RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16234
(609 letters)
>gnl|CDD|216175 pfam00888, Cullin, Cullin family.
Length = 603
Score = 416 bits (1071), Expect = e-139
Identities = 188/447 (42%), Positives = 263/447 (58%), Gaps = 8/447 (1%)
Query: 69 LYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVSSYPK 128
+Y + FE FLE + E+YK E+SK LQ +VS+YM++V + L EE R +LH S+ K
Sbjct: 164 VYKEDFEKPFLEATSEFYKKESSKFLQENSVSEYMKKVEERLEEEEERVRLYLHSSTEKK 223
Query: 129 VKAKCEQHMVADHLNFLQGECVPMVAEERRHDLANMYPLLRSVREGINILIDAVRDHICK 188
+ CE+ ++ HL FL E ++ E+ DL MY LL V G+ L HI K
Sbjct: 224 LIEVCEKVLIEKHLEFLHSEFQRLLDNEKIEDLRRMYRLLSRVPNGLEPLRKYFEKHIKK 283
Query: 189 QGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFD 248
+GL A+S L+ + +V+ +L +H KY + V E F+ D F+ ALDKA IN
Sbjct: 284 EGLAAVSDLAVETDPKDYVQTLLELHDKYDSLVNEAFNNDALFLNALDKAFEEFIN---- 339
Query: 249 PKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLA 308
SKS E LAKYCD LLKKS KGL+E E+++KL + I +FKYI+DKDVF KFY KMLA
Sbjct: 340 -SNSSKSAELLAKYCDSLLKKSLKGLNEEELEEKLDKIIVLFKYIEDKDVFEKFYRKMLA 398
Query: 309 KRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKISGGLNEKFHSEFVKTN-E 367
KRL++ S S D E+ MI KLKQ CGY+FT+K RM DI +S LN F +
Sbjct: 399 KRLLNGTSASDDAEKKMIEKLKQECGYQFTSKLERMFKDISLSKELNNSFKNHLENNLDL 458
Query: 368 IDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLHNIS 427
+ GI S+ +L G WP PT FS+P+ELEK + FE+FY + +GRKL+WLH++
Sbjct: 459 LSEGIDLSVLVLSTGFWPTLPT--EPFSLPEELEKALEKFEEFYSKKHSGRKLTWLHSLG 516
Query: 428 QVELKLSYLKRPYFVTMQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVEC 487
+ ELK + + Y +T+ T+QMA+LLLF + +T ++ LS D + R + SL++
Sbjct: 517 RGELKAEFNDKTYELTVSTYQMAVLLLFNDQEELTVEELSEATGLSDDLLRRTLQSLLKA 576
Query: 488 KLLTSNKEELTEDTEIRLNLGYNNKRT 514
K+L K E+ N+ T
Sbjct: 577 KVLLLTKIPKGEEFSPNTVFSLNSDFT 603
Score = 36.1 bits (83), Expect = 0.055
Identities = 16/99 (16%), Positives = 42/99 (42%), Gaps = 10/99 (10%)
Query: 14 WGSLQETIQGVITLGNVRRATWNDRFSDIYSLCVAYPEPLADRLYQETKLFLDQHL---- 69
W L + I I L + + + ++ +Y+ P L ++LY K +L++++
Sbjct: 1 WEKLLDAID-QILLKSFSSLDYMELYTAVYNYV---PHKLGEKLYNRLKEYLEEYVAALL 56
Query: 70 --YVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERV 106
++ + L+ + + ++ + N+ Y+ R
Sbjct: 57 KSILENDDEVLLKTYYKEWNKFSTSMKILNNIFMYLNRY 95
>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 773
Score = 334 bits (858), Expect = e-105
Identities = 180/568 (31%), Positives = 297/568 (52%), Gaps = 30/568 (5%)
Query: 65 LDQHLYVDIFETQFLEMSGEWYKSEASKLLQTCNVSQYMERVLQVLHEETNRSVRFLHVS 124
+ Y +FE FLE + E+Y+ E+S++++ +V++Y+E+ ++L E +L VS
Sbjct: 213 ENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAHKILEREEELVEIYLKVS 272
Query: 125 SYPKVKAKCEQHMVADHLNFL---QGECVPMVAEERRHDLANMYPLLRSVREGINILIDA 181
+ + E ++ HL+ L + L +Y LL + G+ L +
Sbjct: 273 TKKPLLEVLEDVLITRHLDDLEEQGSGFREALDASNLEKLQVLYRLLSETKYGVQPLQEV 332
Query: 182 VRDHICKQGLEA------------ISGLSGDN--ISTQFVENMLAVHKKYKAFVKELFSG 227
++ +G+ G G + +V+ +L+ H + + V E F G
Sbjct: 333 FERYVKDEGVLINIETNYIFHCKVDVGFLGSRECLPKLYVQKLLSCHDLFPSLVNESFEG 392
Query: 228 DQSFMGALDKACSSVINHKFDPKMPSKSPEYLAKYCDMLLKKSSKGLSESEMDDKLSQSI 287
D S + AL A + IN S EYLAKY D LLKK K ++ D L I
Sbjct: 393 DGSIVKALGNAFKTFINGNESAD--SGPSEYLAKYIDGLLKKDGKQSFIGKIKDLLQDII 450
Query: 288 TVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTD 347
T+F+Y+++KDVF K+Y K+LAKRL++ +S S E MI+ LK+ CG EFT+K M D
Sbjct: 451 TLFRYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVCGQEFTSKLEGMFRD 510
Query: 348 IKISGGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMF 407
I +S E F N+ + + +L WPL P + S +P+EL + F
Sbjct: 511 ISLSSEFTEAFQHSPQSYNK---YLDLFVWVLTQAYWPLSPEEV-SIRLPKELVPILEGF 566
Query: 408 EKFYHGQFNGRKLSWLHNISQVELKLSYLKR---PYFVTMQTFQMAILLLFEKNDAMTCG 464
+KFY + NGRKL W ++ E+K + + T +Q+ + LLF ++ +T
Sbjct: 567 KKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTFE 626
Query: 465 DIQTVLSLSQDQIGRHIASLVECKL--LTSNKEELTEDTEIRLNLGYNNKRTKLKISGAV 522
+I + LS D + R + SL KL L + + ++ +T+ +N +++K ++KI+
Sbjct: 627 EILELTKLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIA 686
Query: 523 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISM 581
+ E Q+ T +V+EDR+ LQA IVRIMK+RK+++H L++EV++Q KS F P +SM
Sbjct: 687 ESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSM 746
Query: 582 IKKCIESLIDKNYVERTANSTDEYSYVA 609
+K+ IE+LI+K Y+ER A+ + Y Y+A
Sbjct: 747 VKRAIETLIEKEYLERQADD-EIYVYLA 773
>gnl|CDD|214545 smart00182, CULLIN, Cullin.
Length = 143
Score = 164 bits (418), Expect = 3e-48
Identities = 66/141 (46%), Positives = 87/141 (61%), Gaps = 1/141 (0%)
Query: 292 YIDDKDVFHKFYAKMLAKRLIHQQSTSMDGEEAMINKLKQACGYEFTNKFHRMLTDIKIS 351
YI DKDVF K+Y K LAKRLI +S S D EE MI KLKQ CGYEFT+K RM DI +S
Sbjct: 1 YIQDKDVFEKYYKKHLAKRLILNRSASDDAEENMITKLKQECGYEFTSKLERMFRDISLS 60
Query: 352 GGLNEKFHSEFVKTNEIDLGIHFSINILQAGSWPLGPTVISSFSVPQELEKCIHMFEKFY 411
LN+ F I ++ +L +G WP T + ++PQELE + FE+FY
Sbjct: 61 KDLNQSFKDMLENNPSAKPIIDLNVRVLTSGYWPTSSTEV-EINLPQELEDALEEFEEFY 119
Query: 412 HGQFNGRKLSWLHNISQVELK 432
+ +GRKL+WLH++ + E+K
Sbjct: 120 LAKHSGRKLTWLHSLGRGEVK 140
>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain. This
is the neddylation site of cullin proteins which are a
family of structurally related proteins containing an
evolutionarily conserved cullin domain. With the
exception of APC2, each member of the cullin family is
modified by Nedd8 and several cullins function in
Ubiquitin-dependent proteolysis, a process in which the
26S proteasome recognises and subsequently degrades a
target protein tagged with K48-linked poly-ubiquitin
chains. Cullins are molecular scaffolds responsible for
assembling the ROC1/Rbx1 RING-based E3 ubiquitin
ligases, of which several play a direct role in
tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
protein, which was originally found to be conjugated to
Cdc53, a cullin component of the SCF
(Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
Saccharomyces cerevisiae, and Nedd8 modification has now
emerged as a regulatory pathway of fundamental
importance for cell cycle control and for embryogenesis
in metazoans. The only identified Nedd8 substrates are
cullins. Neddylation results in covalent conjugation of
a Nedd8 moiety onto a conserved cullin lysine residue.
Length = 68
Score = 105 bits (265), Expect = 8e-28
Identities = 40/68 (58%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 595
V+EDRKL +QAAIVRIMKSRK + HN L+ EV+ Q K F PS++ IKK IESLI+K Y+
Sbjct: 1 VEEDRKLEIQAAIVRIMKSRKTLSHNELVAEVIEQLKKRFPPSVADIKKRIESLIEKEYL 60
Query: 596 ERTANSTD 603
ER + +
Sbjct: 61 ERDEDDRN 68
>gnl|CDD|214883 smart00884, Cullin_Nedd8, Cullin protein neddylation domain. This
is the neddylation site of cullin proteins which are a
family of structurally related proteins containing an
evolutionarily conserved cullin domain. With the
exception of APC2, each member of the cullin family is
modified by Nedd8 and several cullins function in
Ubiquitin-dependent proteolysis, a process in which the
26S proteasome recognises and subsequently degrades a
target protein tagged with K48-linked poly-ubiquitin
chains. Cullins are molecular scaffolds responsible for
assembling the ROC1/Rbx1 RING-based E3 ubiquitin
ligases, of which several play a direct role in
tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
protein, which was originally found to be conjugated to
Cdc53, a cullin component of the SCF
(Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
Saccharomyces cerevisiae, and Nedd8 modification has now
emerged as a regulatory pathway of fundamental
importance for cell cycle control and for embryogenesis
in metazoans. The only identified Nedd8 substrates are
cullins. Neddylation results in covalent conjugation of
a Nedd8 moiety onto a conserved cullin lysine residue.
Length = 68
Score = 101 bits (253), Expect = 4e-26
Identities = 39/68 (57%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 537 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 595
V+EDRKL +QAAIVRIMKSRK + H+ L+ EV+ Q K F PS+S IKK IESLI++ Y+
Sbjct: 1 VEEDRKLEIQAAIVRIMKSRKTLSHSELVSEVIEQLKKRFKPSVSDIKKRIESLIEREYL 60
Query: 596 ERTANSTD 603
ER + +
Sbjct: 61 ERDEDDPN 68
>gnl|CDD|205100 pfam12840, HTH_20, Helix-turn-helix domain. This domain represents
a DNA-binding Helix-turn-helix domain found in
transcriptional regulatory proteins.
Length = 61
Score = 36.0 bits (84), Expect = 0.003
Identities = 9/48 (18%), Positives = 20/48 (41%)
Query: 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEE 496
+ IL + +T ++ L + + + H+ L E L+ +E
Sbjct: 13 LRILRALMGGEPLTASELAERLGIPKQTLSYHLRKLEEAGLVEVVREG 60
>gnl|CDD|236654 PRK10141, PRK10141, DNA-binding transcriptional repressor ArsR;
Provisional.
Length = 117
Score = 35.6 bits (82), Expect = 0.016
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKE 495
+LLL E + C D+ T L SQ +I RH+A L E LL K+
Sbjct: 22 VLLLRESGELCVC-DLCTALDQSQPKISRHLALLRESGLLLDRKQ 65
>gnl|CDD|238042 cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and
similar prokaryotic, metal regulated homodimeric
repressors. ARSR subfamily of helix-turn-helix bacterial
transcription regulatory proteins (winged helix
topology). Includes several proteins that appear to
dissociate from DNA in the presence of metal ions.
Length = 78
Score = 33.0 bits (76), Expect = 0.054
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKE 495
+ IL L + +T ++ L LSQ + RH+ L E L+ S +E
Sbjct: 10 LRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE 55
>gnl|CDD|197713 smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon
Repressor.
Length = 66
Score = 31.4 bits (72), Expect = 0.15
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKE 495
IL L + ++ +L LSQ + H+ L E L+ S +E
Sbjct: 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45
>gnl|CDD|223713 COG0640, ArsR, Predicted transcriptional regulators
[Transcription].
Length = 110
Score = 30.6 bits (68), Expect = 0.68
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 449 MAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKE 495
+ IL L + +T G++ L LSQ + H+ L E L+ +E
Sbjct: 28 LEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVELRRE 74
>gnl|CDD|182157 PRK09940, PRK09940, transcriptional regulator YdeO; Provisional.
Length = 253
Score = 32.0 bits (72), Expect = 0.73
Identities = 36/141 (25%), Positives = 57/141 (40%), Gaps = 30/141 (21%)
Query: 201 NISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDPKMPSKSPEYLA 260
N S + + L++ K F+ L +G S G + +++N K P L
Sbjct: 105 NFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKV----RNIVNMKL------AHPWKLK 154
Query: 261 KYCDMLLKKSSKGLSESEMDDKLSQSITVFKYIDDKDVFHKFYAKMLAKRLIHQQSTSMD 320
CD L +SES + KL Q T F I +L R+ Q + ++
Sbjct: 155 DICDCLY------ISESLLKKKLKQEQTTFSQI------------LLDARM--QHAKNLI 194
Query: 321 GEEAMINKLKQACGYEFTNKF 341
E +NK+ + CGY T+ F
Sbjct: 195 RVEGSVNKIAEQCGYASTSYF 215
>gnl|CDD|219475 pfam07583, PSCyt2, Protein of unknown function (DUF1549). A family
of paralogues in the planctomyces.
Length = 200
Score = 29.8 bits (68), Expect = 2.7
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 3/55 (5%)
Query: 195 SGLSGDNISTQFVENMLAVHKKYKAFVKELFSGDQSFMGALDKACSSVINHKFDP 249
L +T F+ + Q+F+G L C+ +HKFDP
Sbjct: 127 DLLPEQLPATGFLRAGPTDRVDPVDDRVDTVG--QAFLG-LTLGCAQCHDHKFDP 178
>gnl|CDD|221778 pfam12802, MarR_2, MarR family. The Mar proteins are involved in
the multiple antibiotic resistance, a non-specific
resistance system. The expression of the mar operon is
controlled by a repressor, MarR. A large number of
compounds induce transcription of the mar operon. This
is thought to be due to the compound binding to MarR,
and the resulting complex stops MarR binding to the DNA.
With the MarR repression lost, transcription of the
operon proceeds. The structure of MarR is known and
shows MarR as a dimer with each subunit containing a
winged-helix DNA binding motif.
Length = 60
Score = 27.5 bits (62), Expect = 3.4
Identities = 11/44 (25%), Positives = 20/44 (45%)
Query: 448 QMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491
Q +LL + +T ++ L LS+ + R + L E L+
Sbjct: 7 QFRVLLALARAGGLTVAELARRLGLSKQTVSRLVKRLEEKGLVE 50
>gnl|CDD|236376 PRK09084, PRK09084, aspartate kinase III; Validated.
Length = 448
Score = 29.4 bits (67), Expect = 5.7
Identities = 18/95 (18%), Positives = 32/95 (33%), Gaps = 9/95 (9%)
Query: 510 NNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVL 569
+N T+L + A T + + D +L L I +I A++ L
Sbjct: 26 SNPNTRLVVLSASAGVTNLLVALAEGAEPGDERLALLDEIRQI--------QYAILDR-L 76
Query: 570 SQSKSFAPSISMIKKCIESLIDKNYVERTANSTDE 604
I + + I L + + + TDE
Sbjct: 77 GDPNVVREEIERLLENITVLAEAASLATSPALTDE 111
>gnl|CDD|205590 pfam13412, HTH_24, Winged helix-turn-helix DNA-binding.
Length = 48
Score = 26.3 bits (59), Expect = 6.1
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 444 MQTFQMAILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLT 491
+ + IL L ++N ++ ++ L LS + R + L E L+
Sbjct: 1 LDEIDLKILRLLQENPRISQRELAERLGLSLGTVNRRLKRLEEEGLIK 48
>gnl|CDD|225222 COG2345, COG2345, Predicted transcriptional regulator
[Transcription].
Length = 218
Score = 28.8 bits (65), Expect = 7.6
Identities = 29/156 (18%), Positives = 57/156 (36%), Gaps = 15/156 (9%)
Query: 450 AILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTSNKEELTEDTEIRLNLGY 509
IL L +K+ ++ ++ L +S + RH+ L E L E + G
Sbjct: 15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEA--------EGLVEVERQQGGRGR 66
Query: 510 NNKRTKLKISGAVQKETPQE-IERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEV 568
K +L G Q P+ E ++ +D + + A+ ++ R Q A+ +
Sbjct: 67 PAKLYRLTEKGREQF--PKRYGELALALLDALEETGGEEALNAFLEKRAQ----AIGAQY 120
Query: 569 LSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDE 604
A +++ +E L D Y+ +
Sbjct: 121 RPAMGGDADLEEKVERLVELLSDLGYMPELRPVDNG 156
>gnl|CDD|153116 cd01058, AAMH_B, Aromatic and Alkene Monooxygenase Hydroxylase,
subunit B, ferritin-like diiron-binding domain.
Aromatic and Alkene Monooxygenase Hydroxylases, subunit
B (AAMH_B). Subunit B (beta) of the soluble hydroxylase
of multicomponent, aromatic and alkene monooxygenases
are members of a superfamily of ferritin-like
iron-storage proteins. AAMH exists as a hexamer (an
alpha2-beta2-gamma2 homodimer) with each alpha-subunit
housing one nonheme diiron center embedded in a
four-helix bundle. The N-terminal domain of the alpha-
and noncatalytic beta-subunits possess nearly identical
folds; the beta-subunit lacks the C-terminal domain
found in the alpha-subunit. Methane monooxygenase is a
multicomponent enzyme found in methanotrophic bacteria
that catalyzes the hydroxylation of methane and higher
alkenes (as large as octane). Phenol monooxygenase,
found in a diverse group of bacteria, catalyses the
hydroxylation of phenol, chloro- and methyl-phenol and
naphthol. Both enzyme systems consist of three
components: the hydroxylase, a coupling protein and a
reductase. In the MMO hydroxylase, dioxygen and
substrate interact with the diiron center in a
hydrophobic cavity at the active site. The reductase
component and protein coupling factor provide electrons
from NADH for reducing the oxidized binuclear iron-oxo
cluster to its reduced form. Reaction with dioxygen
produces a peroxy-bridged complex and dehydration leads
to the formation of complex Q, which is thought to be
the oxygenating species that carries out the insertion
of an oxygen atom into a C-H bond of the substrate. The
toluene monooxygenase systems, toluene 2-, 3-, and
4-monooxygenase, are similar to MMO but with an
additional component, a Rieske-type ferredoxin. The
alkene monooxygenase from Xanthobacter strain Py2 is
closely related to aromatic monooxygenases and catalyzes
aromatic monohydroxylation of benzene, toluene, and
phenol. Alkane omega-hydroxylase (AlkB) and xylene
monooxygenase are members of a distinct class of
integral membrane diiron proteins and are not included
in this CD.
Length = 304
Score = 28.8 bits (65), Expect = 8.0
Identities = 9/51 (17%), Positives = 26/51 (50%)
Query: 175 INILIDAVRDHICKQGLEAISGLSGDNISTQFVENMLAVHKKYKAFVKELF 225
N++ D + + ++ L+ ++ +GD ++ E ML ++++ + L
Sbjct: 201 QNLVFDPLVGELVRRELDRLAASNGDTLTPLLTEFMLDDAQRHRRWTDALV 251
>gnl|CDD|216248 pfam01022, HTH_5, Bacterial regulatory protein, arsR family.
Members of this family contains a DNA binding
'helix-turn-helix' motif. This family includes other
proteins which are not included in the Prosite
definition.
Length = 47
Score = 26.0 bits (58), Expect = 8.6
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 451 ILLLFEKNDAMTCGDIQTVLSLSQDQIGRHIASLVECKLLTS 492
IL L + + + ++ +L LSQ + H+ L E L+
Sbjct: 7 ILYLLSEGE-LCVCELAEILGLSQSTVSHHLKKLREAGLVEK 47
>gnl|CDD|238643 cd01318, DHOase_IIb, Dihydroorotase (DHOase), subgroup IIb; DHOases
catalyze the reversible interconversion of carbamoyl
aspartate to dihydroorotate, a key reaction in
pyrimidine biosynthesis. This group contains the archeal
members of the DHOase family.
Length = 361
Score = 28.8 bits (65), Expect = 9.0
Identities = 21/91 (23%), Positives = 30/91 (32%), Gaps = 22/91 (24%)
Query: 104 ERVLQVLHEETNRSVRFLHVSS--------YPKVKAKCE--QHMVADHLNFLQGECVPMV 153
R L++ + HVS+ K E H HL +
Sbjct: 161 ARALKLA-RRHGARLHICHVSTPEELKLIKKAKPGVTVEVTPH----HLFLDVEDY---- 211
Query: 154 AEERRHDLANMYPLLRSVREGINILIDAVRD 184
+R L + P LRS RE L+ A+ D
Sbjct: 212 --DRLGTLGKVNPPLRS-REDRKALLQALAD 239
>gnl|CDD|218663 pfam05625, PAXNEB, PAXNEB protein. PAXNEB or PAX6 neighbor is
found in several eukaryotic organisms. PAXNED is an RNA
polymerase II Elongator protein subunit. It is part of
the HAP subcomplex of Elongator, which is a six-subunit
component of the RNA polymerase II holoenzyme. The HAP
subcomplex is required for Elongator structural
integrity and histone acetyltransferase activity. This
protein family has a P-loop motif. However its sequence
has degraded in many members of the family.
Length = 357
Score = 28.8 bits (65), Expect = 9.5
Identities = 12/36 (33%), Positives = 15/36 (41%)
Query: 389 TVISSFSVPQELEKCIHMFEKFYHGQFNGRKLSWLH 424
VI P +EK + K Y G N KL L+
Sbjct: 267 GVIELEPFPGSMEKETNPLYKEYQGLLNIHKLPVLN 302
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
0.319 0.133 0.382
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,902,343
Number of extensions: 2889242
Number of successful extensions: 2414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2397
Number of HSP's successfully gapped: 32
Length of query: 609
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 506
Effective length of database: 6,369,140
Effective search space: 3222784840
Effective search space used: 3222784840
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 (27.5 bits)