RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7582
(661 letters)
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 529 bits (1364), Expect = e-175
Identities = 248/655 (37%), Positives = 355/655 (54%), Gaps = 73/655 (11%)
Query: 7 WIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLL 66
W V+ AYF EKGLVRQ LDS+++FI+ +Q IV++ +I + E P +
Sbjct: 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEI-----------KTEIPG-LKI 49
Query: 67 KFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQK 126
+I + +P E DGS P+ P EARLRNLTY+APLY+ + V G E ++
Sbjct: 50 VLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMI--PVENGIEYEP---EE 104
Query: 127 SFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVY 186
IG +PIM++S C L+GL+ +L E+ E P DPGGYFIINGSE+V+++QE +A N V
Sbjct: 105 VKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVL 164
Query: 187 VFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQE 246
V K + T + + + + V G I P + +
Sbjct: 165 V--DKGEAGSSITHTAKVISSRAGYRAQVTVERRKDG-----------TIYVSFPAVPGK 211
Query: 247 IPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAF-VIQEQNVALNFIGARG 305
IP +I+ RALG DRDI+ + DPE+ + + PSL++A + AL++IG R
Sbjct: 212 IPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASSIAATVEDALDYIGKRV 268
Query: 306 ARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDR 365
A G +E RI+ A +IL K +LPH+G S KKAYFLG M +LL LGRRE DD+
Sbjct: 269 A-IGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDK 327
Query: 366 DHY--------------------------VRMYAQKFIDRGKDFNLELAIKTKIITDGLR 399
DHY ++ +K RG+ +L ++ IIT+ +R
Sbjct: 328 DHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIR 387
Query: 400 YSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTL 459
++LATGNW R GVSQ+L+R + S+LSHLRRV SP+ R + R LH T
Sbjct: 388 HALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQ 441
Query: 460 WGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADAT 519
WG ICP ETPEG GLVKNLALMA ISVG + E L E + +EE +
Sbjct: 442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWS 501
Query: 520 KIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSI--IRDIRDREIRIHTDAGRICR 577
++++NG +G H D E+L +R+LRR I EV++ I E+ ++ D+GR+ R
Sbjct: 502 RVYLNGRLIGYHPDGEELAEKIRELRRSGK-ISDEVNVAYIETGEINEVYVNCDSGRVRR 560
Query: 578 PLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMW 632
PL++ ENG L + H++ LK+ + + LV+ GV+EY+D EEE +A+
Sbjct: 561 PLIVVENGKPKLTREHVEKLKKGELT---FDDLVKMGVIEYLDAEEEENAYVALD 612
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 420 bits (1083), Expect = e-134
Identities = 175/679 (25%), Positives = 278/679 (40%), Gaps = 121/679 (17%)
Query: 3 QEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPP 62
+ I + D LV QLDS++ F +Q + + I
Sbjct: 11 IRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPI------------ESYNG 58
Query: 63 RYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTT 122
L++ L +P P E RLR LTYSAPLYV + V GEE
Sbjct: 59 NTELEYGSYRLGEP---------PKFYPEECRLRGLTYSAPLYVKLRLVVNETGEEI--- 106
Query: 123 QHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMAT 182
+ Q+ ++G IP+M R GGYFIING+E+V+++QE +
Sbjct: 107 KEQEVYMGDIPLMTR------------------------GGYFIINGTERVIVSQEHRSP 142
Query: 183 NTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPY 242
++V KD + + + R S L + + +
Sbjct: 143 GVIFVEK-KDKTGSKVLYVARVI--PYRG-SWLEFEFDPK------------DNLYVRID 186
Query: 243 IKQEIPIMIVFRALGFVADRDILEHI----IYDFDDPEMMEMVKPSLDEA--FVIQEQNV 296
K++IP+ I+ RALG D +I+E + D PE E + +EA I +N
Sbjct: 187 RKRKIPVTILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKITARN- 245
Query: 297 ALNFIGARGARPGVTKER--RIKYAREILQKEMLPHVGVS----DFCETKKAYFLGYMVH 350
AL IG+R + R K A+ +L KE+LPH+G + D KA + M+
Sbjct: 246 ALELIGSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIK 305
Query: 351 RLLLASLGRRELDDRDHY----VR----MYAQKF---IDR---------GKDFNLELAIK 390
L+ LG+ E DD DH +R + F + R K + +
Sbjct: 306 YLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKADKRDTLVP 365
Query: 391 TKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS-PIGRDGKL 449
+I ++L TG +G R+ +SQ +++ S LSH RR+++ + R+
Sbjct: 366 QDLINAKPIHALITGFFG--------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAG 417
Query: 450 AKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYIS-VGSQPSPILEFL-EEWSMENL 507
+ R +H T +G ICP ETPEG +GL+K+LAL A I+ G +P + L ++ +
Sbjct: 418 FEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEI 477
Query: 508 EEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIR-DIRDREI 566
E + AD ++V G G +P +L+ L + RR VS D D
Sbjct: 478 EYL----SADEEDVYVIGQANGTLDEPGELVEELVECRRGGSGEVSVADPEGVDYMDVSP 533
Query: 567 RIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEET 626
+ GR P L ++ + L ++ LV +G +EY+D +
Sbjct: 534 KQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLL--RTEAPLVGTG-MEYLDAEDSGA 590
Query: 627 TMIAMWQVLVQSGVVEYID 645
+IA GVV +++
Sbjct: 591 AVIAKR-----PGVVTHVE 604
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit. 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
forms one of the two distinctive lobes of the Rpb2
structure. This domain is also known as the protrusion
domain. The other lobe (pfam04561) is nested within this
domain.
Length = 394
Score = 385 bits (992), Expect = e-129
Identities = 161/415 (38%), Positives = 216/415 (52%), Gaps = 48/415 (11%)
Query: 18 GLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPT 77
GLV QQLDSF+ F+ +Q +++ P I+ + E P + LK QI L+KP
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDE----------EPEFSLKVGQIKLAKPK 50
Query: 78 HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLR 137
E DG + P EARLRNLTYS+PLYV TV E + +K FIGKIP+MLR
Sbjct: 51 IKESDGKTREIYPREARLRNLTYSSPLYVPAELTVNNTEEI----EKEKVFIGKIPLMLR 106
Query: 138 STYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSM-KDSKYA 196
S C+LNG ++ +L +L ECPLDPGGYFI+NGSEKV+I Q + + N YVF K+
Sbjct: 107 SNACILNGASESELVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRI 166
Query: 197 YKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRAL 256
Y I S S R T + S K + ++A+ + + I ++V
Sbjct: 167 YSASIISNRGRSLRLEIT-SKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVD 225
Query: 257 GFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRI 316
+ D + +F KP L+E FVIQ Q+ AL++IG RG+ G +ERRI
Sbjct: 226 LEIQDDIGINDEEDEFLTD------KPELEEQFVIQTQDEALDYIGGRGSAKGFPRERRI 279
Query: 317 KYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHY-------- 368
A IL +LPH+GVS+ T KA +GYM+HRLLL +LGR LDD DH
Sbjct: 280 LGAVGILDLNLLPHLGVSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLA 339
Query: 369 ------------------VRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATG 405
VR QK + + DF L+ + +K IT G+RY L TG
Sbjct: 340 GELLQSQFRILLNRLERDVRERIQKCLKKKFDFTLQNLVNSKPITSGIRYFLGTG 394
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 368 bits (946), Expect = e-121
Identities = 191/526 (36%), Positives = 283/526 (53%), Gaps = 76/526 (14%)
Query: 7 WIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLL 66
++ +AYF E LVR +DS+++F+ +Q+I+++ I E E +
Sbjct: 6 RVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPI-----------ETEIEDGVYV 54
Query: 67 KFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGE--EPVTTQH 124
+ +I + KP E DGS + P EARLRNLTYSAPLY++++ V GE EP
Sbjct: 55 ELGKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMS--PVEGGEEEEPEEVY- 111
Query: 125 QKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNT 184
IG++P+M+ S C L GL++ +L E+ E PLDPGGYFI+NGSE+VL+ E +A N
Sbjct: 112 ----IGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNK 167
Query: 185 VYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRII--AILPY 242
+ V KD +Y + E+ S R RG ++L + + P
Sbjct: 168 ILV--EKDERYGDRIEVAKVF--SQR-----------RGYRALVTVERNRDGLLEVSFPS 212
Query: 243 IKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIG 302
+ IP +I+ RALG D +I+E + DDPE+++ + +L+EA + Q AL +IG
Sbjct: 213 VPGSIPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIG 268
Query: 303 ARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRREL 362
R A PG TKE RIK A ++ + +LPH+GV KA++LG M +LGRRE
Sbjct: 269 KRVA-PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREE 327
Query: 363 DDRDHY--------------------------VRMYAQKFIDRGKDFNLELAIKTKIITD 396
DD+DHY V+ ++ R ++ +++ A+++ ++T+
Sbjct: 328 DDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTE 387
Query: 397 GLRYSLATGNW-GDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQL 455
L +++ATGNW G R GVSQ+L+R + ++LSHLRRV SP+ R + R L
Sbjct: 388 RLEHAMATGNWVG-------GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDL 440
Query: 456 HNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEE 501
H T WG ICP+ETPEG GLVKN A M IS G + E L+E
Sbjct: 441 HPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit. RNA
polymerases catalyse the DNA dependent polymerization of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Each RNA
polymerase complex contains two related members of this
family, in each case they are the two largest
subunits.The clamp is a mobile structure that grips DNA
during elongation.
Length = 866
Score = 228 bits (584), Expect = 2e-64
Identities = 103/261 (39%), Positives = 134/261 (51%), Gaps = 32/261 (12%)
Query: 19 LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTH 78
LV+QQ+DSF+ F+ + +Q IV+ P I + R LKF IYL KP
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKV 50
Query: 79 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRS 138
E G + PNE RLR+LTYSAPLYVDI TV +G+ + Q+ FIG+IPIMLRS
Sbjct: 51 EE-GGVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRS 105
Query: 139 TYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYK 198
C LNGLT +L +L ECPLDPGGYFIING+EKV+I QE+ + N + V DSK
Sbjct: 106 KLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE---DSKGKRI 162
Query: 199 TEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIV---FRA 255
S +S S L V + RI + +QE + + F
Sbjct: 163 YTKTSIPSYSPYRGSWLEVKSDKK----------KDRIYVRIDLKRQEEALKYIGKRFED 212
Query: 256 LGFVADRDI-LEHIIYDFDDP 275
L ++ + I L DD
Sbjct: 213 LIYMIRKLILLVLGKGKLDDI 233
Score = 205 bits (523), Expect = 2e-56
Identities = 73/175 (41%), Positives = 97/175 (55%), Gaps = 28/175 (16%)
Query: 340 KKAYFLGYMVHRLLLASLGRRELDDRDHY--------------------------VRMYA 373
K+ L YM+ +L+L LG+ +LDD DH V+
Sbjct: 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKL 267
Query: 374 QKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSL 433
QK + + KD +L I +K IT G++ LATGNWG ++ R+G+SQVL+RL S L
Sbjct: 268 QKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSEL 326
Query: 434 SHLRRVNS-PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYIS 487
SH RR++S + R+ K + R LH + WG ICP ETPEG GLVKNLALMA IS
Sbjct: 327 SHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, 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). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain forms one of the two distinctive lobes of the
Rpb2 structure. This domain is also known as the lobe
domain. DNA has been demonstrated to bind to the concave
surface of the lobe domain, and plays a role in
maintaining the transcription bubble. Many of the
bacterial members contain large insertions within this
domain, as region known as dispensable region 1 (DRI).
Length = 185
Score = 170 bits (433), Expect = 2e-49
Identities = 65/196 (33%), Positives = 102/196 (52%), Gaps = 25/196 (12%)
Query: 181 ATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQR-IIAI 239
+N +YV D + + + + + S K I + +I
Sbjct: 1 RSNGIYVEKELD--------------KNGIGAT--YTSSLISNRGSWLKLEIDGKTLIWS 44
Query: 240 LPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALN 299
P K++IPI+I +ALG V+DR+IL+ + YDF+DP+M+E++KP L+EA I Q AL+
Sbjct: 45 RPSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALD 104
Query: 300 FIGARGARPGVTKERRIKYAREILQK-----EMLPHVGVSDFCETK--KAYFLGYMVHRL 352
+IG +E R++ AREIL + H+G+++ E + KA + YM+ RL
Sbjct: 105 YIGKGF-ALRRGEEPRLQRAREILYSRDPKYNLNKHLGLNEPFENERLKAQDILYMIDRL 163
Query: 353 LLASLGRRELDDRDHY 368
L LGRR+ DD DH
Sbjct: 164 LNLKLGRRKPDDIDHL 179
>gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4. 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). Domain 4,
is also known as the external 2 domain.
Length = 63
Score = 111 bits (279), Expect = 1e-29
Identities = 41/64 (64%), Positives = 53/64 (82%), Gaps = 1/64 (1%)
Query: 521 IFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLL 580
++VNG VG HR+PE+L+ TLR+LRR+ I EVS++R+IR REIRI+TDAGRICRPL+
Sbjct: 1 VYVNGKLVGTHRNPEELVETLRELRRKGKI-SPEVSVVRNIRQREIRINTDAGRICRPLI 59
Query: 581 IAEN 584
I EN
Sbjct: 60 IVEN 63
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, 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). Domain 3, s
also known as the fork domain and is proximal to
catalytic site.
Length = 68
Score = 100 bits (250), Expect = 1e-25
Identities = 33/68 (48%), Positives = 44/68 (64%), Gaps = 2/68 (2%)
Query: 422 QVLNRLTFASSLSHLRRVN--SPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKN 479
QVL++ + S LSH RRVN + ++ K + R LH + +G ICP ETPEGA GLV +
Sbjct: 1 QVLDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNS 60
Query: 480 LALMAYIS 487
LAL A I+
Sbjct: 61 LALYARIN 68
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B. This
model represents the archaeal version of DNA-directed
RNA polymerase subunit B (rpoB) and is observed in all
archaeal genomes.
Length = 599
Score = 108 bits (273), Expect = 8e-25
Identities = 46/112 (41%), Positives = 68/112 (60%), Gaps = 4/112 (3%)
Query: 521 IFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLL 580
+++NG +G H DPE+L+ +RKLRR + EV++ E+ I+ DAGRI RPL+
Sbjct: 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLI 59
Query: 581 IAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMW 632
+ ENG L + H++ LKE + W LV+ GV+EY+D EEE IA+
Sbjct: 60 VVENGKPKLTREHVEKLKEGELT---WDDLVKQGVIEYLDAEEEENAYIALD 108
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 106 bits (267), Expect = 5e-24
Identities = 54/142 (38%), Positives = 79/142 (55%), Gaps = 15/142 (10%)
Query: 519 TKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRP 578
K++VNG +G H DPE+L+ +R+ RR +I EV++ E+ I+TDAGR RP
Sbjct: 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEI-SEEVNVSYKEETNEVIINTDAGRARRP 63
Query: 579 LLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQS 638
L++ ENG LL + HI+ LK + + LV+ GV+EY+D EEE IA+
Sbjct: 64 LIVVENGEPLLTEEHIEKLKNGELT---FDDLVKQGVIEYLDAEEEENAYIAV------- 113
Query: 639 GVVEYIDTLEEETTMIAMSPRL 660
Y + L EE T + + P L
Sbjct: 114 ----YEEDLTEEHTHLEIDPSL 131
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 65.5 bits (161), Expect = 5e-11
Identities = 71/328 (21%), Positives = 122/328 (37%), Gaps = 107/328 (32%)
Query: 23 QLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWEKD 82
QLDSFD F+Q+ V L+ + + L+F L +P + +
Sbjct: 31 QLDSFDWFLQLDVPP-----EDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVE- 84
Query: 83 GSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
E + R LTYSAPL V + GE + Q+ ++G IP+M
Sbjct: 85 ---------ECKERGLTYSAPLRVKLRLINKETGE----IKEQEVYMGDIPLM------- 124
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIR 202
T+ G FIING+E+V+++Q R
Sbjct: 125 ----TEN-------------GTFIINGTERVIVSQ----------------------LHR 145
Query: 203 S---CLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYI---------------- 243
S +H TS+ G+ L + RII PY
Sbjct: 146 SPGVYFDHDKDKTSS---------GKLLYSA----RII---PYRGSWLEFEFDPKDILYV 189
Query: 244 ----KQEIPIMIVFRALGFVADRDILEHIIYDFDD-PEMMEMVKPSLDEAFVIQEQNVAL 298
++++P+ ++ RALG+ +D +IL+ + Y+ ++ + +E+ L + ++
Sbjct: 190 RIDRRRKLPVTVLLRALGY-SDEEILD-LFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEE 247
Query: 299 NFIGARGARPGVTKERRIKYAREILQKE 326
A +T+E Y R L+K+
Sbjct: 248 TGEVLAEANDEITEELDGPYIRNTLEKD 275
Score = 39.3 bits (93), Expect = 0.007
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 20/66 (30%)
Query: 431 SSLSHLRRVNS--PIG----------RDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVK 478
S L+H RR+++ P G RD +H T +G ICP ETPEG +GL+
Sbjct: 443 SELTHKRRLSALGPGGLTRERAGFEVRD--------VHPTHYGRICPIETPEGPNIGLIN 494
Query: 479 NLALMA 484
+LA A
Sbjct: 495 SLATYA 500
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of
two alpha chains, one beta chain, and one beta' subunit
[Transcription, DNA-dependent RNA polymerase].
Length = 1065
Score = 63.6 bits (155), Expect = 2e-10
Identities = 57/262 (21%), Positives = 99/262 (37%), Gaps = 60/262 (22%)
Query: 19 LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTH 78
L+ QLDS+D F+Q E + L+ + + L++ L +P +
Sbjct: 20 LLEIQLDSYDWFLQQD--TPPEKRKEEGLEEVFKSIFPIEDYTGNMELEYLSYELGEPKY 77
Query: 79 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRS 138
E + R LTYS PL V + + ++ + + Q+ ++G IP+M
Sbjct: 78 ----------DVEECKERGLTYSVPLKVK-LRLINKEEDGTKEIKEQEVYMGDIPLM--- 123
Query: 139 TYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYK 198
TDR G FIING+E+V+++Q + + K
Sbjct: 124 --------TDR-------------GTFIINGAERVVVSQLHRSPGVFFSSEKDTHKNGKV 162
Query: 199 TEIRSCLEHSSR--PTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRAL 256
+S+R P W+ ++ KK + RI K+++P ++ RAL
Sbjct: 163 L-------YSARIIPYRGSWLEF-----ETDKKDLVYVRIDR-----KRKLPATVLLRAL 205
Query: 257 GFVADRDILEHIIYDFDDPEMM 278
G+ D L E +
Sbjct: 206 GYTIDTLKLNR----VGSYEYI 223
Score = 43.1 bits (102), Expect = 4e-04
Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 4/71 (5%)
Query: 421 SQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGAAVGL 476
SQ +++ + L+H RR+++ P G R+ + R +H T +G ICP ETPEG +GL
Sbjct: 388 SQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGL 447
Query: 477 VKNLALMAYIS 487
+ +L+ A ++
Sbjct: 448 INSLSTYARVN 458
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 58.6 bits (142), Expect = 8e-09
Identities = 85/466 (18%), Positives = 151/466 (32%), Gaps = 117/466 (25%)
Query: 64 YLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQ 123
LL + L P A+ + YS +Y+ + ++ + +
Sbjct: 45 LLLFGKNYKLKYP----------KYNLLSAKSYDSNYSIQIYLPLKFINLKTNK----IK 90
Query: 124 HQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATN 183
IG +P M T R G FIING E+V+++Q + +
Sbjct: 91 FINYLIGNLPKM-----------TQR-------------GTFIINGLERVIVSQ-IIRSP 125
Query: 184 TVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYI 243
+Y + P W+ K I RI
Sbjct: 126 GIYFKKEIKKNS------NKIYSATLIPNRGSWIKFELD-----KNKEIWIRIDKNR--- 171
Query: 244 KQEIPIMIVFRALGFVADRDILEHIIYDFDDP-------------------EMMEMVKPS 284
+ P++I +ALG + D+DI + E+ + + P
Sbjct: 172 --KKPLIIFLKALG-LTDQDIYSRLTKSEFLKKLKPILLNSNSYTNEEILLEIYKNLSPI 228
Query: 285 LDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYF 344
QN+ F + G +I + E + ++ D
Sbjct: 229 EPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS------ 282
Query: 345 LGYMVHRLLLASLGRRELDDRDHY---------------VRMYAQKFI----DRGKDFNL 385
++ +L+ + + DD DH R+ ++ +R ++
Sbjct: 283 ---IIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDI 339
Query: 386 ELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS--PI 443
+ K +I +L + + +SQ +++ S L+H RR++ P
Sbjct: 340 DSLSKFNLINPKPLIALI--------REFFGSSQLSQYMDQTNPLSELTHKRRISILGPG 391
Query: 444 GRDGKLAKP---RQLHNTLWGMICPAETPEGAAVGLVKNLALMAYI 486
G D K R +H + +G ICP ETPEG GL+ +LA A I
Sbjct: 392 GLD-KDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARI 436
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5. 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). Domain 5,
is also known as the external 2 domain.
Length = 46
Score = 49.9 bits (120), Expect = 3e-08
Identities = 16/27 (59%), Positives = 21/27 (77%)
Query: 632 WQVLVQSGVVEYIDTLEEETTMIAMSP 658
+ L++ GV+EY+D EEET MIAMSP
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAMSP 27
Score = 46.4 bits (111), Expect = 4e-07
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 607 WQVLVQSGVVEYIDTLEEETTMIAM 631
+ L++ GV+EY+D EEET MIAM
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAM 25
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 54.1 bits (131), Expect = 2e-07
Identities = 66/268 (24%), Positives = 103/268 (38%), Gaps = 82/268 (30%)
Query: 18 GLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPT 77
G + Q + F FI + + P+I + T E+E + L E L +P
Sbjct: 14 GFNQIQFEGFCRFIDQGLTEELSKFPKI------EDTDQEIE----FQLFVETYQLVEPL 63
Query: 78 HWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLR 137
E+D A +LTYS+ LYV + + Q Q FIG IP+M
Sbjct: 64 IKERD----------AVYESLTYSSELYVPAGLIWKKSRD----MQEQTVFIGNIPLM-- 107
Query: 138 STYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAY 197
+ G FIING +V+I Q + S Y
Sbjct: 108 ----------------------NSLGTFIINGIYRVVINQ------------ILRSPGIY 133
Query: 198 KTEIRSCLEHSSRP--TSTLWVNMMARGGQSL----KKSAIGQRIIAILPYIKQEIPIMI 251
RS L+H+ T T+ + GG+ +K+ I R+ KQ+I I++
Sbjct: 134 ---YRSELDHNGISVYTGTIISD---WGGRLELEIDRKARIWARVSR-----KQKISILV 182
Query: 252 VFRALGFVADRDILEHIIYDFDDPEMME 279
+ A+G R+IL+++ Y PE+
Sbjct: 183 LLSAMGL-NLREILDNVCY----PEIFL 205
Score = 46.4 bits (111), Expect = 4e-05
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 5/82 (6%)
Query: 421 SQVLNRLTFASSLSHLRRVNS--PIGRDGKLA--KPRQLHNTLWGMICPAETPEGAAVGL 476
SQ L++ + + H R+++S P G G+ A + R +H + +G ICP +T EG GL
Sbjct: 375 SQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGL 434
Query: 477 VKNLALMAYI-SVGSQPSPILE 497
+ +LA+ A I GS SP E
Sbjct: 435 IGSLAIHARIGHWGSLESPFYE 456
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Provisional.
Length = 2836
Score = 50.8 bits (121), Expect = 2e-06
Identities = 38/120 (31%), Positives = 65/120 (54%), Gaps = 11/120 (9%)
Query: 420 VSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGAAVG 475
+SQ +++ S ++H RR+++ P G R+ + R +H T +G ICP ETPEG +G
Sbjct: 532 LSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIG 591
Query: 476 LVKNLALMAYIS-VGSQPSPILEFLEEWSMENLEEIAP-----SAIADAT-KIFVNGCWV 528
L+ +LA+ A I+ G SP + + + +E ++ IAD + K+ N C+V
Sbjct: 592 LINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFV 651
Score = 29.2 bits (65), Expect = 8.8
Identities = 45/184 (24%), Positives = 82/184 (44%), Gaps = 46/184 (25%)
Query: 96 RNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIG-----KIPIMLRST------YCLLN 144
R +T+SA + I +++ G ++ KS K+ +++S +C L
Sbjct: 92 RGITFSAQVIASIRLVIMQDG---ISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELP 148
Query: 145 GLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSC 204
+TD+ G FIING EKV+++Q + VF D Y +
Sbjct: 149 MMTDK-------------GTFIINGVEKVIVSQMHRSPG---VFFDSDKGKTYNS---GK 189
Query: 205 LEHSSR--PTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADR 262
L +S+R P W+++ + K + RI K+++PI ++ +ALG +++
Sbjct: 190 LIYSARVIPYRGSWLDI-----EFDVKDHLYFRIDR-----KRKLPISVLLKALG-LSNN 238
Query: 263 DILE 266
DIL+
Sbjct: 239 DILD 242
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Reviewed.
Length = 2890
Score = 44.5 bits (105), Expect = 2e-04
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 8/68 (11%)
Query: 420 VSQVLNRLTFASSLSHLRRVNSPIGRDGKLAK------PRQLHNTLWGMICPAETPEGAA 473
+SQ +++ S ++H RR+ S +G +G L K R +H T +G ICP ETPEG
Sbjct: 525 LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKDRVGFEARDVHPTHYGRICPIETPEGQN 582
Query: 474 VGLVKNLA 481
+GL+ L+
Sbjct: 583 IGLINTLS 590
Score = 36.1 bits (83), Expect = 0.070
Identities = 42/191 (21%), Positives = 73/191 (38%), Gaps = 64/191 (33%)
Query: 91 NEARLRNLTYSAPLYVDI--------TKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCL 142
EA R +TYS PL + + TK+ + G + + + Q FI +IP+M
Sbjct: 83 REAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDI--KEQSIFIREIPLM------- 133
Query: 143 LNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV---FSMKDSKYAYKT 199
T+R FIING E+V++ Q + ++ S +K Y
Sbjct: 134 ----TERT-------------SFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTG 176
Query: 200 EI----RSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRA 255
+I S L L+ + R +++P+ I+FRA
Sbjct: 177 QIIPDRGSWLYFEYDSKDVLYARINKR----------------------RKVPVTILFRA 214
Query: 256 LGFVADRDILE 266
+ + +DI++
Sbjct: 215 MDY-QKQDIIK 224
>gnl|CDD|183063 PRK11264, PRK11264, putative amino-acid ABC transporter ATP-binding
protein YecC; Provisional.
Length = 250
Score = 33.6 bits (77), Expect = 0.29
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 8/49 (16%)
Query: 533 DPE---QLMGTLRKL---RRQMDIIVSEVSIIRDIRDREIRIHTDAGRI 575
DPE +++ T+R+L +R M I+ E+S RD+ DR I + D GRI
Sbjct: 176 DPELVGEVLNTIRQLAQEKRTMVIVTHEMSFARDVADRAIFM--DQGRI 222
>gnl|CDD|212088 cd11519, SLC5sbd_SMCT1, Na(+)/monocarboxylate cotransporter SMCT1
and related proteins; solute-binding domain. SMCT1 is a
high-affinity transporter of various monocarboxylates
including lactate and pyruvate, short-chain fatty acids,
ketone bodies, nicotinate and its structural analogs,
pyroglutamate, benzoate and its derivatives, and iodide.
Human SMCT1 (hSMCT1, also called AIT) is encoded by the
tumor suppressor gene SLC5A8. Its expression is under
the control of the C/EBP transcription factor. Its
tumor-suppressive role is related to uptake of butyrate,
propionate, and pyruvate, these latter are inhibitors of
histone deacetylases. SMCT1 is expressed in the colon,
small intestine, kidney, thyroid gland, retina, and
brain. SMCT1 may contribute to the intestinal/colonic
and oral absorption of monocarboxylate drugs. SMCT1 also
mediates iodide transport from thyrocyte into the
colloid lumen in thyroid gland and through transporting
l-lactate and ketone bodies helps maintain the energy
status and the function of neurons. In the kidney its
expression is limited to the S3 segment of the proximal
convoluted tubule (in contrast to the low-affinity
monocarboxylate transporter SMCT2, belonging to a
different family, which is expressed along the entire
length of the tubule). In the retina, SMCT1 and SMCT2
may play a differential role in monocarboxylate
transport in a cell type-specific manner, SMCT1 is
expressed predominantly in retinal neurons and in
retinal pigmented epithelial (RPE) cells. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 541
Score = 33.6 bits (77), Expect = 0.39
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 461 GMICPAETPEGAAVGLVKNLALMAYISVGSQPSP 494
G++ P GA VGLV A+ ++ +G+Q P
Sbjct: 425 GILFPFANSIGALVGLVSGFAISLWVGIGAQIYP 458
>gnl|CDD|184668 PRK14417, PRK14417, membrane protein; Provisional.
Length = 232
Score = 32.9 bits (75), Expect = 0.42
Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 16/109 (14%)
Query: 465 PAETPEGAAV--GLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIF 522
PA A+ G K +A ++ VG+ P F + ++ + + I IF
Sbjct: 122 PALIALSTALTFGFFKKMAPGVFLGVGALPVMSGYFHGFFGVQEPQTVTWGFIG----IF 177
Query: 523 VNGCWVGIHRDPEQLMGTLRKLRRQM---DIIVSEVSIIRDIRDREIRI 568
+ + I R +LM + + +++ + + + RDIRDR + I
Sbjct: 178 L----IMIVR---RLMAPDSEYSSTVSKAELVFNRLFLDRDIRDRSVWI 219
>gnl|CDD|212074 cd11505, SLC5sbd_SMCT, Na(+)/monocarboxylate cotransporters SMCT1
and 2 and related proteins; solute-binding domain.
SMCT1 is a high-affinity transporter of various
monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. Human SMCT1 (hSMCT1, also
called AIT) is encoded by the tumor suppressor gene
SLC5A8. SMCT1 is expressed in the colon, small
intestine, kidney, thyroid gland, retina, and brain.
SMCT1 may contribute to the intestinal/colonic and oral
absorption of monocarboxylate drugs. It also mediates
iodide transport from thyrocyte into the colloid lumen
in thyroid gland and, through transporting L-lactate and
ketone bodies, helps maintain the energy status and the
function of neurons. SMCT2 is a low-affinity transporter
for short-chain fatty acids, lactate, pyruvate, and
nicotinate. hSMCT2 is encoded by the SLC5A12 gene. SMCT2
is expressed in the kidney, small intestine, skeletal
muscle, and retina. In the kidney, SMCT2 may initiate
lactate absorption in the early parts of the tubule,
SMCT1 in the latter parts of the tubule. In the retina,
SMCT1 and SMCT2 may play a differential role in
monocarboxylate transport in a cell type-specific
manner. This subgroup belongs to the solute carrier 5
(SLC5) transporter family.
Length = 536
Score = 32.4 bits (74), Expect = 0.85
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 461 GMICPAETPEGAAVGLVKNLALMAYISVGSQPSP 494
G++ P +GA GL+ A+ ++ +G+Q P
Sbjct: 425 GILFPFANSKGALSGLLTGFAISLWVGIGAQIYP 458
>gnl|CDD|237880 PRK14984, PRK14984, high-affinity gluconate transporter;
Provisional.
Length = 438
Score = 31.7 bits (72), Expect = 1.2
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 14/55 (25%)
Query: 617 EYIDTLEEETTMIAMW-----------QVLVQSGVVEYIDTLEEETTMIAMSPRL 660
+ DTL +IAM QVLV SGV +YI ++ ET +SP L
Sbjct: 287 QINDTLVSSIKIIAMMLLIIGGGGAFKQVLVDSGVDKYIASMMHETN---ISPLL 338
>gnl|CDD|238102 cd00175, SNc, Staphylococcal nuclease homologues. SNase homologues
are found in bacteria, archaea, and eukaryotes. They
contain no disufide bonds.
Length = 129
Score = 30.3 bits (69), Expect = 1.2
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 348 MVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLEL 387
+ +LLL + E+D +D Y R +++ G++ EL
Sbjct: 51 FLKKLLLGKKVQVEVDSKDRYGRTLGTVYLNGGENIAEEL 90
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 585
Score = 31.8 bits (72), Expect = 1.5
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 249 IMIVFRALGFVADRDILEHIIY---DFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARG 305
I VF+ G +R I E+I D E+ E K + F+++ N +G RG
Sbjct: 411 IATVFQDAGLF-NRSIRENIRLGREGATDEEVYEAAKAAAAHDFILKRSNGYDTLVGERG 469
Query: 306 ARPGVTKERRIKYAREILQ 324
R + +R+ AR IL+
Sbjct: 470 NRLSGGERQRLAIARAILK 488
>gnl|CDD|239884 cd04437, DEP_Epac, DEP (Dishevelled, Egl-10, and Pleckstrin) domain
found in Epac-like proteins. Epac (exchange proteins
directly activated by cAMP) proteins are GEFs
(guanine-nucleotide-exchange factors) for the small
GTPases, Rap1 and Rap2. They are directly regulated by
cyclic AMP, a second messenger that plays a role in the
control of diverse cellular processes, such as cell
adhesion and insulin secretion. Epac-like proteins
share a common domain architecture, containing RasGEF,
DEP and CAP-effector (cAMP binding) domains. The DEP
domain is involved in membrane localization.
Length = 125
Score = 29.6 bits (67), Expect = 2.0
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 572 AGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAM 631
AGR R ++++ L+ R LV +++ ++ + + M
Sbjct: 1 AGRALRNAILSDAPHLI---RDRKYHLRTYRQCCVGTELVD-WLLQQSPCVQSRSQAVGM 56
Query: 632 WQVLVQSGVVEYID 645
WQVL++ GV+ ++D
Sbjct: 57 WQVLLEEGVLLHVD 70
>gnl|CDD|212073 cd11504, SLC5sbd_SMVT, Na(+)/multivitamin cotransporter SMVT and
related proteins; solute-binding domain. This
multivitamin transporter SMVT (product of the SLC5A6
gene) transports biotin, pantothenic acid and lipoate,
and is essential for mediating biotin uptake into
mammalian cells. SMVT is expressed in the placenta,
intestine, heart, brain, lung, liver, kidney and
pancreas. Biotin may regulate its own cellular uptake
through participation in holocarboxylase
synthetase-dependent chromatin remodeling events at SMVT
promoter loci. The cis regulatory elements, Kruppel-like
factor 4 and activator protein-2, regulate the activity
of the human SMVT promoter in the intestine.
Glycosylation of the hSMVT is important for its
transport function. This subgroup belongs to the solute
carrier 5 (SLC5) transporter family.
Length = 527
Score = 31.0 bits (70), Expect = 2.1
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 461 GMICPAETPEGAAVGLVKNLALMAYISVGSQPSP 494
GM P GA VGL+ L + +I +GS
Sbjct: 422 GMFFPWANSTGAVVGLLSGLVMAFWIGIGSFVFR 455
>gnl|CDD|212061 cd11492, SLC5sbd_NIS-SMVT, Na(+)/iodide (NIS) and
Na(+)/multivitamin (SMVT) cotransporters, and related
proteins; solute binding domain. NIS (encoded by the
SLC5A5 gene) transports I-, and other anions including
ClO4-, SCN-, and Br-. SMVT (encoded by the SLC5A6 gene)
transports biotin, pantothenic acid and lipoate. This
subfamily also includes SMCT1 and -2. SMCT1(encoded by
the SLC5A8 gene) is a high-affinity transporter of
various monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. SMCT2 (encoded by the SLC5A12
gene) is a low-affinity transporter for short-chain
fatty acids, lactate, pyruvate, and nicotinate. This
subgroup belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 522
Score = 30.9 bits (71), Expect = 2.2
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 461 GMICPAETPEGAAVGLVKNLALMAYISVGSQPSP 494
GM P +GA VGL+ LA +I +G QP+
Sbjct: 420 GMFFPWANSKGALVGLLVGLAFSLWIGIGGQPAY 453
>gnl|CDD|221470 pfam12224, Amidoligase_2, Putative amidoligase enzyme. This family
of proteins are likely to act as amidoligase enzymes
Protein in this family are found in conserved gene
neighborhoods encoding a glutamine amidotransferase-like
thiol peptidase (in proteobacteria) or an Aig2 family
cyclotransferase protein (in firmicutes).
Length = 250
Score = 30.0 bits (68), Expect = 3.1
Identities = 27/134 (20%), Positives = 41/134 (30%), Gaps = 31/134 (23%)
Query: 443 IGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEW 502
I D + K L P E +V SP L +
Sbjct: 51 IELDSSILKEDAEKRDLADADVPVE--------IV---------------SPPLPY--SE 85
Query: 503 SMENLEEIAPSAIADA-TKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDI 561
+E L+E+ A+ A K C +H +PE T + LR + +R
Sbjct: 86 DLEQLQELV-RALRRAGAKGTNASCGFHVHINPEPPDLTAQTLRNLLQAYALLEDWLRKA 144
Query: 562 ----RDREIRIHTD 571
R R + + D
Sbjct: 145 LPVDRSRRLNPYCD 158
>gnl|CDD|214615 smart00318, SNc, Staphylococcal nuclease homologues.
Length = 137
Score = 28.4 bits (64), Expect = 6.3
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 361 ELDDRDHYVRMYAQKFIDRGKDFNLEL 387
E+D +D Y R +++ G + EL
Sbjct: 72 EVDSKDRYGRFLGTVYLNGGNNIAEEL 98
>gnl|CDD|182747 PRK10807, PRK10807, paraquat-inducible protein B; Provisional.
Length = 547
Score = 29.2 bits (66), Expect = 8.1
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 369 VRMYAQKFIDR-GKDFNLELAIKTKIITDGLRYSLATGN 406
+R+ ++ + G++F++E +K +++ GLR SL TGN
Sbjct: 340 IRIEPERLKMQLGENFDVEQHLK-ELLKRGLRASLKTGN 377
>gnl|CDD|234885 PRK00994, PRK00994, F420-dependent methylenetetrahydromethanopterin
dehydrogenase; Provisional.
Length = 277
Score = 28.8 bits (65), Expect = 9.1
Identities = 20/72 (27%), Positives = 27/72 (37%), Gaps = 18/72 (25%)
Query: 271 DFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPH 330
+ +M+E KP FVI I A PG K AREIL+ +P
Sbjct: 49 EEVVKKMLEEWKPD----FVI--------VISPNPAAPGPKK------AREILKAAGIPC 90
Query: 331 VGVSDFCETKKA 342
+ + D K
Sbjct: 91 IVIGDAPGKKVK 102
>gnl|CDD|206419 pfam14251, DUF4346, Domain of unknown function (DUF4346). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 127 and 502 amino acids in length. There are two
conserved sequence motifs: LDP and DHA. Many members of
this family have been annotated as dihydropteroate
synthases, however no experimental evidence can be found
for this and MJ0107 has been shown not to possess
dihydropteroate synthase activity.
Length = 119
Score = 27.5 bits (62), Expect = 9.4
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 159 LDPGGYFII 167
LDP GYF+I
Sbjct: 14 LDPAGYFLI 22
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 0.136 0.401
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,843,967
Number of extensions: 3545146
Number of successful extensions: 2978
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2917
Number of HSP's successfully gapped: 53
Length of query: 661
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 558
Effective length of database: 6,369,140
Effective search space: 3553980120
Effective search space used: 3553980120
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 (27.6 bits)