RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8861
(550 letters)
>gnl|CDD|235411 PRK05327, rpsD, 30S ribosomal protein S4; Validated.
Length = 203
Score = 302 bits (775), Expect = e-100
Identities = 117/201 (58%), Positives = 140/201 (69%), Gaps = 6/201 (2%)
Query: 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHG-RISGSRTSDYGYQFREK 59
MARY GPK KL RR G+DLF +R L K PGQHG R + SDYG Q REK
Sbjct: 1 MARYTGPKCKLSRRLGVDLFKS-GKRCLKRKYP----PGQHGQRRRKPKLSDYGLQLREK 55
Query: 60 QKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLI 119
QK++R+YG+LEKQFRRYF E AR KG TGE +L+LLESR DNVVYR+GF+ TR +ARQL+
Sbjct: 56 QKLRRIYGVLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLV 115
Query: 120 SHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKM 179
SH LVN K VNI SY++KPGD+I VREK+KK RI +LEL+E W+ VDA+K+
Sbjct: 116 SHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKL 175
Query: 180 EGVFKSEPNRSEFANDINDLL 200
EG FK P R E IN+ L
Sbjct: 176 EGTFKRLPEREEIPVPINEQL 196
>gnl|CDD|200066 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
type. This model finds organelle (chloroplast and
mitochondrial) ribosomal protein S4 as well as bacterial
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 200
Score = 236 bits (605), Expect = 3e-75
Identities = 106/198 (53%), Positives = 133/198 (67%), Gaps = 5/198 (2%)
Query: 3 RYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKV 62
RY GPK KL RR G++LF KS R L K K PGQHG+ + SDYG Q +EKQK+
Sbjct: 1 RYTGPKFKLSRRLGVNLFGKS--RKLLLKRKY--PPGQHGQRR-KKLSDYGLQLQEKQKL 55
Query: 63 KRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHR 122
K MYGI EKQFR+YF E +LKG TGE +L+LLESR DNVVYR+GF+ TR ARQL+SH
Sbjct: 56 KFMYGITEKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHG 115
Query: 123 AFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKKMEGV 182
LVN K V+I SY+++PGDIIS++EK+KK + +LE + SW+ VD K +EG
Sbjct: 116 HILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGK 175
Query: 183 FKSEPNRSEFANDINDLL 200
P RS+ IN+ L
Sbjct: 176 VLRVPERSQLPLPINESL 193
>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 205
Score = 221 bits (564), Expect = 4e-69
Identities = 107/201 (53%), Positives = 132/201 (65%), Gaps = 4/201 (1%)
Query: 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQ 60
MARY GPK KL RR G + +LK KL +PGQHG+ + SDYG Q REKQ
Sbjct: 1 MARYPGPKKKLSRRLGFNPWLKERLCKER---KLPYKPGQHGQERWKKLSDYGLQLREKQ 57
Query: 61 KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLIS 120
K++ YG+LEKQFRRY E RLKG TG +L LLE R DNVVYR+GF+ TR +ARQL+S
Sbjct: 58 KLRAFYGVLEKQFRRYLKEAGRLKGVTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVS 117
Query: 121 HRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLEL-SEHSTPFSWITVDAKKM 179
H LVN K VNI SY + PGD ISVREK+K +I +LEL ++ P +W+ VD +K+
Sbjct: 118 HGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALELAAQRGIPPAWLEVDEEKL 177
Query: 180 EGVFKSEPNRSEFANDINDLL 200
EG FK P RS+ IN+ L
Sbjct: 178 EGTFKRLPERSDLPAPINEQL 198
>gnl|CDD|235522 PRK05591, rplQ, 50S ribosomal protein L17; Validated.
Length = 113
Score = 189 bits (484), Expect = 2e-58
Identities = 71/113 (62%), Positives = 85/113 (75%)
Query: 433 RHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNK 492
R RKL RTSSHR MLRN+ SL+ +E I+TTLPKAKELRRVVE ++TL+KK L +
Sbjct: 1 RKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHAR 60
Query: 493 RLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELL 545
R AF+ LRD++ KLF E+ PRY NGGY RILK+GFR GDNAPMA IEL+
Sbjct: 61 RQAFARLRDKEAVHKLFDEIAPRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113
>gnl|CDD|235359 PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha;
Provisional.
Length = 310
Score = 196 bits (501), Expect = 2e-58
Identities = 67/133 (50%), Positives = 92/133 (69%), Gaps = 2/133 (1%)
Query: 197 NDLLKPRIIDVK--TLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG 254
+ LKP+ I+V+ + N+ K ++EP ERG+G TLGNALRRVLLSS+ G A T V I G
Sbjct: 1 TEFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDG 60
Query: 255 ALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIEL 314
LHE+S++ GV+ED+ +IILNLKG+ LKL+ + L L K G V A DIE D+E+
Sbjct: 61 VLHEFSTIPGVREDVTEIILNLKGLRLKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVEI 120
Query: 315 VNPNHIIAHLSDN 327
VNP+ +IA L++
Sbjct: 121 VNPDLVIATLNEG 133
Score = 154 bits (391), Expect = 1e-42
Identities = 56/100 (56%), Positives = 73/100 (73%), Gaps = 1/100 (1%)
Query: 328 EEAIRQSARVLVDQLNVFAALENTPVKKELDSSLE-KVDPILLRPVDDLELTVRSANCLK 386
EEA+ +A++LV+QL+VF LE +E E + DPILLRP+++LEL+VRS NCLK
Sbjct: 206 EEALALAAKILVEQLSVFVDLEEAEEAEEEVEEEEPEFDPILLRPIEELELSVRSYNCLK 265
Query: 387 AENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRG 426
I+ IGDL+QR+E ELL+T NLG+KSL EIKE LA G
Sbjct: 266 RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAELG 305
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 188 bits (481), Expect = 4e-58
Identities = 76/116 (65%), Positives = 91/116 (78%)
Query: 430 MRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTL 489
MRHR RKL RTSSHR MLRN+ SL+ +E I+TTLPKAKELRRVVE ++TL+KK L
Sbjct: 1 MRHRKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDL 60
Query: 490 SNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELL 545
+N+RLAF+ LRD+ KLF E+ PRY + NGGY RILK+GFR GDNAPMA IEL+
Sbjct: 61 ANRRLAFARLRDKDAVKKLFDEIAPRYAERNGGYTRILKLGFRRGDNAPMAIIELV 116
>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of
Bacterial RNA polymerase. The bacterial alpha subunit
of RNA polymerase (RNAP) consists of two independently
folded domains: an amino-terminal domain (alphaNTD) and
a carboxy-terminal domain (alphaCTD). AlphaCTD is not
required for RNAP assembly but interacts with
transcription activators. AlphaNTD is essential in vivo
and in vitro for RNAP assembly and basal transcription.
It is similar to the eukaryotic RPB3/AC40/archaeal D
subunit, and contains two subdomains: one subdomain is
similar the eukaryotic Rpb11/AC19/archaeal L subunit
which is involved in dimerization; and the other is an
inserted beta sheet subdomain. The alphaNTDs of plant
plastid RNAP (PEP) are also included in this subfamily.
PEP is largely responsible for the transcription of
photosynthetic genes and is closely related to the
multi-subunit bacterial RNAP, which is a large
multi-subunit complex responsible for the synthesis of
all bacterial RNAs. The bacterial RNAP core enzyme
consists of four subunits (beta', beta, alpha and
omega). All residues in the alpha subunit that is
involved in dimerization or in the interaction with
other subunits are located within alphaNTD.
Length = 215
Score = 168 bits (427), Expect = 6e-49
Identities = 61/124 (49%), Positives = 86/124 (69%), Gaps = 1/124 (0%)
Query: 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEG 264
V+ N+ + ++EP ERG G TLGNALRRVLLSS+ G A T V I G LHE+S++ G
Sbjct: 1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPG 60
Query: 265 VQEDIIDIILNLKGVILKLYNRDYA-ILNLKKFGKCVVLASDIELLSDIELVNPNHIIAH 323
V+ED+++I+LNLK ++ K + D +L LK G VV A+DIEL S +E+VNP+ IA
Sbjct: 61 VREDVLEILLNLKEIVFKSDSEDEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIAT 120
Query: 324 LSDN 327
L+++
Sbjct: 121 LTED 124
Score = 29.0 bits (66), Expect = 4.7
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 328 EEAIRQSARVLVDQLNVF 345
EEA+ Q+A++L++ + F
Sbjct: 198 EEALAQAAKILINHFSPF 215
>gnl|CDD|177038 CHL00113, rps4, ribosomal protein S4; Reviewed.
Length = 201
Score = 161 bits (409), Expect = 2e-46
Identities = 76/202 (37%), Positives = 114/202 (56%), Gaps = 12/202 (5%)
Query: 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRI--SGSRTSDYGYQFRE 58
M+RY GP+ K+ RR G A L SK RPG R + S Y + E
Sbjct: 1 MSRYRGPRLKIIRRLG-------ALPGLTSK---TPRPGSDLRNQSRSGKKSQYRIRLEE 50
Query: 59 KQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQL 118
KQK++ YG+ E+Q +Y + KG TG+++L+LLE R DN+++R+G + T ARQL
Sbjct: 51 KQKLRFNYGLTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTIPAARQL 110
Query: 119 ISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLELSEHSTPFSWITVDAKK 178
++H LVN +IV+I SY+ KP DII+V++K K + I N+LE S + +T+D +
Sbjct: 111 VNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREELPNHLTLDKLQ 170
Query: 179 MEGVFKSEPNRSEFANDINDLL 200
+G+ +R IN+LL
Sbjct: 171 YKGLVNQIIDRKWVGLKINELL 192
>gnl|CDD|216356 pfam01196, Ribosomal_L17, Ribosomal protein L17.
Length = 97
Score = 156 bits (398), Expect = 3e-46
Identities = 56/96 (58%), Positives = 71/96 (73%)
Query: 449 MLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKL 508
+LRN+ SL+R+E I+TTL KAKELR E ++TL+KK L +R A S+LRD+++ KL
Sbjct: 1 LLRNLATSLIRHERIETTLAKAKELRPYAEKLITLAKKGDLHARRQALSFLRDKELVKKL 60
Query: 509 FSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIEL 544
F EL PRY NGGY RI+K+G R GDNAPMA IEL
Sbjct: 61 FDELAPRYADRNGGYTRIIKLGPRRGDNAPMAIIEL 96
>gnl|CDD|129169 TIGR00059, L17, ribosomal protein L17. Eubacterial and
mitochondrial. The mitochondrial form, from yeast,
contains an additional 110 amino acids C-terminal to the
region found by this model [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 112
Score = 151 bits (383), Expect = 5e-44
Identities = 63/112 (56%), Positives = 86/112 (76%)
Query: 435 GFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRL 494
+RKL RTS+HR +LRN+ +L+R+E IKTTL KAKELRRVVE ++TL+K + +N+R
Sbjct: 1 SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRRE 60
Query: 495 AFSYLRDRKITIKLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLN 546
A +Y+R+++I KLFSE+ PRY + GGY RILK+G R GD A MA IEL++
Sbjct: 61 AKAYIRNKEIVHKLFSEIAPRYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD
subunit [Transcription].
Length = 317
Score = 157 bits (399), Expect = 1e-43
Identities = 65/129 (50%), Positives = 89/129 (68%)
Query: 199 LLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHE 258
LKP+ + ++ L +AK ++EP ERG+G TLGNALRRVLLSS+ G A T V I G LHE
Sbjct: 1 FLKPKKVKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHE 60
Query: 259 YSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPN 318
+ S+EGVQED++ LNLK + +KL + L L K G V ASDI + D+E+VNP+
Sbjct: 61 FDSIEGVQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPD 120
Query: 319 HIIAHLSDN 327
H+IA L+++
Sbjct: 121 HVIATLTED 129
Score = 109 bits (274), Expect = 2e-26
Identities = 47/99 (47%), Positives = 66/99 (66%)
Query: 328 EEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLELTVRSANCLKA 387
EEA+ +A++L++ L VF L V+ E + + +L P+D+L+L+VRS NCLK
Sbjct: 203 EEALAIAAKILIEHLEVFVELCPKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLKR 262
Query: 388 ENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRG 426
E I IG+L+QR+E ELL+ NLG+KSL EIKE LA G
Sbjct: 263 EGIETIGELVQRTEEELLKVENLGKKSLEEIKEKLAELG 301
>gnl|CDD|233691 TIGR02027, rpoA, DNA-directed RNA polymerase, alpha subunit,
bacterial and chloroplast-type. This family consists of
the bacterial (and chloroplast) DNA-directed RNA
polymerase alpha subunit, encoded by the rpoA gene. The
RNA polymerase catalyzes the transcription of DNA into
RNA using the four ribonucleoside triphosphates as
substrates. The amino terminal domain is involved in
dimerizing and assembling the other RNA polymerase
subunits into a transcriptionally active enzyme. The
carboxy-terminal domain contains determinants for
interaction with DNA and with transcriptional activator
proteins [Transcription, DNA-dependent RNA polymerase].
Length = 297
Score = 151 bits (384), Expect = 8e-42
Identities = 98/291 (33%), Positives = 133/291 (45%), Gaps = 78/291 (26%)
Query: 214 HAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDII 273
+ K ++EP ERG+G TLGNALRRVLLSS+ G A T V I G LHE+S++EGV+ED+ +II
Sbjct: 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEII 60
Query: 274 LNLKGVILKLYNRDYAILNLKKFGKCVVLASDIE-LLSDIELVNPNHIIAHLSD------ 326
LNLK +++K + L K G VV A DI+ D+E+VNP+ +IA L++
Sbjct: 61 LNLKQLVVKSEGDGERTMTLSKKGPGVVTAGDIKAPPGDVEIVNPDLVIATLTEPADLEI 120
Query: 327 ---------------NEEAIRQSARVLVDQ-----LNVFAALENTPVKK----------- 355
N E R + VD L V +ENT V +
Sbjct: 121 ELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNYEVENTRVGQRTDYDKLILEI 180
Query: 356 ELDSSLEKVDPI---------LLRPVDDLELTVRSANC--------LKAENIHCIG---- 394
E + S+ D I L P +L+ + + L+ + I
Sbjct: 181 ETNGSITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEEELEDAKLLSIKIEEL 240
Query: 395 DLIQRSEN-------------------ELLRTPNLGRKSLNEIKEILASRG 426
DL RS N ELL+ N G+KSL EIKE LA G
Sbjct: 241 DLSVRSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAELG 291
>gnl|CDD|214333 CHL00013, rpoA, RNA polymerase alpha subunit.
Length = 327
Score = 114 bits (288), Expect = 3e-28
Identities = 78/300 (26%), Positives = 126/300 (42%), Gaps = 90/300 (30%)
Query: 214 HAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDII 273
+ + I+ P +G T+G ALRR LL + G T I G HEYS++ G++E +++I+
Sbjct: 21 YGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEIL 80
Query: 274 LNLKGVILK--LYNRDYAILNLKKFGKCVVLA------SDIELLS--------------D 311
LNLK ++LK LY A + ++ G V A +E++ +
Sbjct: 81 LNLKEIVLKSNLYGPQKASICVQ--GPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLE 138
Query: 312 IELV------------------------------NPNHII-AHLSDNE------------ 328
IEL N N+ I ++ + NE
Sbjct: 139 IELKIEKGRGYRLKTPKNFQDGSFPIDAVFMPVRNVNYSIHSYGNGNEKQEILFLEIWTN 198
Query: 329 ------EAIRQSARVLVDQLNVF--AALENTPVKKELDSSL---------------EKVD 365
EA+ +++R L+D F A EN ++ + +K
Sbjct: 199 GSITPKEALHEASRNLIDLFIPFLHAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEI 258
Query: 366 PILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR 425
+ ++ LEL+VR+ NCLK NIH + DL+ S+ +LL+ N G+KS E+ E L R
Sbjct: 259 ALKQIFIEQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQKR 318
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 105 bits (264), Expect = 7e-26
Identities = 47/139 (33%), Positives = 65/139 (46%), Gaps = 27/139 (19%)
Query: 215 AKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIIL 274
AK ++EP YG TL NALRRVLLSS+ G A T V I + GVQ++++ L
Sbjct: 1 AKFVLEP----YGLTLANALRRVLLSSVPGMAVTSVYI------EGNTSGVQDEVLAHRL 50
Query: 275 NLKGVILKLYN--------------RDYAILNLKKFGKCVVLASDIELLSD--IELVNPN 318
LK + + L L G V A D++ SD +E+VNP+
Sbjct: 51 GLKPLASDPDGDEYQRDCECEEGCEKCSVTLTLDVKGPGEVTAGDLKSDSDPDVEIVNPD 110
Query: 319 HIIAHLSDNEEAIRQSARV 337
IA L + +E + AR
Sbjct: 111 IPIAKLREGQE-LELEARA 128
>gnl|CDD|202541 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C
terminal domain. The alpha subunit of RNA polymerase
consists of two independently folded domains, referred
to as amino-terminal and carboxyl terminal domains. The
amino terminal domain is involved in the interaction
with the other subunits of the RNA polymerase. The
carboxyl-terminal domain interacts with the DNA and
activators. The amino acid sequence of the alpha subunit
is conserved in prokaryotic and chloroplast RNA
polymerases. There are three regions of particularly
strong conservation, two in the amino-terminal and one
in the carboxyl- terminal.
Length = 67
Score = 94.9 bits (237), Expect = 6e-24
Identities = 30/67 (44%), Positives = 45/67 (67%)
Query: 358 DSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNE 417
+ ++ +L P+++LEL+VRS NCLK I+ +GDL+ +SE +LL+ N G+KSL E
Sbjct: 1 EKEEDEELALLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEE 60
Query: 418 IKEILAS 424
IKE L
Sbjct: 61 IKEKLEE 67
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain.
Members of this family include: alpha subunit from
eubacteria alpha subunits from chloroplasts Rpb3
subunits from eukaryotes RpoD subunits from archaeal.
Length = 117
Score = 87.7 bits (218), Expect = 7e-21
Identities = 32/82 (39%), Positives = 48/82 (58%), Gaps = 2/82 (2%)
Query: 250 VIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRD--YAILNLKKFGKCVVLASDIE 307
V I+G HE+ + GV ED+++IILNLK ++ K+ + L L G V A D+E
Sbjct: 1 VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKGPGEVTAGDLE 60
Query: 308 LLSDIELVNPNHIIAHLSDNEE 329
D+E+VNP+ +IA L +E
Sbjct: 61 SDPDVEIVNPDILIATLRKGQE 82
>gnl|CDD|215762 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal
domain. This family includes small ribosomal subunit
S9 from prokaryotes and S16 from metazoans. This domain
is predicted to bind to ribosomal RNA. This domain is
composed of four helices in the known structure.
However the domain is discontinuous in sequence and the
alignment for this family contains only the first three
helices.
Length = 93
Score = 84.3 bits (209), Expect = 5e-20
Identities = 40/96 (41%), Positives = 52/96 (54%), Gaps = 4/96 (4%)
Query: 2 ARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHG-RISGSRTSDYGYQFREKQ 60
+RY GP KL RR G L + + LRPGQHG R+ R S Y + EKQ
Sbjct: 1 SRYRGPTLKLPRRLGELPRLTAKTKLAGEYG---LRPGQHGWRVKKGRLSRYLLRLDEKQ 57
Query: 61 KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLE 96
K++ YG+LE+Q RRY + +L G G +L LLE
Sbjct: 58 KLRFFYGLLERQLRRYGVLAKKLDGSLGLNLLDLLE 93
>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain
surface is populated by conserved, charged residues that
define a likely RNA-binding site; Found in stress
proteins, ribosomal proteins and tRNA synthetases; This
may imply a hitherto unrecognized functional similarity
between these three protein classes.
Length = 70
Score = 70.4 bits (173), Expect = 2e-15
Identities = 28/56 (50%), Positives = 39/56 (69%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQ 153
R D ++ R+G + +RSEARQLI H LVN K+V SYK+KPGD+I V K+ ++
Sbjct: 2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57
>gnl|CDD|201819 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases, a
yeast protein containing a pseudouridine synthetase and
a deaminase domain, bacterial tyrosyl-tRNA synthetases,
and a number of uncharacterized, small proteins that may
be involved in translation regulation. The S4 domain
probably mediates binding to RNA.
Length = 48
Score = 69.4 bits (171), Expect = 3e-15
Identities = 26/47 (55%), Positives = 34/47 (72%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDII 144
R D V+ R+G +S+RSEARQLI H VN K+V SY++KPGD+I
Sbjct: 2 RLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 67.6 bits (166), Expect = 2e-14
Identities = 26/56 (46%), Positives = 34/56 (60%)
Query: 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152
R D + R+G + +RS+AR+LI VN K V SY +KPGD+ISVR K K
Sbjct: 1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56
>gnl|CDD|173371 PTZ00076, PTZ00076, 60S ribosomal protein L17; Provisional.
Length = 253
Score = 69.8 bits (171), Expect = 2e-13
Identities = 38/116 (32%), Positives = 64/116 (55%), Gaps = 1/116 (0%)
Query: 433 RHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNK 492
R FR+ + HR ++N LLRY ++ TLP+AKEL++ E ++ L+KK+T +
Sbjct: 16 RRLFRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESN 75
Query: 493 RLAFSYLRDRKITIKLFSELGPRYIKINGGYVRIL-KMGFRVGDNAPMAFIELLNQ 547
S LR + KL+ + P Y + R++ + R+ D APMA+IE +++
Sbjct: 76 LKVESMLRTPQGRRKLYEKYVPLYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDR 131
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp.
Length = 88
Score = 48.4 bits (116), Expect = 2e-07
Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 219 MEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG 254
+E G +TLGNALRRVLLS + G A V I
Sbjct: 1 IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPH 36
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
Length = 177
Score = 46.0 bits (110), Expect = 8e-06
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 20/90 (22%)
Query: 57 REKQKVKRM--YGILEKQFRRYFIEGARLKGKTGEIILKL-----LESRFDNVVYRMGFS 109
E+Q + ++ YGIL+ E A L + +L L LE R +VYR G +
Sbjct: 69 EEEQLLGKLKRYGILK--------ENATL-----DDVLSLTVEDILERRLQTIVYRKGLA 115
Query: 110 STRSEARQLISHRAFLVNKKIVNIASYKIK 139
T +ARQ I H VN + V SY +
Sbjct: 116 RTPKQARQFIVHGHIAVNGRRVTSPSYLVS 145
>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
type)/S9(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S9 as well as archaeal
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 162
Score = 43.2 bits (102), Expect = 6e-05
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 8/79 (10%)
Query: 61 KVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLIS 120
++ R+ GIL+ E A+L G + LE R V++ G + T +ARQLI
Sbjct: 76 RLVRL-GILD-------EENAKLDDVLGLTVEDFLERRLQTQVFKKGLARTIHQARQLIV 127
Query: 121 HRAFLVNKKIVNIASYKIK 139
H V+ + V SY ++
Sbjct: 128 HGHIAVDGRRVTSPSYIVR 146
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 44.5 bits (105), Expect = 2e-04
Identities = 21/58 (36%), Positives = 34/58 (58%)
Query: 373 DDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYM 430
DDL ++ R AN I +GDLI ++E +LLR +G K++ E+K+ L + Y+
Sbjct: 1317 DDLGVSQRWANKFSEAGIETVGDLIGKTEEDLLRIEGIGAKAIEELKDGLEAHNLLYI 1374
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
Length = 181
Score = 40.1 bits (94), Expect = 0.001
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 65 MYGILEKQFRRY-FIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRA 123
G+L++ R+ ++ G ++ KLLE R V+++G + + AR LI R
Sbjct: 82 RLGLLDEDERKLDYVLGLTVE--------KLLERRLQTKVFKLGLAKSIHHARVLIRQRH 133
Query: 124 FLVNKKIVNIASYKIK 139
V K+IV+I S+ ++
Sbjct: 134 IRVGKQIVDIPSFLVR 149
>gnl|CDD|224110 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal
structure and biogenesis].
Length = 245
Score = 40.3 bits (95), Expect = 0.001
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152
R D ++ G +R +A++LI LVN + V S + D I V+ + +
Sbjct: 4 RLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQP 58
>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
Length = 194
Score = 37.4 bits (87), Expect = 0.008
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 93 KLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIK 139
LE R +V++ G + + AR LI R V K+IVN+ S+ ++
Sbjct: 105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVR 151
>gnl|CDD|225185 COG2302, COG2302, Uncharacterized conserved protein, contains
S4-like domain [Function unknown].
Length = 257
Score = 37.3 bits (87), Expect = 0.014
Identities = 21/50 (42%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVR 147
R D V+ F +R++A+QLI VN K+V+ ASY+++ GD+IS+R
Sbjct: 182 RLDVVISEG-FGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIR 230
>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA
polymerase. The eukaryotic RPB11 and RPB3 subunits of
RNA polymerase (RNAP), as well as their archaeal (L and
D subunits) and bacterial (alpha subunit) counterparts,
are involved in the assembly of RNAP, a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. At least three distinct RNAP complexes are found
in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for
the synthesis of ribosomal RNA precursor, mRNA
precursor, and 5S and tRNA, respectively. A single
distinct RNAP complex is found in prokaryotes and
archaea, which may be responsible for the synthesis of
all RNAs. The assembly of the two largest eukaryotic
RNAP subunits that provide most of the enzyme's
catalytic functions depends on the presence of
RPB3/RPB11 heterodimer subunits. This is also true for
the archaeal (D/L subunits) and bacterial (alpha
subunit) counterparts.
Length = 86
Score = 32.0 bits (73), Expect = 0.12
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 212 SNHAKVIMEPFERGYGYTLGNALRRVLLSS 241
N+ ++E +TLGN+LRR+LL S
Sbjct: 8 KNYVDFVLEN----EDHTLGNSLRRILLKS 33
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family. In E.
coli, RluD (SfhB) modifies uridine to pseudouridine at
23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504
and 2580, and RluA modifies U746 and tRNA U32. An
additional homolog from E. coli outside this family,
TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to
pseudouridine [Protein synthesis, tRNA and rRNA base
modification].
Length = 299
Score = 33.8 bits (78), Expect = 0.16
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVR 147
R D+ + + +RS ++LI + VN K+ K+K GD I+VR
Sbjct: 7 RLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVR 56
>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein;
Provisional.
Length = 267
Score = 33.2 bits (76), Expect = 0.27
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 107 GFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAK 151
GF +RS+ LIS VN + V +K GD++SV K +
Sbjct: 201 GFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGR 245
>gnl|CDD|129570 TIGR00478, tly, hemolysin TlyA family protein. Hemolysins are
exotoxins that attack blood cell membranes and cause
cell rupture, often by forming a pore in the membrane.
At least two members of this protein family have been
characterized indirectly as pore-forming hemolysins, one
from the spirochete Serpula (Treponema) hyodysenteriae
and one from Mycobacterium tuberculosis. However,
homology domains in this protein suggest
methyltransferase activity (pfam01728) and RNA-binding
activity (pfam01479) [Unknown function, General].
Length = 228
Score = 32.5 bits (74), Expect = 0.39
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148
R D ++ R G +R +A++LI LVN K V+ S + I + +
Sbjct: 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQ 51
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific
[Translation, ribosomal structure and biogenesis].
Length = 289
Score = 32.7 bits (75), Expect = 0.40
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 89 EIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146
E+ + R D + ++ +RS ++LI VN K V SYK+KPGD++ +
Sbjct: 5 EVPEEEAGQRLDKFLAKL-LPISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRI 60
>gnl|CDD|200567 cd10942, CE4_u11, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 252
Score = 31.7 bits (72), Expect = 0.85
Identities = 20/88 (22%), Positives = 30/88 (34%), Gaps = 8/88 (9%)
Query: 168 PFSWITVDA----KKMEGVFKSEPNRSEFANDINDLLKPRIIDVKTLGSNHAKVIMEPFE 223
PF+W VD +G+ + + L+ +D ++ PF
Sbjct: 158 PFAWAAVDGFYYLDSFDGLRGPPQEEVDTPAALAQALR-SALDAVVARGGFLTIVFHPFL 216
Query: 224 RGYGYTLG---NALRRVLLSSMIGCAPT 248
G L LRR+ S I CAP
Sbjct: 217 SGSPERLAVFEQVLRRIANDSRIWCAPA 244
>gnl|CDD|187730 cd08702, Arna_FMT_C, C-terminal subdomain of the formyltransferase
domain on ArnA, which modifies lipid A with
4-amino-4-deoxy-l-arabinose. Domain found in ArnA with
similarity to the C-terminal domain of
Formyltransferase. ArnA is a bifunctional enzyme
required for the modification of lipid A with
4-amino-4-deoxy-l-arabinose (Ara4N) that leads to
resistance to cationic antimicrobial peptides (CAMPs)
and clinical antimicrobials such as polymyxin. The
C-terminal domain of ArnA is a dehydrogenase domain that
catalyzes the oxidative decarboxylation of
UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose
(UDP-Ara4O) and the N-terminal domain is a
formyltransferase domain that catalyzes the addition of
a formyl group to UDP-4-amino-4-deoxy-L-arabinose
(UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose
(UDP-L-Ara4FN). This domain family represents the
C-terminal subdomain of the formyltransferase domain,
downstream of the N-terminal subdomain containing the
catalytic center. ArnA forms a hexameric structure (a
dimer of trimers), in which the dehydrogenase domains
are arranged at the center with the transformylase
domains on the outside of the complex.
Length = 92
Score = 28.7 bits (65), Expect = 2.3
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 5/47 (10%)
Query: 495 AFSYLRDRKITI--KLFSELGPRYIKINGGYVRILKMGFRV--GDNA 537
AF+++ +KI I + Y G + + V GD A
Sbjct: 28 AFTFVGGQKIKIWKARPVD-DAFYNGEPGKVLSVDGDPLIVACGDGA 73
>gnl|CDD|216240 pfam01008, IF-2B, Initiation factor 2 subunit family. This family
includes initiation factor 2B alpha, beta and delta
subunits from eukaryotes, initiation factor 2B subunits
1 and 2 from archaebacteria and some proteins of unknown
function from prokaryotes. Initiation factor 2 binds to
Met-tRNA, GTP and the small ribosomal subunit. Members
of this family have also been characterized as
5-methylthioribose- 1-phosphate isomerases, an enzyme of
the methionine salvage pathway. The crystal structure of
Ypr118w, a non-essential, low-copy number gene product
from Saccharomyces cerevisiae, reveals a dimeric protein
with two domains and a putative active site cleft.
Length = 281
Score = 30.3 bits (69), Expect = 2.5
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRA--FLV-----NKKIVNIASYKIKPGDII 144
R ++ + SS EA++ + A F+ +KI IA+ IK GD I
Sbjct: 58 RLLRIISELHSSSDVEEAKESLIEAADEFIDEIEEARRKIGAIAAELIKDGDTI 111
>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated.
Length = 237
Score = 29.8 bits (68), Expect = 3.4
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 106 MGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG--DIISV 146
+G++ T EA+++I+ LV+ ++ YK G D+IS+
Sbjct: 48 LGYADTAREAKKIINEGKVLVDGRVRK--DYKFPVGLMDVISI 88
>gnl|CDD|181104 PRK07758, PRK07758, hypothetical protein; Provisional.
Length = 95
Score = 28.0 bits (62), Expect = 3.8
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 377 LTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRG 426
L+ + L+ IH + +L + SE E+L+ +G SL ++++ L G
Sbjct: 42 LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESG 91
>gnl|CDD|224109 COG1188, COG1188, Ribosome-associated heat shock protein implicated
in the recycling of the 50S subunit (S4 paralog)
[Translation, ribosomal structure and biogenesis].
Length = 100
Score = 28.0 bits (63), Expect = 4.0
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVR 147
R D ++ F RS A+++I VN + S ++K GDI+++R
Sbjct: 10 RLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRAK-PSKEVKVGDILTIR 58
>gnl|CDD|239013 cd02058, PAI-2, Plasminogen Activator Inhibitor-2 (PAI-2). PAI-2 is
a serine protease inhibitor that belongs to the
ov-serpin branch of the serpin superfamily. It is is an
effective inhibitor of urinary plasminogen activator
(urokinase or uPA) and is involved in cell
differentiation, tissue growth and regeneration.
Length = 380
Score = 29.3 bits (66), Expect = 5.1
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 386 KAENIHC-----IGDLIQRSENELLRTPN--LGRKSLNEIKEILASRGKYY 429
+E+IH + ++ + N LL++ N G K+ +++ L KYY
Sbjct: 63 NSEDIHSGFQSLLSEINKPGTNYLLKSANRLYGEKTYPFLEKFLQLTQKYY 113
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 29.5 bits (67), Expect = 5.5
Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 23/91 (25%)
Query: 66 YGILEKQFRRYFIEGARLKGKTGEIIL------KLLESRFDNVVYRMGFSSTRSEAR-QL 118
Y + F YF E A +++ + LE+R G + A L
Sbjct: 163 YSLYATLFPVYFEEAA--------MLIFLFLLGRYLEAR------AKGRARRAIRALLDL 208
Query: 119 ISHRAFLV--NKKIVNIASYKIKPGDIISVR 147
A +V + + + +++ GDI+ VR
Sbjct: 209 APKTATVVRGDGEEEEVPVEEVQVGDIVLVR 239
>gnl|CDD|226648 COG4185, COG4185, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 187
Score = 28.6 bits (64), Expect = 5.9
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 297 GKCVVLAS-DIELLSDIELVNPNHIIAHLS--DNEEAIRQSARVLVDQLN 343
GK V AS LL I VN + I A +S + A Q+ARV +D++
Sbjct: 14 GKSTVYASTLAPLLPGIVFVNADEIAAQISPDNPTSAAIQAARVAIDRIA 63
>gnl|CDD|188295 TIGR03180, UraD_2, OHCU decarboxylase. Previously thought to only
proceed spontaneously, the decarboxylation of
2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU)
has been recently been shown to be catalyzed by this
enzyme in Mus musculus. Homologs of this enzyme are
found adjacent to and fused with uricase in a number of
prokaryotes and are represented by this model. This
model is a separate (but related) clade from that
represented by TIGR3164. This model places a second
homolog in streptomyces species which (are not in the
vicinity of other urate catabolism associated genes)
below the trusted cutoff.
Length = 158
Score = 28.2 bits (63), Expect = 7.5
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 70 EKQFRRYFIEGARLKGKTGEIILKLLESRFDN 101
E++F R F+ R G++ E +L L++R N
Sbjct: 104 EEKFGRIFL--IRAAGRSAEEMLDALQARLQN 133
>gnl|CDD|239386 cd03112, CobW_like, The function of this protein family is unkown.
The amino acid sequence of YjiA protein in E. coli
contains several conserved motifs that characterizes it
as a P-loop GTPase. YijA gene is among the genes
significantly induced in response to DNA-damage caused
by mitomycin. YijA gene is a homologue of the CobW gene
which encodes the cobalamin synthesis protein/P47K.
Length = 158
Score = 28.0 bits (63), Expect = 8.7
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 301 VLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSA---RVLV 339
LA L I LV+ H HL EA Q A R+L+
Sbjct: 112 ELAERYLLDGVITLVDAKHANQHLDQQTEAQSQIAFADRILL 153
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 28.9 bits (66), Expect = 8.9
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 318 NHIIAHLSDNEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVDPILLRPVDDLEL 377
I+A L E + ++ DQL++FA E +P+ + L+ +DP L P + L L
Sbjct: 790 REILAQLESASEKAKAASA-EEDQLSLFAEPEESPLLEA----LKALDPDNLTPREALNL 844
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
0.321 0.138 0.385
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,377,444
Number of extensions: 2883077
Number of successful extensions: 2843
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2822
Number of HSP's successfully gapped: 78
Length of query: 550
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 448
Effective length of database: 6,413,494
Effective search space: 2873245312
Effective search space used: 2873245312
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: 61 (27.2 bits)