RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1131
(353 letters)
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 226 bits (578), Expect = 3e-72
Identities = 75/147 (51%), Positives = 101/147 (68%), Gaps = 6/147 (4%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPK-PSDLHLQCGYKVERHIRDGDLVIFN 144
++ +LVR G GAKYI+R G++ +L+ K HL+ G VERH+ DGD+V+FN
Sbjct: 154 KLRKLVRNGP---NGAKYIIR--GKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFN 208
Query: 145 RQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIH 204
RQPTLH+MS+ HRVRVL T R+N SPYNADFDGDEMNLHVPQS+E RAE +
Sbjct: 209 RQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELM 268
Query: 205 VTPRQIITPQNNRPVMGIVQDTLTAVR 231
+ P I++P+N +P++G +QD L +
Sbjct: 269 LVPNNILSPKNGKPIIGPIQDMLLGLY 295
Score = 196 bits (501), Expect = 9e-61
Identities = 62/120 (51%), Positives = 81/120 (67%), Gaps = 2/120 (1%)
Query: 226 TLTAVRKMTKRDVFL--DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNL 283
L +K + D VERH+ DGD+V+FNRQPTLH+MS+ HRVRVL T R+N
Sbjct: 176 NLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNP 235
Query: 284 SCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVR 343
SPYNADFDGDEMNLHVPQS+E RAE + + P I++P+N +P++G +QD L +
Sbjct: 236 LVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
Score = 121 bits (307), Expect = 3e-32
Identities = 43/86 (50%), Positives = 57/86 (66%), Gaps = 6/86 (6%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPK-PSDLHLQCGYKVERHIRDGDLVIFNR 59
+ +LVR G GAKYI+R G++ +L+ K HL+ G VERH+ DGD+V+FNR
Sbjct: 155 LRKLVRNGP---NGAKYIIR--GKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNR 209
Query: 60 QPTLHKMSMMGHRVRVLPWSTFRMNL 85
QPTLH+MS+ HRVRVL T R+N
Sbjct: 210 QPTLHRMSIQAHRVRVLEGKTIRLNP 235
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 205 bits (523), Expect = 2e-59
Identities = 80/175 (45%), Positives = 112/175 (64%), Gaps = 9/175 (5%)
Query: 73 VRVLPWSTFRMNL-RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL--HLQCGY 129
RV W N+ + E V G ++PGA Y++R +G RI L K +L L+ G+
Sbjct: 353 ERVTEW-----NIEELREYVLNGPEKHPGANYVIRPDGRRIKLTDKNK-EELAEKLEPGW 406
Query: 130 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLH 189
VERH+ DGD+V+FNRQP+LH+MS+M HRVRVLP TFR+NL+ PYNADFDGDEMNLH
Sbjct: 407 IVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLH 466
Query: 190 VPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE 244
VPQ+ E RAE + + I++P+ P++G +QD ++ +T++ K E
Sbjct: 467 VPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEE 521
Score = 170 bits (433), Expect = 4e-47
Identities = 57/97 (58%), Positives = 74/97 (76%)
Query: 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL 300
VERH+ DGD+V+FNRQP+LH+MS+M HRVRVLP TFR+NL+ PYNADFDGDEMNL
Sbjct: 406 WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNL 465
Query: 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
HVPQ+ E RAE + + I++P+ P++G +QD
Sbjct: 466 HVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQD 502
Score = 124 bits (315), Expect = 2e-31
Identities = 46/87 (52%), Positives = 62/87 (71%), Gaps = 3/87 (3%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL--HLQCGYKVERHIRDGDLVIFN 58
+ E V G ++PGA Y++R +G RI L K +L L+ G+ VERH+ DGD+V+FN
Sbjct: 363 LREYVLNGPEKHPGANYVIRPDGRRIKLTDKNK-EELAEKLEPGWIVERHLIDGDIVLFN 421
Query: 59 RQPTLHKMSMMGHRVRVLPWSTFRMNL 85
RQP+LH+MS+M HRVRVLP TFR+NL
Sbjct: 422 RQPSLHRMSIMAHRVRVLPGKTFRLNL 448
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 2, contains the active site. The
invariant motif -NADFDGD- binds the active site
magnesium ion.
Length = 165
Score = 187 bits (478), Expect = 5e-59
Identities = 66/128 (51%), Positives = 83/128 (64%), Gaps = 2/128 (1%)
Query: 77 PWSTFRMN-LRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHI 135
P ++N ++ +LV G + PGAKYI R G + DL + + + L G V RH+
Sbjct: 36 PEIVTKLNIKKLRKLVSNGPNVPPGAKYIKRIKGAKRDLEYKKR-IAIELWYGDIVLRHV 94
Query: 136 RDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSME 195
DGD+V+ NRQPTLH+MS+M HR RVL T R+N S SPYNADFDGDEMNLHVPQS E
Sbjct: 95 IDGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEE 154
Query: 196 TRAEVENI 203
RAE +
Sbjct: 155 ARAEAREL 162
Score = 153 bits (389), Expect = 7e-46
Identities = 51/89 (57%), Positives = 62/89 (69%)
Query: 227 LTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCT 286
L +++ + D V RH+ DGD+V+ NRQPTLH+MS+M HR RVL T R+N S
Sbjct: 74 LEYKKRIAIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVC 133
Query: 287 SPYNADFDGDEMNLHVPQSMETRAEVENI 315
SPYNADFDGDEMNLHVPQS E RAE +
Sbjct: 134 SPYNADFDGDEMNLHVPQSEEARAEAREL 162
Score = 121 bits (307), Expect = 1e-33
Identities = 40/85 (47%), Positives = 53/85 (62%), Gaps = 1/85 (1%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQ 60
+ +LV G + PGAKYI R G + DL + + + L G V RH+ DGD+V+ NRQ
Sbjct: 47 LRKLVSNGPNVPPGAKYIKRIKGAKRDLEYKKR-IAIELWYGDIVLRHVIDGDVVLLNRQ 105
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNL 85
PTLH+MS+M HR RVL T R+N
Sbjct: 106 PTLHRMSIMAHRPRVLEGKTIRLNP 130
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 193 bits (492), Expect = 3e-55
Identities = 80/174 (45%), Positives = 110/174 (63%), Gaps = 7/174 (4%)
Query: 73 VRVLPWSTFRMNL-RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL-HLQCGYK 130
RV PW N+ + E V G +PGA Y++R +G RI +R K L+ G+
Sbjct: 349 ERVTPW-----NIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEELAERLEPGWV 403
Query: 131 VERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHV 190
VERH+ DGD+V+FNRQP+LH+MSMMGH+V+VLP TFR+NL+ PYNADFDGDEMNLHV
Sbjct: 404 VERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 463
Query: 191 PQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE 244
PQ+ E RAE + + I+TP+ P++G + D ++ +T + K E
Sbjct: 464 PQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEE 517
Score = 158 bits (402), Expect = 6e-43
Identities = 58/110 (52%), Positives = 79/110 (71%)
Query: 243 VERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHV 302
VERH+ DGD+V+FNRQP+LH+MSMMGH+V+VLP TFR+NL+ PYNADFDGDEMNLHV
Sbjct: 404 VERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 463
Query: 303 PQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFL 352
PQ+ E RAE + + I+TP+ P++G + D ++ +T +
Sbjct: 464 PQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLF 513
Score = 116 bits (292), Expect = 2e-28
Identities = 45/86 (52%), Positives = 61/86 (70%), Gaps = 1/86 (1%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL-HLQCGYKVERHIRDGDLVIFNR 59
+ E V G +PGA Y++R +G RI +R K L+ G+ VERH+ DGD+V+FNR
Sbjct: 359 LREYVLNGPDSWPGANYVIRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNR 418
Query: 60 QPTLHKMSMMGHRVRVLPWSTFRMNL 85
QP+LH+MSMMGH+V+VLP TFR+NL
Sbjct: 419 QPSLHRMSMMGHKVKVLPGKTFRLNL 444
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 178 bits (453), Expect = 1e-49
Identities = 76/166 (45%), Positives = 104/166 (62%), Gaps = 7/166 (4%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL-------HLQCGYKVERHIRDG 138
+M ELV G ++PGA I + +G +I L F L+ G VERH+ DG
Sbjct: 372 KMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADG 431
Query: 139 DLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRA 198
D+VIFNRQP+LHK+S++ HRV+VLP +TFR++ + PYNADFDGDEMNLHVPQ + RA
Sbjct: 432 DIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARA 491
Query: 199 EVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE 244
E + +I+P+ P++G +QD +TA +TK D DK E
Sbjct: 492 EAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNE 537
Score = 148 bits (375), Expect = 2e-39
Identities = 60/113 (53%), Positives = 81/113 (71%)
Query: 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL 300
D VERH+ DGD+VIFNRQP+LHK+S++ HRV+VLP +TFR++ + PYNADFDGDEMNL
Sbjct: 422 DIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNL 481
Query: 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
HVPQ + RAE + +I+P+ P++G +QD +TA +TK D D
Sbjct: 482 HVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFD 534
Score = 102 bits (256), Expect = 7e-24
Identities = 42/91 (46%), Positives = 58/91 (63%), Gaps = 7/91 (7%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDL-------HLQCGYKVERHIRDGD 53
M ELV G ++PGA I + +G +I L F L+ G VERH+ DGD
Sbjct: 373 MKELVINGPDEFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGD 432
Query: 54 LVIFNRQPTLHKMSMMGHRVRVLPWSTFRMN 84
+VIFNRQP+LHK+S++ HRV+VLP +TFR++
Sbjct: 433 IVIFNRQPSLHKLSILAHRVKVLPGATFRLH 463
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 158 bits (401), Expect = 6e-43
Identities = 57/166 (34%), Positives = 78/166 (46%), Gaps = 18/166 (10%)
Query: 82 RMNLRMF--ELVRRGNSQY--PGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRD 137
+M L +F +V N + GAKY R R+ + V R + D
Sbjct: 314 KMALELFKPFVVTELNIEGLRTGAKYAKRMVERRLPE-------------VWDVLREVID 360
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLP-WSTFRMNLSCTSPYNADFDGDEMNLHVPQSMET 196
GD V+ NR PTLH++S+M VLP R++ YNADFDGDEM +HVP S E
Sbjct: 361 GDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEA 420
Query: 197 RAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 242
AE + T I+TP P++ +QDT+ +T D L
Sbjct: 421 AAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPS 466
Score = 154 bits (391), Expect = 1e-41
Identities = 48/131 (36%), Positives = 69/131 (52%), Gaps = 2/131 (1%)
Query: 224 QDTLTAVRKMTKRDV-FLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLP-WSTFRM 281
+ ++M +R + + V R + DGD V+ NR PTLH++S+M VLP R+
Sbjct: 334 RTGAKYAKRMVERRLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRL 393
Query: 282 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTA 341
+ YNADFDGDEM +HVP S E AE + T I+TP P++ +QDT+
Sbjct: 394 HPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGG 453
Query: 342 VRKMTKRDVFL 352
+T D L
Sbjct: 454 PYLLTIVDAKL 464
Score = 76.5 bits (189), Expect = 3e-15
Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 16/84 (19%)
Query: 3 ELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPT 62
EL G GAKY R R+ + V R + DGD V+ NR PT
Sbjct: 327 ELNIEGLRT--GAKYAKRMVERRLPE-------------VWDVLREVIDGDPVLLNRAPT 371
Query: 63 LHKMSMMGHRVRVLP-WSTFRMNL 85
LH++S+M VLP R++
Sbjct: 372 LHRLSIMQAFEPVLPEGKAIRLHP 395
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 68.9 bits (169), Expect = 1e-12
Identities = 35/127 (27%), Positives = 65/127 (51%), Gaps = 9/127 (7%)
Query: 226 TLTAVRKMTKR--DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNL 283
+ + +KM ++ D +E I++ V+ NR PTLH++ + ++ R++
Sbjct: 375 NIKSAKKMIEQEDPEVWDVLEDVIKEHP-VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHP 433
Query: 284 SCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT----- 338
+ +NADFDGD+M +HVP S E +AE + + I+ P++ +P++ QD
Sbjct: 434 LVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLY 493
Query: 339 -LTAVRK 344
LT +
Sbjct: 494 YLTTEKP 500
Score = 68.5 bits (168), Expect = 1e-12
Identities = 30/98 (30%), Positives = 52/98 (53%), Gaps = 6/98 (6%)
Query: 141 VIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEV 200
V+ NR PTLH++ + ++ R++ + +NADFDGD+M +HVP S E +AE
Sbjct: 403 VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEA 462
Query: 201 ENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRK 232
+ + I+ P++ +P++ QD LT +
Sbjct: 463 RALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKP 500
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 64.6 bits (158), Expect = 1e-12
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 209 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVE 244
I++PQN +P++G QD + + +T+RD F D+ E
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREE 36
Score = 62.6 bits (153), Expect = 6e-12
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 321 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
I++PQN +P++G QD + + +T+RD F D
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFD 33
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 67.7 bits (165), Expect = 2e-12
Identities = 34/119 (28%), Positives = 63/119 (52%), Gaps = 2/119 (1%)
Query: 220 MGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF 279
GIV + A + + + D + V + + G V+ NR PTLH++ + ++
Sbjct: 389 QGIVNNIKAAKKLIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAI 448
Query: 280 RMN-LSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
+++ L C + +NADFDGD+M +HVP S+E + E + + +++P P++ QD
Sbjct: 449 QLHPLVCPA-FNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQD 506
Score = 63.5 bits (154), Expect = 5e-11
Identities = 29/98 (29%), Positives = 54/98 (55%), Gaps = 2/98 (2%)
Query: 129 YKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMN-LSCTSPYNADFDGDEMN 187
+ V + + G V+ NR PTLH++ + ++ +++ L C + +NADFDGD+M
Sbjct: 410 WSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPA-FNADFDGDQMA 468
Query: 188 LHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 225
+HVP S+E + E + + +++P P++ QD
Sbjct: 469 VHVPLSLEAQTEARLLMLASNNVLSPATGEPIVTPSQD 506
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 66.5 bits (163), Expect = 5e-12
Identities = 34/127 (26%), Positives = 62/127 (48%), Gaps = 16/127 (12%)
Query: 221 GIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMM--------GHRVR 272
+ + A K+ +++ + ++ + + G V+ NR PTLH++ + G +
Sbjct: 418 HLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAIC 477
Query: 273 VLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVM 332
+ P L C +NADFDGD+M +HVP S+E +AE + + +++P P+
Sbjct: 478 LHP-------LVCKG-FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPIS 529
Query: 333 GIVQDTL 339
QD L
Sbjct: 530 VPSQDML 536
Score = 58.0 bits (141), Expect = 3e-09
Identities = 32/106 (30%), Positives = 53/106 (50%), Gaps = 16/106 (15%)
Query: 130 KVERHIRDGDLVIFNRQPTLHKMSMM--------GHRVRVLPWSTFRMNLSCTSPYNADF 181
++ + + G V+ NR PTLH++ + G + + P L C +NADF
Sbjct: 439 EILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP-------LVCKG-FNADF 490
Query: 182 DGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTL 227
DGD+M +HVP S+E +AE + + +++P P+ QD L
Sbjct: 491 DGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDML 536
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 66.2 bits (161), Expect = 9e-12
Identities = 37/124 (29%), Positives = 68/124 (54%), Gaps = 11/124 (8%)
Query: 141 VIFNRQPTLHKMSMMGHRVRVLPWSTFRMN-LSCTSPYNADFDGDEMNLHVPQSMETRAE 199
V+ NR PTLH++ + ++ +++ L CT+ +NADFDGD+M +HVP S+E + E
Sbjct: 1854 VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTA-FNADFDGDQMAVHVPISLEAQLE 1912
Query: 200 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD---------KVERHIRDG 250
+ ++ +++P N RP++ +D + + +T ++ D +VE + DG
Sbjct: 1913 ARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKEDDLPSFGAFCEVEHSLSDG 1972
Query: 251 DLVI 254
L I
Sbjct: 1973 TLHI 1976
Score = 65.0 bits (158), Expect = 2e-11
Identities = 30/95 (31%), Positives = 57/95 (60%), Gaps = 2/95 (2%)
Query: 253 VIFNRQPTLHKMSMMGHRVRVLPWSTFRMN-LSCTSPYNADFDGDEMNLHVPQSMETRAE 311
V+ NR PTLH++ + ++ +++ L CT+ +NADFDGD+M +HVP S+E + E
Sbjct: 1854 VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTA-FNADFDGDQMAVHVPISLEAQLE 1912
Query: 312 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMT 346
+ ++ +++P N RP++ +D + + +T
Sbjct: 1913 ARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLT 1947
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 64.1 bits (156), Expect = 4e-11
Identities = 39/113 (34%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMN-LSCTSPYNADFDGDEMN 299
D +E I+D V+ NR PTLH++ + ++ +++ L CT +NADFDGD+M
Sbjct: 488 DVLEEVIQD-HPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCT-AFNADFDGDQMA 545
Query: 300 LHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMT-KRDVF 351
+HVP S + +AE + ++ I +P + RP+ QD + V +T +RD F
Sbjct: 546 VHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGF 598
Score = 63.7 bits (155), Expect = 6e-11
Identities = 35/104 (33%), Positives = 58/104 (55%), Gaps = 3/104 (2%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMN-LSCTSPYNADFDGDEMNLHVPQSMET 196
V+ NR PTLH++ + ++ +++ L CT +NADFDGD+M +HVP S +
Sbjct: 496 DHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCT-AFNADFDGDQMAVHVPLSTQA 554
Query: 197 RAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMT-KRDVF 239
+AE + ++ I +P + RP+ QD + V +T +RD F
Sbjct: 555 QAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGF 598
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 62.5 bits (152), Expect = 1e-10
Identities = 36/118 (30%), Positives = 65/118 (55%), Gaps = 2/118 (1%)
Query: 221 GIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFR 280
GIV + A + + + D + +V + +G V+ NR PTLH++ + ++ +
Sbjct: 397 GIVNNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQ 456
Query: 281 MN-LSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
++ L C + +NADFDGD+M +HVP S+E +AE + + I++P P++ QD
Sbjct: 457 LHPLVCPA-FNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
Score = 59.8 bits (145), Expect = 9e-10
Identities = 30/90 (33%), Positives = 52/90 (57%), Gaps = 2/90 (2%)
Query: 137 DGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMN-LSCTSPYNADFDGDEMNLHVPQSME 195
+G V+ NR PTLH++ + ++ +++ L C + +NADFDGD+M +HVP S+E
Sbjct: 425 EGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPA-FNADFDGDQMAVHVPLSLE 483
Query: 196 TRAEVENIHVTPRQIITPQNNRPVMGIVQD 225
+AE + + I++P P++ QD
Sbjct: 484 AQAEARLLMLASNNILSPATGEPIVTPSQD 513
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 61.5 bits (149), Expect = 3e-10
Identities = 32/93 (34%), Positives = 52/93 (55%)
Query: 133 RHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 192
+ I +G V+ NR PTLHK S+ +++ +++ S +NADFDGD+M +HVP
Sbjct: 1802 QEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPL 1861
Query: 193 SMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 225
S E AE + + ++ I+ P + + V QD
Sbjct: 1862 SQEAIAECKVLMLSSMNILLPASGKAVAIPSQD 1894
Score = 61.5 bits (149), Expect = 3e-10
Identities = 32/93 (34%), Positives = 52/93 (55%)
Query: 245 RHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 304
+ I +G V+ NR PTLHK S+ +++ +++ S +NADFDGD+M +HVP
Sbjct: 1802 QEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPL 1861
Query: 305 SMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
S E AE + + ++ I+ P + + V QD
Sbjct: 1862 SQEAIAECKVLMLSSMNILLPASGKAVAIPSQD 1894
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 57.0 bits (139), Expect = 7e-09
Identities = 45/134 (33%), Positives = 72/134 (53%), Gaps = 32/134 (23%)
Query: 220 MGIVQDTLTAVRKMTKR------DVFLDKVERHIRDGDLVIFNRQPTLHKMSMM------ 267
G+ T+ + +KM +R DV L++V I+ V+ NR PTLH++ +
Sbjct: 378 RGLAT-TIKSAKKMVEREDPEVWDV-LEEV---IK-EHPVLLNRAPTLHRLGIQAFEPVL 431
Query: 268 --GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITP 325
G +++ P L CT +NADFDGD+M +HVP S+E +AE + ++ I++P
Sbjct: 432 IEGKAIQLHP-------LVCT-AFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSP 483
Query: 326 QNNRPVMGIV--QD 337
N +P+ IV QD
Sbjct: 484 ANGKPI--IVPSQD 495
Score = 55.1 bits (134), Expect = 3e-08
Identities = 35/95 (36%), Positives = 54/95 (56%), Gaps = 20/95 (21%)
Query: 141 VIFNRQPTLHKMSMM--------GHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 192
V+ NR PTLH++ + G +++ P L CT +NADFDGD+M +HVP
Sbjct: 411 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP-------LVCT-AFNADFDGDQMAVHVPL 462
Query: 193 SMETRAEVENIHVTPRQIITPQNNRPVMGIV--QD 225
S+E +AE + ++ I++P N +P+ IV QD
Sbjct: 463 SLEAQAEARVLMLSSNNILSPANGKPI--IVPSQD 495
>gnl|CDD|236918 PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional.
Length = 852
Score = 29.2 bits (66), Expect = 3.9
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 62 TLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPS 121
T+ S G +++ + ++ L++RG +Y + R G + L+ P +
Sbjct: 707 TVQDFSDGGLGIKINGQAQLLEGQKVNLLLKRGQQEYVFPTQVTRVMGNEVGLQLMPLTT 766
Query: 122 DLHL---QC 127
H+ QC
Sbjct: 767 QQHIDFVQC 775
>gnl|CDD|234862 PRK00912, PRK00912, ribonuclease P protein component 3;
Provisional.
Length = 237
Score = 28.4 bits (64), Expect = 4.6
Identities = 24/97 (24%), Positives = 35/97 (36%), Gaps = 20/97 (20%)
Query: 143 FNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD----------FD----GDEMNL 188
FN + L S G R R L S FR NL+ Y+ +D + + L
Sbjct: 136 FNLRDILK--SRGGRRARTL--SNFRDNLALARKYDFPLVLTSGAMSCYDLRSPREMIAL 191
Query: 189 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 225
ME ++ + P II + NR V +
Sbjct: 192 AELFGMEEDEALKALSYYPESII--KKNRNRKNYVIE 226
Score = 28.4 bits (64), Expect = 4.6
Identities = 24/97 (24%), Positives = 35/97 (36%), Gaps = 20/97 (20%)
Query: 255 FNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNAD----------FD----GDEMNL 300
FN + L S G R R L S FR NL+ Y+ +D + + L
Sbjct: 136 FNLRDILK--SRGGRRARTL--SNFRDNLALARKYDFPLVLTSGAMSCYDLRSPREMIAL 191
Query: 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
ME ++ + P II + NR V +
Sbjct: 192 AELFGMEEDEALKALSYYPESII--KKNRNRKNYVIE 226
>gnl|CDD|187601 cd05343, Mgc4172-like_SDR_c, human Mgc4172-like, classical (c)
SDRs. Human Mgc4172-like proteins, putative SDRs. These
proteins are members of the SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 28.6 bits (64), Expect = 5.0
Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 26/73 (35%)
Query: 46 ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLRMFELVRRGNSQYPGAKYIV 105
ER++ DG ++ N SM GHRV + F Y K+ V
Sbjct: 132 ERNVDDGHIININ--------SMSGHRVPPVSVFHF----------------YAATKHAV 167
Query: 106 R--DNGERIDLRF 116
G R +LR
Sbjct: 168 TALTEGLRQELRE 180
>gnl|CDD|235728 PRK06184, PRK06184, hypothetical protein; Provisional.
Length = 502
Score = 28.4 bits (64), Expect = 5.8
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 72 RVRVLPW-STFRMNLRMFELVRRGN 95
R+ + W S FRMN R+ + R G
Sbjct: 258 RLHSVTWASAFRMNARLADRYRVGR 282
>gnl|CDD|218386 pfam05021, NPL4, NPL4 family. The HRD4 gene was identical to NPL4,
a gene previously implicated in nuclear transport. Using
a diverse set of substrates and direct ubiquitination
assays, analysis revealed that HRD4/NPL4 is required for
a poorly characterized step in ER-associated degradation
after ubiquitination of target proteins but before their
recognition by the 26S proteasome. Npl4p physically
associates with Cdc48p via Ufd1p to form a
Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex
functions in the recognition of several
polyubiquitin-tagged proteins and facilitates their
presentation to the 26S proteasome for processive
degradation or even more specific processing.
Length = 306
Score = 28.0 bits (63), Expect = 6.9
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 213 PQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMG 268
P NR MG QD L A+ K K +ER + D L++F L K+ ++
Sbjct: 222 PIENREAMGESQD-LRALAKYLKSHKPKPFLER-LSDFHLLLF-----LAKLGILD 270
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 28.1 bits (63), Expect = 8.3
Identities = 20/119 (16%), Positives = 30/119 (25%), Gaps = 14/119 (11%)
Query: 144 NRQPTLHKMSMMGHRVRV-----LPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRA 198
R G R S+ M + LH P E
Sbjct: 342 ERCAWRLCKQEPGEDYRRPALDHASLSSVEMRAKDGGRGLESPTERQRLLHSPPPAEGDL 401
Query: 199 EVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDV-FLDKVERHIRDGDLVIFN 256
++ I R R +D V + K +DK+ R ++FN
Sbjct: 402 DLAGILEEVRIA---HRFRK-----RDESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFN 452
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
0.324 0.138 0.426
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,435,728
Number of extensions: 1785524
Number of successful extensions: 2146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2122
Number of HSP's successfully gapped: 53
Length of query: 353
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 255
Effective length of database: 6,590,910
Effective search space: 1680682050
Effective search space used: 1680682050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.3 bits)