RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8269
(386 letters)
>gnl|CDD|227533 COG5208, HAP5, CCAAT-binding factor, subunit C [Transcription].
Length = 286
Score = 144 bits (364), Expect = 2e-40
Identities = 59/85 (69%), Positives = 71/85 (83%)
Query: 109 DLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTL 168
LK LPLARIKK+MK D+ VKMISAEAP+LF+K E+FI ELT+RAWI+ E+NKRRTL
Sbjct: 104 LLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTL 163
Query: 169 QRNDIAMAITKYDMFDFLIDIVPRE 193
Q++DIA A+ K +MFDFLIDIVPR
Sbjct: 164 QKSDIAAAVKKSEMFDFLIDIVPRN 188
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
(CBF/NF-Y) and archaeal histone. This family includes
archaebacterial histones and histone like transcription
factors from eukaryotes.
Length = 65
Score = 85.4 bits (212), Expect = 5e-21
Identities = 22/63 (34%), Positives = 34/63 (53%)
Query: 115 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 174
LP+AR+K+IMK D IS +A L ++ E FI + A + KR+T+ I
Sbjct: 3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62
Query: 175 MAI 177
+A+
Sbjct: 63 LAV 65
>gnl|CDD|216649 pfam01694, Rhomboid, Rhomboid family. This family contains
integral membrane proteins that are related to
Drosophila rhomboid protein. Members of this family are
found in bacteria and eukaryotes. Rhomboid promotes the
cleavage of the membrane-anchored TGF-alpha-like growth
factor Spitz, allowing it to activate the Drosophila EGF
receptor. Analysis has shown that Rhomboid-1 is an
intramembrane serine protease (EC:3.4.21.105).
Parasite-encoded rhomboid enzymes are also important for
invasion of host cells by Toxoplasma and the malaria
parasite.
Length = 146
Score = 85.7 bits (213), Expect = 4e-20
Identities = 42/138 (30%), Positives = 60/138 (43%), Gaps = 9/138 (6%)
Query: 222 MLLSTFSHQSPLHIFANMFVLHSFMPSSVEDLGKEQFVGFYLTAGVVASLLSYVHKILVR 281
++ S F H LH+ NM L F LG +F+ YL +G+ SLLSY +
Sbjct: 10 LITSMFLHAGWLHLLFNMLALLFFGIPLERILGSVRFLLLYLLSGLAGSLLSY---LFSP 66
Query: 282 KPGLSIGASGAIMAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWR 341
S+GASGAI +L + P + + P GI+LL+ L
Sbjct: 67 ASSPSVGASGAIFGLLGALLVLLPRNRILLFNFPGALLLLL----GIILLNLLLGFLPG- 121
Query: 342 LFDHAAHLGGALFGILYS 359
+ AHLGG + G+L
Sbjct: 122 -ISNFAHLGGLIAGLLLG 138
>gnl|CDD|223777 COG0705, COG0705, Membrane associated serine protease [Amino acid
transport and metabolism].
Length = 228
Score = 67.5 bits (165), Expect = 6e-13
Identities = 39/145 (26%), Positives = 64/145 (44%), Gaps = 2/145 (1%)
Query: 225 STFSHQSPLHIFANMFVLHSFMPSSVEDLGKEQFVGFYLTAGVVASLLSYVHKILVRKPG 284
+ F H LH+ NM L F + LG +F+ FYL +G++A L + +
Sbjct: 74 AIFLHAGFLHLLFNMLALWVFGSNLERRLGTLRFLLFYLLSGLLAGLAQVL--FGPKGGA 131
Query: 285 LSIGASGAIMAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWRLFD 344
S+GASGAI +L + P + +LF+ R + + ++ F G
Sbjct: 132 PSLGASGAIFGLLGAYFLLFPFARILLLFLSLPRPALILILIWLLYSLFSGAGSFGPSVA 191
Query: 345 HAAHLGGALFGILYSKYGEQTWAHR 369
+AHLGG + G+L + + R
Sbjct: 192 WSAHLGGLIGGLLLAALLSRKLRKR 216
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 54.1 bits (131), Expect = 1e-09
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 109 DLKTQALPLARIKKIMKLDDGV-KMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRT 167
L LP +R+ + +K IS++AP+ +A E + E+ A + KR+T
Sbjct: 3 RLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKT 62
Query: 168 LQRNDIAMAI 177
+ DI +A+
Sbjct: 63 ITPRDIQLAV 72
>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit
(DRAP1 homolog) [Transcription].
Length = 113
Score = 51.1 bits (122), Expect = 3e-08
Identities = 22/82 (26%), Positives = 42/82 (51%)
Query: 116 PLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAM 175
P+AR+KKIM+LD+ + + P++ SKA E+F+ E+ + + + +
Sbjct: 25 PIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKR 84
Query: 176 AITKYDMFDFLIDIVPREEVKT 197
A + FDFL ++ + +T
Sbjct: 85 ATESDEKFDFLKNMEQFKNRET 106
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 43.9 bits (104), Expect = 7e-06
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 112 TQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRN 171
LP A +++I++ G + +S+ A +A E ++ E+ A E KR+T++
Sbjct: 17 DLLLPKAPVRRILR-KAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75
Query: 172 DIAMAITKYDMF 183
DI +A+ +
Sbjct: 76 DIKLALKRLGRR 87
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 38.7 bits (90), Expect = 0.001
Identities = 17/74 (22%), Positives = 34/74 (45%)
Query: 114 ALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDI 173
P+ R+K+++K + I A AP+ + E E+ A DNK++ + +
Sbjct: 26 IFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHL 85
Query: 174 AMAITKYDMFDFLI 187
+AI + + L+
Sbjct: 86 QLAIRNDEELNKLL 99
>gnl|CDD|185445 PTZ00101, PTZ00101, rhomboid-1 protease; Provisional.
Length = 278
Score = 34.1 bits (78), Expect = 0.097
Identities = 38/149 (25%), Positives = 63/149 (42%), Gaps = 23/149 (15%)
Query: 222 MLLSTFSHQSPLHIFANMFVLHSFMPSSVE-DLGKEQFVGFYLTAGVVASLLSYVHKILV 280
++L F H + H F N+F M ++E + G + + Y G+ ++LS V
Sbjct: 105 LILPIFLHANIFHTFFNVF-FQLRMGFTLEKNYGIVKIIILYFLTGIYGNILSSS----V 159
Query: 281 RKPGLSIGASGAIMAVLA-HTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFR 339
+ +GAS + M +L T EL +L+ +V E + I+ + +
Sbjct: 160 TYCPIKVGASTSGMGLLGIVTS------ELILLW--HVIRHRERVVFNIIFFSLISFFYY 211
Query: 340 WRL----FDHAAHLGGAL----FGILYSK 360
+ DH HLGG L GILY+
Sbjct: 212 FTFNGSNIDHVGHLGGLLSGISMGILYNS 240
>gnl|CDD|129039 smart00803, TAF, TATA box binding protein associated factor. TAFs
(TATA box binding protein associated factors) are part
of the transcription initiation factor TFIID multimeric
protein complex. TFIID is composed of the TATA box
binding protein (TBP) and a number of TAFs. The TAFs
provide binding sites for many different transcriptional
activators and co-activators that modulate transcription
initiation by Pol II. TAF proteins adopt a histone-like
fold.
Length = 65
Score = 29.9 bits (68), Expect = 0.27
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 129 GVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMAI 177
G+ +S EA L ++ E I E+ A +KR TL +DI A+
Sbjct: 16 GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64
>gnl|CDD|181601 PRK08978, PRK08978, acetolactate synthase 2 catalytic subunit;
Reviewed.
Length = 548
Score = 31.4 bits (72), Expect = 0.97
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 10 PAFEASNDIPKWRKDLRK-----RWNALHPGDRVYVPIL 43
PA + +I WR+ + W HPG+ +Y P L
Sbjct: 319 PALQQPLNIDAWRQHCAQLRAEHAWRYDHPGEAIYAPAL 357
>gnl|CDD|233674 TIGR01992, PTS-IIBC-Tre, PTS system, trehalose-specific IIBC
component. This model represents the fused enzyme II B
and C components of the trehalose-specific PTS sugar
transporter system. Trehalose is converted to
trehalose-6-phosphate in the process of translocation
into the cell. These transporters lack their own IIA
domains and instead use the glucose IIA protein (IIAglc
or Crr). The exceptions to this rule are Staphylococci
and Streptococci which contain their own A domain as a
C-terminal fusion. This family is closely related to the
sucrose transporting PTS IIBC enzymes and the B and C
domains of each are described by subfamily-domain level
TIGRFAMs models (TIGR00826 and TIGR00852, respectively).
In E. coli, B. subtilis and P. fluorescens the presence
of this gene is associated with the presence of
trehalase which degrades T6P to glucose and glucose-6-P.
Trehalose may also be transported (in Salmonella) via
the mannose PTS or galactose permease systems, or (in
Sinorhizobium, Thermococcus and Sulfolobus, for
instance) by ABC transporters.
Length = 462
Score = 30.5 bits (69), Expect = 1.7
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 342 LFDHAAHLGGALFGILYS 359
LF AA LGGA+FG+LY+
Sbjct: 297 LFTSAAWLGGAIFGLLYA 314
>gnl|CDD|131051 TIGR01996, PTS-II-BC-sucr, PTS system, sucrose-specific IIBC
component. This model represents the fused enzyme II B
and C components of the sucrose-specific PTS sugar
transporter system. Sucrose is converted to
sucrose-6-phosphate in the process of translocation into
the cell. Some of these transporters lack their own IIA
domains and instead use the glucose IIA protein (IIAglc
or Crr). The exceptions to this rule are Staphylococci,
Streptococci, Lactococci, Lactobacilli, etc. which
contain their own A domain as a C-terminal fusion. This
family is closely related to the trehalose transporting
PTS IIBC enzymes and the B and C domains of each are
described by subfamily-domain level TIGRFAMs models
(TIGR00826 and TIGR00852, respectively).
Length = 461
Score = 29.2 bits (66), Expect = 3.9
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 14/85 (16%)
Query: 285 LSIGASGAIMAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRW---- 340
L + + I+A + L +L P++ I G + L +G + RW
Sbjct: 231 LPVLVAVWILAKIEKFLRKVVPNALDLLLTPFLTL----LITGFLTLLVIGPIGRWVGDV 286
Query: 341 ------RLFDHAAHLGGALFGILYS 359
L+D LGG LFG LYS
Sbjct: 287 LTDGLQWLYDLPGGLGGLLFGGLYS 311
>gnl|CDD|110227 pfam01209, Ubie_methyltran, ubiE/COQ5 methyltransferase family.
Length = 233
Score = 28.6 bits (64), Expect = 5.1
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 17 DIPKWRKDLRKRWNALHPGDRVYV-----PILFLNGVVFLAWFYPRLHPVLYKYFASNPQ 71
+ P + K L++ + L PG RV P L + +F + P + K FA + +
Sbjct: 128 NFPDYLKVLKEAFRVLKPGGRVVCLEFSKPENPLLSQAYELYFKYVM-PFMGKMFAKSYK 186
Query: 72 S 72
S
Sbjct: 187 S 187
>gnl|CDD|225817 COG3278, CcoN, Cbb3-type cytochrome oxidase, subunit 1
[Posttranslational modification, protein turnover,
chaperones].
Length = 482
Score = 28.1 bits (63), Expect = 8.6
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 17/80 (21%)
Query: 233 LHIFANMFVLHSF-------MPSSVEDLGKEQF-----VGFYLTAGVVASLLSYVHKILV 280
LHI N+ V SF S V+D + + VGF+LTAG + + +V K
Sbjct: 177 LHIVNNLSVPVSFFGWKSYSAYSGVQDALVQWWYGHNAVGFFLTAGFLGMMYYFVPKQ-A 235
Query: 281 RKP----GLSIGASGAIMAV 296
+P LSI A++ +
Sbjct: 236 GRPIYSYRLSIVHFWALIFL 255
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
0.325 0.139 0.429
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,486,399
Number of extensions: 2050053
Number of successful extensions: 2360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2349
Number of HSP's successfully gapped: 42
Length of query: 386
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 287
Effective length of database: 6,546,556
Effective search space: 1878861572
Effective search space used: 1878861572
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 60 (26.8 bits)