RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14634
(388 letters)
>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site
selection and in elongation by RNA polymerase II
[Transcription].
Length = 521
Score = 98.2 bits (244), Expect = 3e-22
Identities = 41/174 (23%), Positives = 83/174 (47%)
Query: 132 ISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCMTEGV 191
+ K Y + +TN+ L + G + +VFR+ ISN F E+ R +
Sbjct: 259 VGKGSTYSKPYGRKEVKTNRYLDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKL 318
Query: 192 ALPTKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQ 251
++P+ +V+ K ++ + M + ++++ ++V K+ P N +KT+L ++R A
Sbjct: 319 SMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPKRSNVIHEKTELRQKRQRAI 378
Query: 252 SKGDDEEASILQRKIDDLEERANELDKARTSTISSISYINNRNRRKNVEEAEKA 305
+ + A QR+++++E+ S ++ +N RNRR+N E A
Sbjct: 379 ELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLA 432
Score = 38.5 bits (89), Expect = 0.005
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 325 SASRKVIEYIETKEE------LNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNNTGI 378
S + + +E I ++ N+ R+ R + + V PIF VIGCF R+ IG G
Sbjct: 192 SYAEEAVEDISRTDDFAELYDFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGY 251
Query: 379 PLYRV 383
+YR+
Sbjct: 252 LVYRI 256
>gnl|CDD|190531 pfam03126, Plus-3, Plus-3 domain. This domain is about 90 residues
in length and is often found associated with the
pfam02213 domain. The function of this domain is
uncertain. It is possible that this domain is involved
in DNA binding as it has three conserved positively
charged residues, hence this domain has been named the
plus-3 domain. It is found in yeast Rtf1 which may be a
transcription elongation factor.
Length = 105
Score = 79.6 bits (197), Expect = 2e-18
Identities = 31/58 (53%), Positives = 38/58 (65%)
Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQC 186
+ +I+GV E K Y LG T+K LK+ HG SERVFR+ F+SN FTE EF RW C
Sbjct: 48 LAQITGVKEGKKPYQLGGKTTDKYLKVTHGKSERVFRISFVSNSPFTEEEFERWLQSC 105
Score = 63.4 bits (155), Expect = 1e-12
Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 338 EELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNN--TGIPLYRV 383
+++NRIRL R + KL+ P F V+GCFVR+ IG + TG YR+
Sbjct: 1 DDINRIRLGRSLLAKLLFYPGFESTVVGCFVRVNIGPDKETGQQSYRL 48
>gnl|CDD|197843 smart00719, Plus3, Short conserved domain in transcriptional
regulators. Plus3 domains occur in the Saccharomyces
cerevisiae Rtf1p protein, which interacts with Spt6p,
and in parsley CIP, which interacts with the bZIP
protein CPRF1.
Length = 109
Score = 79.7 bits (197), Expect = 2e-18
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 129 IGEISGVCETGKIYSLGKTRTNKGLKLRHGNSERVFRLEFISNQEFTESEFIRWKDQCM 187
+ +++GV E K YSLG TN L++ +G+SE+V ++ FISNQ+FTE EF RWK
Sbjct: 51 LVQVTGVKEADKPYSLGGKTTNVLLEVLNGDSEKVVQINFISNQDFTEEEFQRWKQAIK 109
Score = 56.9 bits (138), Expect = 3e-10
Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 338 EELNRIRLSRFKMEKLVHLPIFGQIVIGCFVRIGIGNN-TGIPLYRV 383
+ LN +RL R +E+L+ P F V+GCFVR+ IG N P+YR+
Sbjct: 5 DNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKQPIYRL 51
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 37.4 bits (87), Expect = 0.014
Identities = 17/111 (15%), Positives = 49/111 (44%), Gaps = 9/111 (8%)
Query: 197 DEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDD 256
E+E K + ++ ++ ++++ + E + Y K +E + + +
Sbjct: 331 KELEEKEERLE------ELKKKLKELEKRLEELEERHELYEEAK-AKKEELERLKKRLTG 383
Query: 257 EEASILQRKIDDLEERANELDKARTSTISSISYINNR--NRRKNVEEAEKA 305
L++++++LE+ E+++ + + I + +K +EE +KA
Sbjct: 384 LTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKA 434
>gnl|CDD|180307 PRK05892, PRK05892, nucleoside diphosphate kinase regulator;
Provisional.
Length = 158
Score = 30.1 bits (68), Expect = 1.2
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 21/78 (26%)
Query: 216 EEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDD-------EEASILQRKIDD 268
E ++ ++ ++R +R M GD +E + L +I++
Sbjct: 17 EAELARLRARRDRLAVEV-----------NDRGMIGDHGDQAEAIQRADELARLDDRINE 65
Query: 269 LEERANELDKARTSTISS 286
L+ R L T S
Sbjct: 66 LDRR---LRTGPTPWSGS 80
>gnl|CDD|215418 PLN02782, PLN02782, Branched-chain amino acid aminotransferase.
Length = 403
Score = 29.4 bits (66), Expect = 3.6
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 46 FKPTPYNYAMKKTQLMKERDMAQSKIGESQPFRDGNLSSLPRAGI 90
PT Y Y MK RD SK GE Q F GN+ P AG+
Sbjct: 79 LVPTDYMYIMKCN-----RDGEFSK-GELQRF--GNIELSPSAGV 115
>gnl|CDD|182343 PRK10262, PRK10262, thioredoxin reductase; Provisional.
Length = 321
Score = 29.3 bits (65), Expect = 4.1
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 300 EEAEKAIMVSCCCCCSGFSYRSVK-------SSASRKVIEYIETKEELNRI-RLSRFKME 351
EEA K VS C C GF YR+ K ++A + + E++ I R F+ E
Sbjct: 125 EEAFKGRGVSACATCDGFFYRNQKVAVIGGGNTAVEEALYLSNIASEVHLIHRRDGFRAE 184
Query: 352 KLV 354
K++
Sbjct: 185 KIL 187
>gnl|CDD|226456 COG3947, COG3947, Response regulator containing CheY-like receiver
and SARP domains [Signal transduction mechanisms].
Length = 361
Score = 29.1 bits (65), Expect = 4.4
Identities = 29/119 (24%), Positives = 45/119 (37%), Gaps = 11/119 (9%)
Query: 195 TKDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKG 254
T DE++ + + + E D E+ER + K + E
Sbjct: 243 TIDELKELVGQYKGDYL---PEADYPWAEDERERLEQLYMKLLGKVARAYLEAGKP---- 295
Query: 255 DDEEASILQR--KIDDLEERANELDKARTSTI-SSISYINNRNRRKNVEEAEKAIMVSC 310
+E + QR +D L E+ N+ A +T+ IS I + R V EAE I V
Sbjct: 296 -NEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDD 353
>gnl|CDD|219577 pfam07787, DUF1625, Protein of unknown function (DUF1625).
Sequences making up this family are derived from
hypothetical proteins expressed by both prokaryotic and
eukaryotic species. The region in question is
approximately 250 residues long.
Length = 247
Score = 28.5 bits (64), Expect = 5.0
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 211 MYQWKEEDVEQIVREKERFKPTPY 234
MYQW EE V + + + T
Sbjct: 1 MYQWVEESVSETYGKVGGTETTYS 24
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 29.1 bits (66), Expect = 5.1
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 194 PTKDEVERKSKEIQ-----NGMMYQWKEEDVEQIVR 224
PT DE+ER +EI+ + Y +E++ IVR
Sbjct: 172 PTDDEIERYVEEIELYKEVTSLQYSPSDEEIRLIVR 207
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 29.2 bits (66), Expect = 5.4
Identities = 25/96 (26%), Positives = 47/96 (48%), Gaps = 16/96 (16%)
Query: 215 KEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGDDEEASILQRKIDDLEERAN 274
K E+++++ R + + +++ L KE+D A SK E L++++ +LEE
Sbjct: 403 KPEELDELDRRIIQLE-------IEREALKKEKDEA-SK---ERLEDLEKELAELEEEYA 451
Query: 275 ELD---KARTSTISSISYINNR--NRRKNVEEAEKA 305
+L+ KA + I I I R +E+AE+
Sbjct: 452 DLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAERE 487
>gnl|CDD|234210 TIGR03439, methyl_EasF, probable methyltransferase domain, EasF
family. This model represents an uncharacterized domain
of about 300 amino acids with homology to
S-adenosylmethionine-dependent methyltransferases.
Proteins with this domain are exclusively fungal. A few,
such as EasF from Neotyphodium lolii, are associated
with the biosynthesis of ergot alkaloids, a class of
fungal secondary metabolites. EasF may, in fact, be the
AdoMet:dimethylallyltryptophan N-methyltransferase, the
enzyme that follows tryptophan dimethylallyltransferase
(DMATS) in ergot alkaloid biosynthesis. Several other
members of this family, including mug158 (meiotically
up-regulated gene 158 protein) from Schizosaccharomyces
pombe, contain an additional uncharacterized domain
DUF323 (pfam03781).
Length = 319
Score = 28.8 bits (65), Expect = 5.5
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 155 LRHGNS---ERVFRLEFISNQEF-TESEFIRWKDQCM---TEGVALPTKDEVERKSKEIQ 207
L H N FR E + EF E + + + + V++ + V RK ++I+
Sbjct: 225 LVHANEILGHEAFREE---DWEFLGEWDEELGRHEAFYIPKKDVSIGLEGVVIRKGEKIR 281
Query: 208 NGMMYQWKEEDVEQIVRE 225
++ +++ EQ+ +
Sbjct: 282 FECSGKYDKDEREQLCQS 299
>gnl|CDD|204187 pfam09278, MerR-DNA-bind, MerR, DNA binding. Members of this
family of DNA-binding domains are predominantly found in
the prokaryotic transcriptional regulator MerR. They
adopt a structure consisting of a core of three alpha
helices, with an architecture that is similar to that of
the 'winged helix' fold.
Length = 65
Score = 26.3 bits (59), Expect = 6.1
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 256 DEEASILQRKIDDLEERANELDKART 281
+ ++L+ K+ +LE R EL R
Sbjct: 35 ADVRALLREKLAELEARIAELQALRA 60
>gnl|CDD|218079 pfam04420, CHD5, CHD5-like protein. Members of this family are
probably coiled-coil proteins that are similar to the
CHD5 (Congenital heart disease 5) protein. In
Saccharomyces cerevisiae this protein localises to the
ER and is thought to play a homeostatic role.
Length = 161
Score = 27.6 bits (62), Expect = 7.7
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 262 LQRKIDDLEERANELDKARTSTISSISYI 290
L RK+D L + +L K T+ S ++
Sbjct: 71 LNRKLDKLTDELEKLKKELTAQKSKFKWV 99
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 28.0 bits (63), Expect = 9.2
Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 196 KDEVERKSKEIQNGMMYQWKEEDVEQIVREKERFKPTPYNYAMKKTQLMKERDMAQSKGD 255
E + +S + + + E + E+++ E+ER M + +L ++ ++ + +G
Sbjct: 233 MMEAQERSYQEHVKQLIEKMEAEREKLLAEQER---------MLEHKLQEQEELLK-EGF 282
Query: 256 DEEASILQRKIDDLE 270
EA LQ++I DL+
Sbjct: 283 KTEAESLQKEIQDLK 297
>gnl|CDD|224006 COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI
component in bacteria) [Carbohydrate transport and
metabolism].
Length = 574
Score = 27.9 bits (63), Expect = 9.6
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 12/69 (17%)
Query: 215 KEEDVEQIVREKERFKPTPYNYAMKKT--QLMKERDMAQSKGDDEEASILQRKI-----D 267
K E + E ER + A+ +L ++ A G +E+A+I + +
Sbjct: 30 KTPAAEDVEAEIERL-----DAALAAARAELEALKEKAAEDGGEEKAAIFEAHLMLLEDP 84
Query: 268 DLEERANEL 276
+L E A EL
Sbjct: 85 ELTEEAEEL 93
>gnl|CDD|173163 PRK14700, PRK14700, recombination factor protein RarA; Provisional.
Length = 300
Score = 27.7 bits (61), Expect = 10.0
Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 24/101 (23%)
Query: 137 ETGKIYSLGKTRTNKGLKLRHGNSERVF-----RLEFISNQEFTESEFIRWKDQCMTEGV 191
E+GKI +G T N L R+F RL ++ Q+ E
Sbjct: 5 ESGKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKAL------------ 52
Query: 192 ALPTKDEVERKSK-EIQNGM---MYQWKEEDVEQIVREKER 228
++DEV K K +I +G+ M+ + E D +I+ ER
Sbjct: 53 ---SQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILNLLER 90
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
0.318 0.133 0.387
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,592,945
Number of extensions: 1868927
Number of successful extensions: 2217
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2194
Number of HSP's successfully gapped: 75
Length of query: 388
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 289
Effective length of database: 6,546,556
Effective search space: 1891954684
Effective search space used: 1891954684
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: 60 (26.9 bits)