaps = 42/134 (31%)
Query: 7 LRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDK 66
L+ +RVE + L++LEKEL +L+ K A A A + L +V
Sbjct: 710 LKAKPSELPERVEALLEE--LKELEKELEQLKAKLA-------AAAAGDLLAQAKEVNG- 759
Query: 67 INLLT----------------DFKTKMDDAV------------TIVKLTEEMDSTDAGLL 98
+ +L D K K+ V +V +T+ D TD GL
Sbjct: 760 VKVLAAQVEGVDAKALRTLADDLKDKLGSGVVVLATVEDGKVSLVVAVTK--DLTDKGL- 816
Query: 99 EEAASIIKELNKAL 112
+A ++KEL K +
Sbjct: 817 -KAGDLVKELAKIV 829
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 30.1 bits (68), Expect = 2.3
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 28 QQLEK---ELAELEMKAADSSFWDN--RAEAQETLQALTDVKDKI 67
+++EK +LA+ E K DS +D +AE LQ K +
Sbjct: 570 KEMEKLNAQLAQAEEKLGDSELYDQSRKAELTACLQQQASAKSGL 614
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and
archaea also match the model The seed members used to
make the model include Nitrate reductases from
Pseudomonas fluorescens (GP:11344601), E.coli and
B.subtilis. All seed members are experimentally
characterized. Some unpublished nitrate reductases, that
are shorter sequences, and probably fragments fall in
between the noise and trusted cutoffs. Pfam models
pfam00384 (Molybdopterin oxidoreductase) and
pfam01568(Molydopterin dinucleotide binding domain) will
also match the nitrate reductase, alpha subunit [Energy
metabolism, Anaerobic].
Length = 1235
Score = 29.9 bits (67), Expect = 2.7
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 156 RWGEKQRYKTRVVEKSLGEEAGIKSAVIEVE---GRYAYGYLSGEKGTH 201
RWGEK ++ + GEE ++ +++ + + Y G+ H
Sbjct: 393 RWGEKGKWNLEQRDGKTGEEIELQLSLLGSQDEIAEVGFPYFGGDGTEH 441
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 29.8 bits (68), Expect = 2.7
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 7/39 (17%)
Query: 222 AEVMPLLPEE---SMDVQIPEEDLEISFSRAGGKGGQNV 257
AEV ++ +E S DV +P++ L S A GK GQNV
Sbjct: 290 AEVSSVVVDEDEHSADVVVPDDQL----SLAIGKNGQNV 324
>gnl|CDD|227071 COG4727, COG4727, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 287
Score = 29.2 bits (65), Expect = 3.9
Identities = 16/66 (24%), Positives = 22/66 (33%), Gaps = 4/66 (6%)
Query: 122 SGPY-DKEGAVISITAGAGGTDAQDWADMLLRMYV-RWGEKQRYKTRVVEKSLGEEAGIK 179
S Y + V+ + A A A D LR RW + Y V+ G
Sbjct: 166 SVRYQNSNQWVLELLALA--WGALDHDGSDLRNRAQRWLRQASYAPSPVDIDSHARMGAS 223
Query: 180 SAVIEV 185
+ V V
Sbjct: 224 TFVPNV 229
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 28.1 bits (64), Expect = 4.2
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 13/52 (25%)
Query: 21 IRASAG-LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLT 71
+RA+ G L+QLE AELE KAA + AEA+ + +K+ LT
Sbjct: 37 VRATKGNLKQLEARRAELEAKAA-----EELAEAEA-------LAEKLEGLT 76
>gnl|CDD|238817 cd01639, IMPase, IMPase, inositol monophosphatase and related
domains. A family of Mg++ dependent phosphatases,
inhibited by lithium, many of which may act on inositol
monophosphate substrate. They dephosphorylate inositol
phosphate to generate inositol, which may be recycled
into inositol lipids; in eukaryotes IMPase plays a vital
role in intracellular signaling. IMPase is one of the
proposed targets of Li+ therapy in manic-depressive
illness. This family contains some bacterial members of
the inositol monophosphatase family classified as
SuhB-like. E. coli SuhB has been suggested to
participate in posstranscriptional control of gene
expression, and its inositol monophosphatase activity
doesn't appear to be sufficient for its cellular
function. It has been proposed, that SuhB plays a role
in the biosynthesis of phosphatidylinositol in
mycobacteria.
Length = 244
Score = 28.3 bits (64), Expect = 6.0
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 317 AVKA--EWGQQIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFIKSYLKYKY 369
A++A + G+ + KL +V D+V+ +D +E I LK Y
Sbjct: 5 AIEAARKAGEILLEAY---EKLGLNVEEKGSPVDLVTEVDKAVEKLIIEILKKAY 56
>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 732
Score = 28.6 bits (64), Expect = 6.1
Identities = 17/57 (29%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 324 QQIRNYVFHPYKLVKDVRTGHETSDIVSVMD--------GELEPFIK----SYLKYK 368
+ I Y Y L V G ET DI+ V+ + FI+ SY K K
Sbjct: 52 EHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSKTPIPKGIIEFIRLCTQSYGKVK 108
>gnl|CDD|132914 cd07043, STAS_anti-anti-sigma_factors, Sulphate Transporter and
Anti-Sigma factor antagonist) domain of anti-anti-sigma
factors, key regulators of anti-sigma factors by
phosphorylation. Anti-anti-sigma factors play an
important role in the regulation of several sigma
factors and their corresponding anti-sigma factors. Upon
dephosphorylation they bind the anti-sigma factor and
induce the release of the sigma factor from the
anti-sigma factor. In a feedback mechanism the
anti-anti-sigma factor can be inactivated via
phosphorylation by the anti-sigma factor. Well studied
examples from Bacillus subtilis are SpoIIAA (regulating
sigmaF and sigmaC which play an important role in
sporulation) and RsbV (regulating sigmaB involved in the
general stress response). The STAS domain is also found
in the C- terminal region of sulphate transporters and
stressosomes.
Length = 99
Score = 26.7 bits (60), Expect = 6.8
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 73 FKTKMDDAVTIVKLTEEMDSTDAGLLEEA 101
+ V +V+L+ E+D+ A L EA
Sbjct: 1 ITVEERGGVLVVRLSGELDAATAPELREA 29
>gnl|CDD|147765 pfam05791, Bacillus_HBL, Bacillus haemolytic enterotoxin (HBL).
This family consists of several Bacillus haemolytic
enterotoxins (HblC, HblD, HblA, NheA, and NheB) which
can cause food poisoning in humans.
Length = 181
Score = 27.7 bits (62), Expect = 6.9
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 7/50 (14%)
Query: 49 NRAEAQETLQALTDVKDKINL-LTDFKTKMDDAVTIVKLTEEMDSTDAGL 97
N+ E + L+ L D K+K+ FKT +D +I+K AG+
Sbjct: 119 NQKEVDQLLEELKDFKNKLAKDTRSFKTDVDQLTSILK------GQGAGI 162
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is
an essential multifunctional transcription elongation
factor that is universally conserved among prokaryotes
and archaea. NusA anti-termination function plays an
important role in the expression of ribosomal rrn
operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 26.0 bits (58), Expect = 7.3
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 229 PEESMDVQIPEEDLEISFSRAGGKGGQNVNKVE 261
E+ V +P++ L A GKGGQNV
Sbjct: 23 EEKRARVVVPDDQL----GLAIGKGGQNVRLAS 51
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 25.6 bits (57), Expect = 9.9
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 14/60 (23%)
Query: 239 EEDLEISFSRAG---GKGGQNVNKV--ETAVRITHIPTG--------VTVRCTEERSQLA 285
E + + S G GKGG + ++ ET +I IP VT+ T E + A
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKI-KIPDSGSGSEERIVTITGTPEAVEKA 59
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.313 0.129 0.353
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,036,049
Number of extensions: 1867908
Number of successful extensions: 1911
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1867
Number of HSP's successfully gapped: 122
Length of query: 379
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 280
Effective length of database: 6,546,556
Effective search space: 1833035680
Effective search space used: 1833035680
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: 60 (26.7 bits)