RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4154
(346 letters)
>gnl|CDD|217417 pfam03194, LUC7, LUC7 N_terminus. This family contains the N
terminal region of several LUC7 protein homologues and
only contains eukaryotic proteins. LUC7 has been shown
to be a U1 snRNA associated protein with a role in
splice site recognition. The family also contains human
and mouse LUC7 like (LUC7L) proteins and human cisplatin
resistance-associated overexpressed protein (CROP).
Length = 252
Score = 261 bits (668), Expect = 1e-86
Identities = 122/247 (49%), Positives = 167/247 (67%), Gaps = 36/247 (14%)
Query: 16 GESNKYNVKFFDSKVCKSFLLTCCPHEILSSTRMDLGECPKIHDLALRADYEKASKNRDY 75
G+ ++ +VKF D +VC+S+L+ CPH++ +T+MDLG CPK+HDL L+ADYE+ASK++DY
Sbjct: 18 GDESRQSVKFDDREVCRSYLVGFCPHDLFQNTKMDLGPCPKVHDLKLKADYERASKSQDY 77
Query: 76 YYDIDRMDLGECPKIHDLALRADYEKASKNRDYYYDIDAMEHLQAFISDCDRRTELAKQR 135
+ Y+++A+E L+ F+ DCDR+ + AKQR
Sbjct: 78 FP--------------------------------YEVEALEILERFVHDCDRKIDKAKQR 105
Query: 136 LLETQEVLSAEVAE-KANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKK 194
L TQE + A+ KA + +L E+IGK LA+AE LG EG V+E++KLM E+E+L+ KK
Sbjct: 106 LELTQEEQTKIAADSKAEELAELDEEIGKLLAEAEALGEEGKVDEAMKLMKEVEELKAKK 165
Query: 195 AEAEDT--YRNSMPAS-SYQQQKLRVCEVCSAYLGIHDNDRRLADHFGGKLHLGFIKIRE 251
E ED+ RN+ P+S QQQKLRVCEVC AYL DNDRRLADHFGGKLHLG++K+RE
Sbjct: 166 KELEDSDEVRNAAPSSAQAQQQKLRVCEVCGAYLSRLDNDRRLADHFGGKLHLGYVKVRE 225
Query: 252 KLAELQA 258
KLAEL+
Sbjct: 226 KLAELKE 232
Score = 85.2 bits (211), Expect = 3e-19
Identities = 39/77 (50%), Positives = 55/77 (71%), Gaps = 1/77 (1%)
Query: 255 ELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAE-KANAVHQLAEDIGKKLAKAE 313
E++A+E L+ F+ DCDR+ + AKQRL TQE + A+ KA + +L E+IGK LA+AE
Sbjct: 81 EVEALEILERFVHDCDRKIDKAKQRLELTQEEQTKIAADSKAEELAELDEEIGKLLAEAE 140
Query: 314 ELGAEGFVEESLKLMTE 330
LG EG V+E++KLM E
Sbjct: 141 ALGEEGKVDEAMKLMKE 157
>gnl|CDD|227527 COG5200, LUC7, U1 snRNP component, mediates U1 snRNP association
with cap-binding complex [RNA processing and
modification].
Length = 258
Score = 136 bits (344), Expect = 3e-38
Identities = 67/235 (28%), Positives = 107/235 (45%), Gaps = 35/235 (14%)
Query: 23 VKFFDSKVCKSFLLTCCPHEILSSTRMDLGECPKIHDLALRADYEKASKNRDYYYDIDRM 82
F D KVC S L+ CP ++ +T+ LG+CP H+ + Y
Sbjct: 26 THFTDKKVCISMLVGFCPFDLFRNTKRSLGKCPTSHE--------------EKY------ 65
Query: 83 DLGECPKIHDLALRADYEKASKNRDYYYDIDAMEHLQAFISDCDRRTELAKQRLLETQEV 142
+A+YE+ + R Y+ + + L + C+ A T E
Sbjct: 66 -------------KAEYERNGRERAEEYEWEYLRLLVRIVLSCNDGIRAAGLEDRTTPE- 111
Query: 143 LSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKKAEAEDTYR 202
++ EK +++ E IG+ + + L VE + E+E LR+++ E ++
Sbjct: 112 EFGKIKEKEELFNRVDESIGELGMEGDALAKRKLVERACSAFNELERLREERKEIKEAVY 171
Query: 203 NSMP-ASSYQQQKLRVCEVCSAYLGIHDNDRRLADHFGGKLHLGFIKIREKLAEL 256
+ + QKL+VC +C AYL D DRRLADHF GKLHLG++ +R LA+L
Sbjct: 172 SMVENNGQGTHQKLQVCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVRSDLADL 226
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5'
exonuclease domain of Bacillus stearothermophilus DNA
polymerase I and similar family-A DNA polymerases.
Bacillus stearothermophilus-like Polymerase I (Pol I), a
subgroup of the family-A DNA polymerases, contains an
inactive DnaQ-like 3'-5' exonuclease domain in the same
polypeptide chain as the polymerase region. The
exonuclease-like domain of these proteins possess the
same fold as the Klenow fragment (KF) of Escherichia
coli Pol I, but does not contain the four critical
metal-binding residues necessary for activity. The
function of this domain is unknown. It might act as a
spacer between the polymerase and the 5'-3' exonuclease
domains. Some members of this subgroup, such as those
from Bacillus sphaericus and Thermus aquaticus, are
thermostable DNA polymerases.
Length = 178
Score = 34.9 bits (81), Expect = 0.024
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 12/81 (14%)
Query: 110 YDID--AMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAK 167
YD+ A +L + + + + +EVL+ +A KA A+ +LA + ++L +
Sbjct: 99 YDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEE 158
Query: 168 AEELGAEGFVEESLKLMTEIE 188
E L+L E+E
Sbjct: 159 ----------NEQLELYYEVE 169
Score = 30.7 bits (70), Expect = 0.79
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 253 LAELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKA 312
LA+L A +L + + + + +EVL+ +A KA A+ +LA + ++L +
Sbjct: 101 LADL-AKRYLGRELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEEN 159
Query: 313 E 313
E
Sbjct: 160 E 160
>gnl|CDD|172460 PRK13954, mscL, large-conductance mechanosensitive channel;
Provisional.
Length = 119
Score = 33.3 bits (76), Expect = 0.056
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 161 IGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKK 194
I L K EE E VEE++ L+TEI DL ++K
Sbjct: 86 IANTLMKKEEAEEEAVVEENVVLLTEIRDLLREK 119
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 32.9 bits (75), Expect = 0.24
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 248 KIREKLAELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVHQ-LAEDIG 306
+ R+K + QA E Q ++ +R +L K+RL ++ AE A K A+ Q AE+
Sbjct: 79 EQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAA 138
Query: 307 KKLAKAEELGAE 318
K A A + AE
Sbjct: 139 AKAAAAAKAKAE 150
Score = 30.5 bits (69), Expect = 1.1
Identities = 30/104 (28%), Positives = 47/104 (45%), Gaps = 1/104 (0%)
Query: 96 RADYEKASKNRDYYYDIDAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVH 155
+ ++A + R A E Q ++ +R +L K+RL ++ AE A K A+
Sbjct: 71 QKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALK 130
Query: 156 Q-LAEDIGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKKAEAE 198
Q AE+ K A A + AE + + + KKKAEAE
Sbjct: 131 QKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAE 174
>gnl|CDD|131530 TIGR02477, PFKA_PPi, diphosphate--fructose-6-phosphate
1-phosphotransferase. Diphosphate--fructose-6-phosphate
1-phosphotransferase catalyzes the addition of phosphate
from diphosphate (PPi) to fructose 6-phosphate to give
fructose 1,6-bisphosphate (EC 2.7.1.90). The enzyme is
also known as pyrophosphate-dependent
phosphofructokinase. The usage of PPi-dependent enzymes
in glycolysis presumably frees up ATP for other
processes. TIGR02482 represents the ATP-dependent
6-phosphofructokinase enzyme contained within Pfam
pfam00365: Phosphofructokinase. This model hits
primarily bacterial, plant alpha, and plant beta
sequences [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 539
Score = 31.5 bits (72), Expect = 0.65
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 14/93 (15%)
Query: 137 LETQE---VLSAEVAEKANAVHQLAEDIGKKLAKAEELG--------AEGFVE---ESLK 182
L+T ++ EVA K + QL + I + K G EG +E E
Sbjct: 259 LQTHPNVCIIGEEVAAKKMTLSQLTDYIADVIVKRAAKGKNFGVILIPEGLIEFIPEVQA 318
Query: 183 LMTEIEDLRKKKAEAEDTYRNSMPASSYQQQKL 215
L+ E+ +L + E N S + L
Sbjct: 319 LIKELNNLLAQNVLEEGRKDNVQSKLSPSSKAL 351
>gnl|CDD|133410 cd04783, HTH_MerR1, Helix-Turn-Helix DNA binding domain of the
MerR1 transcription regulator. Helix-turn-helix (HTH)
transcription regulator MerR1. MerR1 transcription
regulators, such as Tn21 MerR and Tn501 MerR, mediate
response to mercury exposure in eubacteria. These
proteins are comprised of distinct domains that harbor
the regulatory (effector-binding) site and the active
(DNA-binding) site. Their conserved N-terminal domains
contain winged HTH motifs that mediate DNA binding,
while the C-terminal domains have three conserved
cysteines that define a mercury binding site. These
proteins share the N-terminal DNA binding domain with
other transcription regulators of the MerR superfamily
that promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 126
Score = 29.9 bits (68), Expect = 0.71
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 232 RRLADHFGGKLHLGFIKIREKLAELQAMEH-LQAFISDCDRRTELAKQRLLETQE 285
R LA+ KL ++ EK+A+LQ M LQ +S C ++ E
Sbjct: 79 RELAEQ---KLA----EVDEKIADLQRMRASLQELVSQCAATKNNVSCPIIAALE 126
>gnl|CDD|235001 PRK02107, PRK02107, glutamate--cysteine ligase; Provisional.
Length = 523
Score = 31.3 bits (72), Expect = 0.86
Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 7/52 (13%)
Query: 93 LALRADYEKASKNRDYYYDIDAMEHLQAFISDCDRRTELAKQRLLETQEVLS 144
LAL Y R + E +A + LA+Q LE + LS
Sbjct: 466 LALAEAY--REYLRAEPLSALSEEDFEA-----EAEASLARQAELEAADTLS 510
>gnl|CDD|133398 cd04770, HTH_HMRTR, Helix-Turn-Helix DNA binding domain of Heavy
Metal Resistance transcription regulators.
Helix-turn-helix (HTH) heavy metal resistance
transcription regulators (HMRTR): MerR1 (mercury), CueR
(copper), CadR (cadmium), PbrR (lead), ZntR (zinc),
and other related proteins. These transcription
regulators mediate responses to heavy metal stress in
eubacteria. They belong to the MerR superfamily of
transcription regulators that promote transcription of
various stress regulons by reconfiguring the operator
sequence located between the -35 and -10 promoter
elements. A typical MerR regulator is comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their N-terminal domains are homologous and
contain a DNA-binding winged HTH motif, while the
C-terminal domains are often dissimilar and bind
specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 123
Score = 29.5 bits (67), Expect = 1.0
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 249 IREKLAELQAMEH-LQAFISDCDRRTE 274
+ K+AELQA+ L +S CD
Sbjct: 91 VEAKIAELQALRAELAGLLSACDGDES 117
>gnl|CDD|237851 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
Length = 539
Score = 30.7 bits (69), Expect = 1.4
Identities = 29/122 (23%), Positives = 49/122 (40%), Gaps = 16/122 (13%)
Query: 56 KIHDLALRADYEKASKNRDYYYDIDRMDLGECPKIHDLALRADYEKASKNRDYYYDIDAM 115
+I +A R DY+ S ++D + +L R + + S R Y+D +
Sbjct: 261 EIEGIANRTDYDLGSHSKD-------------QEQLNLTARVNPNEDSTARLTYFDQASG 307
Query: 116 EHLQAFI---SDCDRRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELG 172
H+ ++ S R LA +E+ A EK AV E K + ++E+L
Sbjct: 308 RHVVPYVIEPSAGVGRCMLAVMCEGYAEELTKAIPGEKLAAVGDALEAFLKSVGRSEKLA 367
Query: 173 AE 174
E
Sbjct: 368 GE 369
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 30.4 bits (69), Expect = 1.6
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 156 QLAEDIGKKLAKAEELGAEGFVEESLKLMTEI-EDLRKKKAEAEDTYRNSMPASSYQQQK 214
+ I K E++ EES +++ EI +L++K+ E D S+ A + +
Sbjct: 547 ADMQAIEDGKKKKEDV-----TEESREMLKEILSELKEKRKEIGDHLAGSLKAENRSLKT 601
Query: 215 LRVCEVCSAYLGI 227
+ C C L I
Sbjct: 602 IGKCPECGGDLII 614
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 30.4 bits (69), Expect = 1.7
Identities = 42/204 (20%), Positives = 74/204 (36%), Gaps = 32/204 (15%)
Query: 118 LQAFISDCDRRTELAKQR---LLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAE 174
L IS +++ ++ ++R L E L A++ E + + +LAE+ LA+ EE
Sbjct: 293 LANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEE----LAELEE---- 344
Query: 175 GFVEESLKLMTEIEDLRKKKAEAEDTYRNSMPASSYQQQKLR--VCEVCSAYLGIHDNDR 232
+ +L E+E L + E E +++L +V L I +
Sbjct: 345 ----KLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNN 400
Query: 233 RLADHFGGKLHLGFIKIREKLAELQAM-EHLQAFISDCDRRTELAKQRLLETQEVLSAEV 291
+ ++ +L L+ E LQ I + +L + L E Q L
Sbjct: 401 EI------------ERLEARLERLEDRRERLQQEIE--ELLKKLEEAELKELQAELEELE 446
Query: 292 AEKANAVHQLAEDIGKKLAKAEEL 315
E +L EEL
Sbjct: 447 EELEELQEELERLEEALEELREEL 470
Score = 28.1 bits (63), Expect = 8.6
Identities = 32/188 (17%), Positives = 60/188 (31%), Gaps = 28/188 (14%)
Query: 127 RRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTE 186
L E E L +A + L E I + E L AE +EE +L+ E
Sbjct: 813 TLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAE--IEELEELIEE 870
Query: 187 IEDLRKKKAEAEDTYRNSMPASSYQQQKLRVCEVCSAYLGIHDNDRRLADHFGGKLHLGF 246
+E + + ++ + ++L + R +
Sbjct: 871 LESELEALLNERASLEEALALLRSELEEL-------------SEELRELES--------- 908
Query: 247 IKIREKLAELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIG 306
++ + +E L+ ++ + R E + R+ QE LS E + L I
Sbjct: 909 ----KRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEEYSLTLEEAEALENKIE 964
Query: 307 KKLAKAEE 314
+A
Sbjct: 965 DDEEEARR 972
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 30.0 bits (69), Expect = 1.8
Identities = 25/118 (21%), Positives = 43/118 (36%), Gaps = 26/118 (22%)
Query: 91 HDL-ALRADYE---KASKNRDYYYDIDAMEHLQAFISDCDRRTELAK-QRLLETQEVLSA 145
D+ +R + E +A R + D+D + L D +RR + + L + LS
Sbjct: 2 LDIKLIRENPEAVKEALAKRGFPLDVDELLEL-----DEERRELQTELEELQAERNALSK 56
Query: 146 EVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKKAEAEDTYRN 203
E+ + ED +A+ +EL E I+ L + E E
Sbjct: 57 EIGQAKRK----GEDAEALIAEVKELKEE------------IKALEAELDELEAELEE 98
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 29.9 bits (68), Expect = 1.9
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 240 GKLHLGFIKIREKLAELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVH 299
G LHLG++ KL + Q H + F D + E +++LS E NA
Sbjct: 16 GPLHLGYLVPLMKLVQFQQAGH-EVFFLIGDLTAIIGDPSKSEERKLLSREE-VLENAKA 73
Query: 300 QLA 302
QLA
Sbjct: 74 QLA 76
>gnl|CDD|215380 PLN02710, PLN02710, farnesyltranstransferase subunit beta.
Length = 439
Score = 29.4 bits (66), Expect = 2.8
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 19/71 (26%)
Query: 7 FANFSINFPGESNKYNVKFFDSKVCKSFLLTCCPHEILSSTRMDLGECPKIHDLALRADY 66
++ +F SN+ F S + ++L C ++ D LR
Sbjct: 327 YSKVGFDFIKASNQQMGPLFHSIALQQYILLCS----------------QVLDGGLR--- 367
Query: 67 EKASKNRDYYY 77
+K K+RDYY+
Sbjct: 368 DKPGKSRDYYH 378
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 29.5 bits (67), Expect = 3.0
Identities = 27/110 (24%), Positives = 44/110 (40%), Gaps = 18/110 (16%)
Query: 135 RLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKK 194
L+ QE L E+A +L + E +EE +L E+E L+KK
Sbjct: 708 EYLQEQEDLLKEIASLLKVPPELLPKV------------ERLLEELKELEKELERLKKKL 755
Query: 195 AEAEDTYRNSMPASSYQQQKLRVCEVCSAYLGIHDND--RRLADHFGGKL 242
A AE S+ + +++ +V + + D R +AD KL
Sbjct: 756 AAAELADL----LSNAKAEEIGGVKVLAKEVDGADMKELREIADDLKKKL 801
>gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase.
Length = 357
Score = 29.4 bits (66), Expect = 3.1
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 239 GGKLHLGFIKIREKLAELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAV 298
GG H+G +KI +AM H IS D++ E A + L ++S++ AE A
Sbjct: 190 GGVGHMG-VKIA------KAMGHHVTVISSSDKKREEALEHLGADDYLVSSDAAEMQEAA 242
Query: 299 HQL 301
L
Sbjct: 243 DSL 245
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 29.1 bits (65), Expect = 3.2
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 133 KQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEEL----GAEGFVEESLK-LMTEI 187
K+ E +E L EK + +L E + E L +EE LK L E+
Sbjct: 134 KEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEV 193
Query: 188 EDLRKKKAEAED 199
DL+K+ E E
Sbjct: 194 YDLKKRWDELEP 205
>gnl|CDD|133406 cd04779, HTH_MerR-like_sg4, Helix-Turn-Helix DNA binding domain of
putative transcription regulators from the MerR
superfamily. Putative helix-turn-helix (HTH) MerR-like
transcription regulators (subgroup 4). Based on sequence
similarity, these proteins are predicted to function as
transcription regulators that mediate responses to
stress in eubacteria. They belong to the MerR
superfamily of transcription regulators that promote
transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of two distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 134
Score = 28.2 bits (63), Expect = 3.7
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 109 YYDIDAMEHLQAFISDC-DRRTELAKQR-LLETQEVLSAEVAEKANAVHQLAEDIGKKLA 166
YYD A++ LQ I +R LA+ + LE + E E A V + + I
Sbjct: 37 YYDETALDRLQ-LIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEH 95
Query: 167 KAEEL 171
+ ++L
Sbjct: 96 RLKQL 100
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at their
amino terminus. This family represents the rest of these
proteins.
Length = 244
Score = 28.6 bits (64), Expect = 4.0
Identities = 22/79 (27%), Positives = 35/79 (44%)
Query: 240 GKLHLGFIKIREKLAELQAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVH 299
K++++ E Q +E + + +RR E E +E L AEV E V
Sbjct: 33 ETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERERLEAEVDEATAEVA 92
Query: 300 QLAEDIGKKLAKAEELGAE 318
+L E+ KK A+ +L E
Sbjct: 93 KLEEEREKKEAETRQLQQE 111
Score = 28.2 bits (63), Expect = 6.2
Identities = 29/137 (21%), Positives = 42/137 (30%), Gaps = 14/137 (10%)
Query: 127 RRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTE 186
RR E E +E L AEV E V +L E+ KK A+ +L E L
Sbjct: 64 RRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQE--------LREA 115
Query: 187 IEDLRKKKAEAEDTYRNSMPASSYQQQKLRVCEVCSAYLGIHDNDRRLADHFGGKLHLGF 246
E + + E + V L DN + +
Sbjct: 116 QEAHERARQELLEAAAAPTAPPHVAAP------VNGEQLEPDDNGEEASADLETDPDMKD 169
Query: 247 IKIREKLAELQAMEHLQ 263
E++ + E LQ
Sbjct: 170 RSEEERVTYAEKNERLQ 186
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 28.9 bits (66), Expect = 4.5
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 141 EVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEIE 188
E + AE A+ +L E + KL + L L+L EIE
Sbjct: 445 EEAAEYAAEDADVTLRLHEVLKPKLLEEPGL---------LELYEEIE 483
>gnl|CDD|133412 cd04785, HTH_CadR-PbrR-like, Helix-Turn-Helix DNA binding domain of
the CadR- and PbrR-like transcription regulators.
Helix-turn-helix (HTH) CadR- and PbrR-like transcription
regulators. CadR and PbrR regulate expression of the
cadmium and lead resistance operons, respectively. These
proteins are comprised of distinct domains that harbor
the regulatory (effector-binding) site and the active
(DNA-binding) site. Their conserved N-terminal domains
contain predicted winged HTH motifs that mediate DNA
binding, while the C-terminal domains have three
conserved cysteines which comprise a putative metal
binding site. Some members in this group have a
histidine-rich C-terminal extension. These proteins
share the N-terminal DNA binding domain with other
transcription regulators of the MerR superfamily that
promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 126
Score = 27.5 bits (62), Expect = 4.7
Identities = 11/42 (26%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 243 HLGFIKIREKLAELQAMEH-LQAFISDCDRRTELAKQRLLET 283
HL +R ++A+L+ +E L+ ++ C +A R++E
Sbjct: 87 HLA--DVRARIADLRRLEAELKRMVAACS-GGRVADCRIIEA 125
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 28.9 bits (65), Expect = 4.8
Identities = 38/209 (18%), Positives = 77/209 (36%), Gaps = 34/209 (16%)
Query: 116 EHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEG 175
++ I ++ E K+RL E +E LS+ E N +L E + E+L
Sbjct: 719 GEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLE 778
Query: 176 FVEESLKLMTEIEDLRKKKAEAE--DTYRNSMPASSYQQQKLRVCEVCSAYLGIHDNDRR 233
L+ + + +AE + + + A + + +++
Sbjct: 779 EALNDLEARLSHSRIPEIQAELSKLEEEVSRIEAR------------------LREIEQK 820
Query: 234 LADHFGGKLHLGFIKIREKLAELQAMEHLQAFISDC-DRRTELAKQ-RLLETQ-EVLSAE 290
L +L L ++ E + ++ LQ D ++ + K+ L + E L E
Sbjct: 821 L-----NRLTL-----EKEYLE-KEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEE 869
Query: 291 VAEKANAVHQLAEDIGKKLAKAEELGAEG 319
+ E A+ L +G + +EL A+
Sbjct: 870 LEELEAALRDLESRLGDLKKERDELEAQL 898
Score = 28.9 bits (65), Expect = 4.9
Identities = 21/109 (19%), Positives = 39/109 (35%), Gaps = 6/109 (5%)
Query: 100 EKASKNRDYYYDIDA-MEHLQAFISDCDRRTELA---KQRLLETQEVLSAEVAEKANAVH 155
+ SK + I+A + ++ ++ E Q L E + L ++ +
Sbjct: 798 AELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIE 857
Query: 156 QLAEDIGKKLAKAEEL-GAEGFVEESLK-LMTEIEDLRKKKAEAEDTYR 202
L + + EEL A +E L L E ++L + E E
Sbjct: 858 NLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIE 906
>gnl|CDD|178009 PLN02383, PLN02383, aspartate semialdehyde dehydrogenase.
Length = 344
Score = 28.6 bits (64), Expect = 5.4
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 281 LETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEQTSSCSPGHV 340
+T+EVL + Q A ++ A +E G + EE +KL+ E + V
Sbjct: 181 QQTREVLEGKPPTCNIFAQQYAFNLFSHNAPMQENG---YNEEEMKLVKETRKIWNDDDV 237
Query: 341 PL 342
+
Sbjct: 238 KV 239
>gnl|CDD|235735 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 28.2 bits (63), Expect = 6.8
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 158 AEDIGKKLAKAEELGAEGFVEESLKLMTEIEDLRKKK 194
E++ KL KA +L +G ++K + E E L+K K
Sbjct: 274 REEMSNKLKKAIDLKKKGQ---NIKFLNEEEFLQKCK 307
>gnl|CDD|206160 pfam13990, YjcZ, YjcZ-like protein. This family of proteins is
functionally uncharacterized. The family includes the
YjcZ protein from E. coli. This family of proteins is
found in enteric bacteria. Proteins in this family are
approximately 300 amino acids in length. There are two
conserved sequence motifs: FGD and MPR.
Length = 270
Score = 28.1 bits (63), Expect = 7.3
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 18/65 (27%)
Query: 278 QRLLETQEVLSAEVAEKANAVHQLAEDIGKKLAKAEELGAEGFVEESLKLMTEQTSSCSP 337
+RL + L+ + AE+ A++ A+G +E L+ + + TSS P
Sbjct: 25 ERL---TQELTGQSAERQWAMNGNL--------------AQG-LEARLQWLEKLTSSLDP 66
Query: 338 GHVPL 342
GH+ L
Sbjct: 67 GHLAL 71
>gnl|CDD|224881 COG1970, MscL, Large-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 130
Score = 27.3 bits (61), Expect = 7.6
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 163 KKLAKAEELGAEGFVEESLKLMTEIEDLRKKK 194
+KL K E L+TEI DL KK+
Sbjct: 99 RKLEKEEPEAPAPAPPAEEVLLTEIRDLLKKQ 130
>gnl|CDD|214384 CHL00174, accD, acetyl-CoA carboxylase beta subunit; Reviewed.
Length = 296
Score = 27.9 bits (63), Expect = 7.7
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 212 QQKLRVCEVCSAYLGIHDNDR 232
+ K+ +CE C +L + +DR
Sbjct: 54 KSKMNICEQCGYHLKMSSSDR 74
>gnl|CDD|235937 PRK07111, PRK07111, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 735
Score = 28.0 bits (63), Expect = 8.3
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 112 IDAMEHLQAFISDCDRRTELAKQRLLETQEVLSAEVAEKANA-VHQLAEDIGKKLAK-AE 169
I+A + + F D R ELA ++LL EV V +G+ L K +E
Sbjct: 456 IEAKKDIDKFFELLDERLELAIEQLLHRYEVQK-------TLKVKDFPFLMGQGLWKGSE 508
Query: 170 ELGAEGFVEESLK 182
LG + +E LK
Sbjct: 509 NLGPDDSIEPVLK 521
>gnl|CDD|177993 PLN02365, PLN02365, 2-oxoglutarate-dependent dioxygenase.
Length = 300
Score = 27.8 bits (62), Expect = 9.0
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 19/94 (20%)
Query: 92 DLALRADYEKASKNRDYY-----YDIDAMEHLQAFISDCDRRTELAKQRLLETQEVLSAE 146
D+ L + Y S+ Y YD+ + + + F C + QR E
Sbjct: 66 DVILGSGYMAPSEVNPLYEALGLYDMASPQAVDTF---CSQLDASPHQR----------E 112
Query: 147 VAEK-ANAVHQLAEDIGKKLAKAEELGAEGFVEE 179
+K A A+H LA D+ +KLA++ L F +
Sbjct: 113 TIKKYAKAIHDLAMDLARKLAESLGLVEGDFFQG 146
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
0.317 0.132 0.376
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,348,800
Number of extensions: 1683461
Number of successful extensions: 2361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2304
Number of HSP's successfully gapped: 157
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)