RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16472
(630 letters)
>gnl|CDD|240267 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional.
Length = 390
Score = 356 bits (916), Expect = e-118
Identities = 153/281 (54%), Positives = 190/281 (67%), Gaps = 40/281 (14%)
Query: 39 SHRKFSAPRHGSMGFYPKKRSARHRGKVKCFPKDDPTKPVHLTAFIGYKAGMTHIVREAD 98
SHRKF PRHGS+GF P+KR RHRG+++ FPKDDPT+P HLTAF+GYKAGMTHIVR+ D
Sbjct: 2 SHRKFEHPRHGSLGFLPRKRCRRHRGRIRSFPKDDPTQPPHLTAFMGYKAGMTHIVRDVD 61
Query: 99 RPGSKINKKEIVEAVTILETPPMVIVGVIGYVETPHGLRSFKTVWAEHLSQECRRRFYKN 158
RPGSK++KKE+VEAVTI+E PPMV+VG++GY ETP GLR+ TVWA HLS E RRRFYKN
Sbjct: 62 RPGSKLHKKEVVEAVTIIEAPPMVVVGIVGYRETPRGLRALTTVWAHHLSDEFRRRFYKN 121
Query: 159 WYKSRQKAFTKASKKWQDKLGKKTIAQDLRKMAKYCKVIRVIAHTQNQQQSLHQNQQSHT 218
WYKS++KAFTK K KK + L+++ KYC VIRVIAHT
Sbjct: 122 WYKSKKKAFTKYKKFAAT---KKAEERTLKRIKKYCSVIRVIAHT--------------- 163
Query: 219 KDQPIQSNVNKTQPDSHESHVQMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPI 278
Q L QKKAH+MEIQ+NGGSVA+K+ +A+ LE+ +
Sbjct: 164 ---------------------QPSKLPLGQKKAHVMEIQVNGGSVAEKVDFAKSLLEKEV 202
Query: 279 PVGQVFAQDEMIDCIGVTKGKGFKGEMIAMKLLKKRQKKAH 319
PV VF Q+EMID IGVTKG GF+G ++ + + +K H
Sbjct: 203 PVDSVFQQNEMIDVIGVTKGHGFEG-VVKRWGVTRLPRKTH 242
Score = 216 bits (551), Expect = 4e-64
Identities = 84/123 (68%), Positives = 99/123 (80%)
Query: 308 MKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKG 367
L QKKAH+MEIQ+NGGSVA+K+ +A+ LE+ +PV VF Q+EMID IGVTKG G
Sbjct: 165 PSKLPLGQKKAHVMEIQVNGGSVAEKVDFAKSLLEKEVPVDSVFQQNEMIDVIGVTKGHG 224
Query: 368 FKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPSRVQFTVARAGQKGYHHRTELNKKIYRM 427
F+GV RW +LPRKTH+GLRKVACIGAWHP+RVQ+TV RAGQ GYHHRTELNKKIYR+
Sbjct: 225 FEGVVKRWGVTRLPRKTHRGLRKVACIGAWHPARVQYTVPRAGQHGYHHRTELNKKIYRI 284
Query: 428 GAG 430
G
Sbjct: 285 GVA 287
Score = 200 bits (510), Expect = 3e-58
Identities = 83/118 (70%), Positives = 92/118 (77%), Gaps = 4/118 (3%)
Query: 436 GKVSVTSRWHTKKLPRKTHKGLRKVACIGAWHPSRVQFTVARAGQKGYHHRTELFLCKKK 495
G V RW +LPRKTH+GLRKVACIGAWHP+RVQ+TV RAGQ GYHHRTE L KK
Sbjct: 224 GFEGVVKRWGVTRLPRKTHRGLRKVACIGAWHPARVQYTVPRAGQHGYHHRTE--LNKKI 281
Query: 496 YL--SMVIKNNASTDYDLTEKSITPMGGFPHYGEVNNDFLMIKGCCMGPKKRVITLRK 551
Y NNA+T+ DLTEK+ITPMGGFPHYG V NDFLM+KGC +GPKKRVITLRK
Sbjct: 282 YRIGVAEDPNNATTEADLTEKTITPMGGFPHYGTVRNDFLMLKGCVVGPKKRVITLRK 339
Score = 95.2 bits (237), Expect = 6e-21
Identities = 41/73 (56%), Positives = 52/73 (71%)
Query: 545 RVITLRKMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCI 604
RVI + L QKKAH+MEIQ+NGGSVA+K+ +A+ LE+ +PV VF Q+EMID I
Sbjct: 158 RVIAHTQPSKLPLGQKKAHVMEIQVNGGSVAEKVDFAKSLLEKEVPVDSVFQQNEMIDVI 217
Query: 605 GVTKGKGFKECVH 617
GVTKG GF+ V
Sbjct: 218 GVTKGHGFEGVVK 230
>gnl|CDD|235260 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed.
Length = 337
Score = 176 bits (450), Expect = 3e-50
Identities = 87/264 (32%), Positives = 130/264 (49%), Gaps = 52/264 (19%)
Query: 40 HRKFSAPRHGSMGFYPKKRSARHRGKVKCFPKDDPTKPVHLTAFIGYKAGMTHIVREADR 99
RK PR GS+ F P+KR+ +++ +P+ D +P L F GYKAGMTH++ DR
Sbjct: 1 MRKIHRPRRGSLAFSPRKRAKSIVPRIRSWPEID-GEPK-LLGFAGYKAGMTHVIMIDDR 58
Query: 100 PGSKINKKEIVEAVTILETPPMVIVGVIGYVETPHGLRSFKTVWAEHLSQECRRRFYKNW 159
P S KEI VT+LETPPM + + Y + P+GL+ VWAE L +E RR
Sbjct: 59 PNSPTEGKEIFVPVTVLETPPMRVAAIRAYEKDPYGLKVLTEVWAEDLDKELERRITLPK 118
Query: 160 YKSRQKAFTKASKKWQDKLGKKTIAQDLRKMAKYCKVIRVIAHTQNQQQSLHQNQQSHTK 219
++KAF K L + I +RVI HTQ +
Sbjct: 119 KDEKKKAFEKL----LKLLEEGKIVD-----------VRVIVHTQPK------------- 150
Query: 220 DQPIQSNVNKTQPDSHESHVQMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIP 279
+ + V K +P+ +MEI++ GGSV +++ +A++ L + I
Sbjct: 151 ---LVTGVPKKKPE-------------------IMEIRIGGGSVEERLEYAKELLGKEIS 188
Query: 280 VGQVFAQDEMIDCIGVTKGKGFKG 303
+ VF + +++D I VTKGKGF+G
Sbjct: 189 ISDVFKEGQLVDVIAVTKGKGFQG 212
Score = 138 bits (349), Expect = 5e-36
Identities = 54/116 (46%), Positives = 80/116 (68%), Gaps = 2/116 (1%)
Query: 315 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGVTSR 374
+KK +MEI++ GGSV +++ +A++ L + I + VF + +++D I VTKGKGF+GV R
Sbjct: 157 KKKPEIMEIRIGGGSVEERLEYAKELLGKEISISDVFKEGQLVDVIAVTKGKGFQGVVKR 216
Query: 375 WHTKKLPRKTH--KGLRKVACIGAWHPSRVQFTVARAGQKGYHHRTELNKKIYRMG 428
W K LPRK G R + +G W+PSRV +TV +AGQ G+H RTE NK+I ++G
Sbjct: 217 WGVKLLPRKHKRRGGSRHIGTLGPWNPSRVMWTVPQAGQMGFHQRTEYNKRILKIG 272
Score = 110 bits (277), Expect = 2e-26
Identities = 50/110 (45%), Positives = 63/110 (57%), Gaps = 15/110 (13%)
Query: 443 RWHTKKLPRKTH--KGLRKVACIGAWHPSRVQFTVARAGQKGYHHRTELFLCKKKYLSMV 500
RW K LPRK G R + +G W+PSRV +TV +AGQ G+H RTE K+ L
Sbjct: 216 RWGVKLLPRKHKRRGGSRHIGTLGPWNPSRVMWTVPQAGQMGFHQRTEY---NKRILK-- 270
Query: 501 IKNNASTDYDLTEKSITPMGGFPHYGEVNNDFLMIKGCCMGPKKRVITLR 550
I ++ ITP GGF HYG V ND+++IKG GP KR+I LR
Sbjct: 271 IGDDGD--------EITPKGGFLHYGLVRNDYVLIKGSVPGPAKRLIRLR 312
Score = 60.2 bits (147), Expect = 8e-10
Identities = 23/54 (42%), Positives = 39/54 (72%)
Query: 559 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGF 612
+KK +MEI++ GGSV +++ +A++ L + I + VF + +++D I VTKGKGF
Sbjct: 157 KKKPEIMEIRIGGGSVEERLEYAKELLGKEISISDVFKEGQLVDVIAVTKGKGF 210
>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3.
Length = 199
Score = 152 bits (385), Expect = 1e-42
Identities = 59/117 (50%), Positives = 69/117 (58%), Gaps = 13/117 (11%)
Query: 316 KKAHLMEIQLNGGSVADKIAWARQHLE--QPIPVGQVFAQDEMIDCIGVTKGKGFKGVTS 373
KAH+ME ++NGG + E Q I V VF + E +D GVTKGKGF+GV
Sbjct: 71 PKAHVMEFRVNGG----------EEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVMK 120
Query: 374 RWHTKKLPRKTHKG-LRKVACIGAWHPSRVQFTVARAGQKGYHHRTELNKKIYRMGA 429
RW K+LPRK +G RK IGAWHP RV V AGQ G HHRTE N KIYR+
Sbjct: 121 RWGFKRLPRKHGRGYHRKPGSIGAWHPGRVFPGVKMAGQMGNHHRTEQNLKIYRIDQ 177
Score = 97.0 bits (242), Expect = 4e-23
Identities = 41/112 (36%), Positives = 52/112 (46%), Gaps = 31/112 (27%)
Query: 440 VTSRWHTKKLPRKTHKG-LRKVACIGAWHPSRVQFTVARAGQKGYHHRTELFLCKKKYLS 498
V RW K+LPRK +G RK IGAWHP RV V AGQ G HHRTE L
Sbjct: 118 VMKRWGFKRLPRKHGRGYHRKPGSIGAWHPGRVFPGVKMAGQMGNHHRTEQNL------- 170
Query: 499 MVIKNNASTDYDLTEKSITPMGGFPHYGEVNNDFLMIKGCCMGPKKRVITLR 550
+ + + N+ L++KG GPKKR++T+R
Sbjct: 171 KIYRIDQE-----------------------NNLLLVKGSVPGPKKRLVTIR 199
Score = 94.3 bits (235), Expect = 3e-22
Identities = 60/221 (27%), Positives = 75/221 (33%), Gaps = 104/221 (47%)
Query: 87 KAGMTHIVREADRPGSKINKKEIVEAVTILETPPMVIVGVIGYVETPHGLRSFKTVWAEH 146
KAGMTHI KK ++E VT++E PPMV+V V Y ET
Sbjct: 1 KAGMTHIF---------TEKKGVLEPVTVIEVPPMVVVQVKTYEET-------------- 37
Query: 147 LSQECRRRFYKNWYKSRQKAFTKASKKWQDKLGKKTIAQDLRKMAKYCKVIRVIAHTQNQ 206
G K I L + KY V RV+ HTQ
Sbjct: 38 ------------------------------NDGYKAIQVGLESIKKYRVVKRVLGHTQ-- 65
Query: 207 QQSLHQNQQSHTKDQPIQSNVNKTQPDSHESHVQMKLLKKRQKKAHLMEIQLNGGSVADK 266
+ KAH+ME ++NGG
Sbjct: 66 -------------------------------------KRGTPPKAHVMEFRVNGG----- 83
Query: 267 IAWARQHLE--QPIPVGQVFAQDEMIDCIGVTKGKGFKGEM 305
+ E Q I V VF + E +D GVTKGKGF+G M
Sbjct: 84 -----EEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVM 119
Score = 59.3 bits (144), Expect = 5e-10
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 544 KRVITLRKMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLE--QPIPVGQVFAQDEMI 601
KRV+ + + KAH+ME ++NGG + E Q I V VF + E +
Sbjct: 58 KRVLGHTQKRGTPP---KAHVMEFRVNGG----------EEFEPGQTIAVSDVFREGEYV 104
Query: 602 DCIGVTKGKGFK 613
D GVTKGKGF+
Sbjct: 105 DVTGVTKGKGFQ 116
>gnl|CDD|234286 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model
describes exclusively the archaeal class of ribosomal
protein L3. A separate model (TIGR03625) describes the
bacterial/organelle form, and both belong to Pfam family
pfam00297. Eukaryotic proteins are excluded from this
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 330
Score = 154 bits (392), Expect = 4e-42
Identities = 78/260 (30%), Positives = 122/260 (46%), Gaps = 53/260 (20%)
Query: 44 SAPRHGSMGFYPKKRSARHRGKVKCFPKDDPTKPVHLTAFIGYKAGMTHIVREADRPGSK 103
PR GS+ F P+KR+ R +++ +P+ D L F GYKAGMTH++ DR S
Sbjct: 1 HRPRRGSLAFSPRKRAKRIVPRIRSWPEVD--GEPKLQGFAGYKAGMTHVIMVDDRKNSP 58
Query: 104 INKKEIVEAVTILETPPMVIVGVIGYVETPHGLRSFKTVWAEHLSQECRRRFYKNWYKSR 163
KEI VT+LE PP+ + + Y + P+GL+ VWA +L +E R+ +
Sbjct: 59 TEGKEISVPVTVLEAPPLRVAAIRAYGKDPYGLKVLTEVWANNLDKELSRKI------TL 112
Query: 164 QKAFTKASKKWQDKLGKKTIAQDLRKMAKYCKVIRVIAHTQNQQQSLHQNQQSHTKDQPI 223
K + K + + + A D +R+I HTQ + +
Sbjct: 113 PKNYDVEEKLEKIEELLENDADD----------VRLIVHTQPK----------------L 146
Query: 224 QSNVNKTQPDSHESHVQMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQV 283
+ V K +P+ +MEI++ GGSV ++ +A L + I V V
Sbjct: 147 VTGVPKKKPE-------------------IMEIRIGGGSVEERFEYALSILGKEISVSDV 187
Query: 284 FAQDEMIDCIGVTKGKGFKG 303
F + +++D I VTKGKGF+G
Sbjct: 188 FKEGQLVDVIAVTKGKGFQG 207
Score = 130 bits (330), Expect = 1e-33
Identities = 57/115 (49%), Positives = 77/115 (66%), Gaps = 2/115 (1%)
Query: 316 KKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGVTSRW 375
KK +MEI++ GGSV ++ +A L + I V VF + +++D I VTKGKGF+GV RW
Sbjct: 153 KKPEIMEIRIGGGSVEERFEYALSILGKEISVSDVFKEGQLVDVIAVTKGKGFQGVVKRW 212
Query: 376 HTKKLPRKT--HKGLRKVACIGAWHPSRVQFTVARAGQKGYHHRTELNKKIYRMG 428
K LPRK KG R + +G W PSRV++TV +AGQ GYH RTE NK+I ++G
Sbjct: 213 GVKLLPRKHKRRKGGRHIGTLGPWTPSRVRWTVPQAGQMGYHQRTEYNKRILKIG 267
Score = 107 bits (270), Expect = 1e-25
Identities = 56/140 (40%), Positives = 71/140 (50%), Gaps = 19/140 (13%)
Query: 440 VTSRWHTKKLPRKT--HKGLRKVACIGAWHPSRVQFTVARAGQKGYHHRTELFLCKKKYL 497
V RW K LPRK KG R + +G W PSRV++TV +AGQ GYH RTE K+ L
Sbjct: 208 VVKRWGVKLLPRKHKRRKGGRHIGTLGPWTPSRVRWTVPQAGQMGYHQRTEY---NKRIL 264
Query: 498 SMVIKNNASTDYDLTEKSITPMGGFPHYGEVNNDFLMIKGCCMGPKKRVITLRKMKLLKK 557
I + ITP GGF +YG V ND+++IKG GP KR+I LR
Sbjct: 265 K--IGEDGDE--------ITPKGGFVNYGLVRNDYVLIKGSVPGPSKRLIRLRD----AI 310
Query: 558 RQKKAHLMEIQLNGGSVADK 577
R K ++ S+ K
Sbjct: 311 RPPKPPEGAPEITYISLESK 330
Score = 55.0 bits (133), Expect = 4e-08
Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 545 RVITLRKMKLLKKR-QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDC 603
R+I + KL+ +KK +MEI++ GGSV ++ +A L + I V VF + +++D
Sbjct: 137 RLIVHTQPKLVTGVPKKKPEIMEIRIGGGSVEERFEYALSILGKEISVSDVFKEGQLVDV 196
Query: 604 IGVTKGKGF 612
I VTKGKGF
Sbjct: 197 IAVTKGKGF 205
>gnl|CDD|223165 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
structure and biogenesis].
Length = 218
Score = 119 bits (302), Expect = 6e-31
Identities = 39/118 (33%), Positives = 54/118 (45%), Gaps = 9/118 (7%)
Query: 315 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGVTSR 374
+ K HL E ++ GG VA+K ++ VF + E++D GVTKGKGF+GV R
Sbjct: 74 KPKRHLAEFRVGGGDVAEKFEVGQEIT------VDVFKEGELVDVTGVTKGKGFQGVMKR 127
Query: 375 WHTKKLPRKTHKGL--RKVACIG-AWHPSRVQFTVARAGQKGYHHRTELNKKIYRMGA 429
W K P L R+ IG P RV AG G T N ++ ++
Sbjct: 128 WGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEVVKVDV 185
Score = 68.4 bits (168), Expect = 4e-13
Identities = 29/115 (25%), Positives = 38/115 (33%), Gaps = 33/115 (28%)
Query: 440 VTSRWHTKKLPRKTHKGL--RKVACIG-AWHPSRVQFTVARAGQKGYHHRTELFLCKKKY 496
V RW K P L R+ IG P RV AG G T L
Sbjct: 124 VMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNL----- 178
Query: 497 LSMVIKNNASTDYDLTEKSITPMGGFPHYGEVNNDFLMIKGCCMGPKKRVITLRK 551
V+K D V N+ +++KG G KKR++ +R
Sbjct: 179 --EVVK------VD-----------------VENNLILVKGAVPGAKKRLVVVRP 208
Score = 56.8 bits (138), Expect = 4e-09
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
Query: 248 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGEM 305
+ K HL E ++ GG VA+K ++ VF + E++D GVTKGKGF+G M
Sbjct: 74 KPKRHLAEFRVGGGDVAEKFEVGQEIT------VDVFKEGELVDVTGVTKGKGFQGVM 125
Score = 54.1 bits (131), Expect = 3e-08
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 559 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGF 612
+ K HL E ++ GG VA+K ++ VF + E++D GVTKGKGF
Sbjct: 74 KPKRHLAEFRVGGGDVAEKFEVGQEIT------VDVFKEGELVDVTGVTKGKGF 121
Score = 51.8 bits (125), Expect = 2e-07
Identities = 25/67 (37%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 80 LTAFIGYKAGMTHIVREADRPGSKINKKEIVEAVTILETPPMVIVGVIGYVETPHGLRSF 139
+ F+GYK GMTH+ E I VT++E PP V+V V Y ET G R+
Sbjct: 1 MLGFLGYKVGMTHVFDERG----------ISVPVTVIEVPPNVVVQVKTY-ETD-GYRAV 48
Query: 140 KTVWAEH 146
V A
Sbjct: 49 -QVGAGD 54
>gnl|CDD|234285 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 40.9 bits (97), Expect = 7e-04
Identities = 27/92 (29%), Positives = 36/92 (39%), Gaps = 12/92 (13%)
Query: 345 IPVGQ-----VFAQDEMIDCIGVTKGKGFKGVTSRWHTKKLPRKTH---KGLRKVACIGA 396
VG +F + +D G +KGKGF GV R + P +H K R IG
Sbjct: 88 YEVGDEITVDIFEAGQKVDVTGTSKGKGFAGVMKRHNFSGGP-ASHGNSKSHRAPGSIGQ 146
Query: 397 --WHPSRVQFTVARAGQKGYHHRTELNKKIYR 426
P RV AG G T N ++ +
Sbjct: 147 RQT-PGRVFKGKKMAGHMGNERVTVQNLEVVK 177
Score = 30.9 bits (71), Expect = 1.6
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 278 IPVGQ-----VFAQDEMIDCIGVTKGKGFKGEM 305
VG +F + +D G +KGKGF G M
Sbjct: 88 YEVGDEITVDIFEAGQKVDVTGTSKGKGFAGVM 120
>gnl|CDD|234564 PRK00001, rplC, 50S ribosomal protein L3; Validated.
Length = 210
Score = 40.9 bits (97), Expect = 9e-04
Identities = 28/89 (31%), Positives = 38/89 (42%), Gaps = 10/89 (11%)
Query: 345 IPVGQ-----VFAQDEMIDCIGVTKGKGFKGVTSRWHTKKLPRKTH---KGLRKVACIGA 396
VGQ +F + +D G +KGKGF GV R + P +H + R+ IGA
Sbjct: 89 YEVGQEITVDIFEAGQKVDVTGTSKGKGFAGVIKRHNFSGGP-ASHGNSRSHRRPGSIGA 147
Query: 397 WH-PSRVQFTVARAGQKGYHHRTELNKKI 424
P RV AG G T N ++
Sbjct: 148 RQTPGRVFKGKKMAGHMGNERVTVQNLEV 176
Score = 31.6 bits (73), Expect = 0.92
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 8/37 (21%)
Query: 278 IPVGQ-----VFAQDEMIDCIGVTKGKGFKGEMIAMK 309
VGQ +F + +D G +KGKGF G +K
Sbjct: 89 YEVGQEITVDIFEAGQKVDVTGTSKGKGFAG---VIK 122
Score = 28.9 bits (66), Expect = 7.2
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 589 IPVGQ-----VFAQDEMIDCIGVTKGKGF 612
VGQ +F + +D G +KGKGF
Sbjct: 89 YEVGQEITVDIFEAGQKVDVTGTSKGKGF 117
>gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated.
Length = 207
Score = 36.1 bits (84), Expect = 0.027
Identities = 29/88 (32%), Positives = 39/88 (44%), Gaps = 9/88 (10%)
Query: 345 IPVGQV-----FAQDEMIDCIGVTKGKGFKGVTSRWHTKKLPRKTH--KGLRKVACIGA- 396
VGQ F+ ++++ G + GKGF G+ R + + P TH K R IGA
Sbjct: 91 FEVGQPLTVDAFSVGQLVNVSGKSIGKGFAGLQKRHNFSRGP-MTHGSKNHRAPGSIGAG 149
Query: 397 WHPSRVQFTVARAGQKGYHHRTELNKKI 424
P RV AG+ G T N KI
Sbjct: 150 TTPGRVYPGKKMAGRLGNKKVTIKNLKI 177
>gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in the type IA family of DNA topoisomerases
(TopoIA). This subgroup contains proteins similar to
the Type I DNA topoisomerases: E. coli topisomerases I
and III, eukaryotic topoisomerase III and, ATP-dependent
reverse gyrase found in archaea and thermophilic
bacteria. Type IA DNA topoisomerases remove (relax)
negative supercoils in the DNA. These enzymes cleave one
strand of the DNA duplex, covalently link to the 5'
phosphoryl end of the DNA break and allow the other
strand of the duplex to pass through the gap. Reverse
gyrase is also able to insert positive supercoils in the
presence of ATP and negative supercoils in the presence
of AMPPNP. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). For
topoisomerases the conserved glutamate is believed to
act as a general base in strand joining and, as a
general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 142
Score = 29.5 bits (67), Expect = 2.3
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 155 FYKNWYKSRQKAFTKASKKWQDKLGKKTIAQDLRKMAKYCKVIRVIA 201
Y +W K K+ KK + L+K+AK I V+A
Sbjct: 52 EYVDWDKDWPLELFPFEPKYVVIPDKKKQLKALKKLAKKADEI-VLA 97
>gnl|CDD|220625 pfam10191, COG7, Golgi complex component 7 (COG7). COG7 is a
component of the conserved oligomeric Golgi complex
which is required for normal Golgi morphology and
localisation. Mutation in COG7 causes a congenital
disorder of glycosylation.
Length = 768
Score = 30.9 bits (70), Expect = 2.7
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 244 LKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKG 303
L++ L + L G V+D + + LE+ + V A+ + CI +T+G G
Sbjct: 370 LEESNLSIQLSAVPLEGAEVSDCV----RELEESVAKVFVLAEAAVERCIKITQGLALCG 425
Query: 304 EMIAMKLLKKRQ 315
++A+ + +
Sbjct: 426 LILALDSIFLKY 437
Score = 30.1 bits (68), Expect = 4.6
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 311 LKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKG 367
L++ L + L G V+D + + LE+ + V A+ + CI +T+G
Sbjct: 370 LEESNLSIQLSAVPLEGAEVSDCV----RELEESVAKVFVLAEAAVERCIKITQGLA 422
Score = 30.1 bits (68), Expect = 4.6
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 555 LKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKG 611
L++ L + L G V+D + + LE+ + V A+ + CI +T+G
Sbjct: 370 LEESNLSIQLSAVPLEGAEVSDCV----RELEESVAKVFVLAEAAVERCIKITQGLA 422
>gnl|CDD|223607 COG0533, QRI7, Metal-dependent proteases with possible chaperone
activity [Posttranslational modification, protein
turnover, chaperones].
Length = 342
Score = 29.5 bits (67), Expect = 6.0
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 571 GGSVADKIAWARQHLEQPIPV-GQVFAQDEM----IDCIGVTKGKGFKECVHSNASCAK 624
G V ++A +R H+E P+ + A+ + ID I VT G G + A+ AK
Sbjct: 38 YGGVVPELA-SRHHVENIPPLIEEALAEAGVSLEDIDAIAVTAGPGLGGALLVGATAAK 95
>gnl|CDD|238097 cd00168, SCP, SCP: SCP-like extracellular protein domain, found in
eukaryotes and prokaryotes. This family includes plant
pathogenesis-related protein 1 (PR-1), which accumulates
after infections with pathogens, and may act as an
anti-fungal agent or be involved in cell wall loosening.
This family also includes CRISPs, mammalian
cysteine-rich secretory proteins, which combine SCP with
a C-terminal cysteine rich domain, and allergen 5 from
vespid venom. Roles for CRISP, in response to pathogens,
fertilization, and sperm maturation have been proposed.
One member, Tex31 from the venom duct of Conus textile,
has been shown to possess proteolytic activity sensitive
to serine protease inhibitors. The human GAPR-1 protein
has been reported to dimerize, and such a dimer may form
an active site containing a catalytic triad. SCP has
also been proposed to be a Ca++ chelating serine
protease. The Ca++-chelating function would fit with
various signaling processes that members of this family,
such as the CRISPs, are involved in, and is supported by
sequence and structural evidence of a conserved pocket
containing two histidines and a glutamate. It also may
explain how helothermine, a toxic peptide secreted by
the beaded lizard, blocks Ca++ transporting ryanodine
receptors. Little is known about the biological roles of
the bacterial and archaeal SCP domains.
Length = 122
Score = 27.8 bits (62), Expect = 7.3
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 392 ACIGAWHPSRVQFTVARAG-QKGYHHRTE-LNKKIYRMGAGIHT 433
A + AW+ + + G G H T+ + K ++G G+
Sbjct: 66 AAVQAWYNEIKNYNFGQPGFSSGTGHYTQVVWKNTTKIGCGVAF 109
>gnl|CDD|216553 pfam01528, Herpes_glycop, Herpesvirus glycoprotein M. The
herpesvirus glycoprotein M (gM) is an integral membrane
protein predicted to contain 8 transmembrane segments.
Glycoprotein M is not essential for viral replication.
Length = 374
Score = 28.8 bits (65), Expect = 8.6
Identities = 11/39 (28%), Positives = 15/39 (38%)
Query: 12 RKFSAPRHGSMGFYPKKRSARHRVKKASHRKFSAPRHGS 50
R + R S +Y R+ R VK R+ S S
Sbjct: 326 RAYLYHRRRSTRYYALVRTVRETVKSYKRRRRSKLSQAS 364
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.133 0.407
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,327,779
Number of extensions: 3002151
Number of successful extensions: 2596
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2570
Number of HSP's successfully gapped: 49
Length of query: 630
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 527
Effective length of database: 6,369,140
Effective search space: 3356536780
Effective search space used: 3356536780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.8 bits)