RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7977
(1225 letters)
>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160 kDa)
subunit. CPSF is involved in mRNA polyadenylation and
binds the AAUAAA conserved sequence in pre-mRNA. CPSF has
also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA binding.
Length = 318
Score = 197 bits (504), Expect = 3e-56
Identities = 68/221 (30%), Positives = 109/221 (49%), Gaps = 10/221 (4%)
Query: 1005 HNLLIIDQNTFEILHAHQLFPGEYALSLIS--SKFGEDPNTYFVLGTAVVHPEENEPKQG 1062
+ ++D T+E++ +L E LS+ S + E Y V+GTA E+ + G
Sbjct: 2 SCIRLVDPITWEVIDTLELEENEAVLSVKSVNLEDSEGRKEYLVVGTAFDLGEDPAARSG 61
Query: 1063 RIIIFHYDDG----KLQQIAEKEIKGACYSMCEFNGKLLASINSTVRLFEWTNEKELRLE 1118
RI +F + KL+ + + E+KGA ++CEF G+LLA +R+++ + +L +
Sbjct: 62 RIYVFEIIEPETNRKLKLVHKTEVKGAVTALCEFQGRLLAGQGQKLRVYDLG-KDKLLPK 120
Query: 1119 CSHFNNIIA-LFLKVKGDFILVGDLMRSLTLLQYKTMEGSFEEISRDYNPNWMTSIEIL- 1176
I + LKV G+ I+VGDLM+S+T L Y +RD P W+T+ E L
Sbjct: 121 AFLDTPITYVVSLKVFGNRIIVGDLMKSVTFLGYDEEPYRLILFARDTQPRWVTAAEFLV 180
Query: 1177 DDELFLGAENSYNLFICQKD-SAATSDEDRTHLQEVGTVHL 1216
D + LGA+ NL + + D A S + L HL
Sbjct: 181 DYDTILGADKFGNLHVLRYDPEAPESLDGDPRLLHRAEFHL 221
>gnl|CDD|220751 pfam10433, MMS1_N, Mono-functional DNA-alkylating methyl
methanesulfonate N-term. MMS1 is a protein that
protects against replication-dependent DNA damage in
Saccharomyces cerevisiae. MMS1 belongs to the DDB1
family of cullin 4 adaptors and the two proteins are
homologous. MMS1 bridges the interaction of MMS22 and
Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein
involved in the regulation of DNA replication subsequent
to DNA damage. The N-terminal region of MMS1 and the
C-terminal of MMS22 are required for the the MMS1-MMS22
interaction. The human HIV-1 virion-associated protein
Vpr assembles with DDB1 through interaction with DCAF1
(chromatin assembly factor) to form an E3 ubiquitin
ligase that targets cellular substrates for
proteasome-mediated degradation and subsequent G2
arrest.
Length = 513
Score = 194 bits (494), Expect = 6e-53
Identities = 91/307 (29%), Positives = 135/307 (43%), Gaps = 38/307 (12%)
Query: 73 SLWNGWSERYLLGDLAGRLFMLLLEKEEKMDGTFSVKEPKVELLGEISIPECLTYLDNG- 131
+N + LL GR++ L + + + V+ + +G+ S+ LD G
Sbjct: 223 WSYNEKHDDILLAREDGRIYYLEISNDGE------VESITILGIGKCSVAIAFAILDKGN 276
Query: 132 ---VVFVGSRLGDSQLVKLNRSPDENGTYVSVMESFTNLAPIIDMVVVDLERQGQG---- 184
V+FV S GD L K++ + ++ F N API+D VVVD
Sbjct: 277 EGDVLFVASDTGDGGLFKISARDN-----PRCVQDFPNWAPILDFVVVDSGNSKNESQDP 331
Query: 185 ---QLVTCSGGFKEGSLRIIRNGIGIEEHACI--DLPGIKGIWALSIGSPKNLDNTLVLS 239
++ TCSG K GSLR +R+GI E I +L GI+G+W L GS N L++S
Sbjct: 332 SQDRIFTCSGVGKRGSLRELRHGIEAEIGLVIEEELRGIRGLWLLPSGS--NGGYYLLVS 389
Query: 240 FVGHTRVLTLS---GAEVEETEMG-GFTSDQQTFYCGNVDPRTVLQVTPSAAILISTESK 295
F TRVL L G EVEE + G QT GN ++QVT ++ L E
Sbjct: 390 FPFETRVLQLPVDPGEEVEEVDEDSGLDLSVQTLAAGNTSDGVIIQVTENSIRLSDLELG 449
Query: 296 ARVSSWEPPNGKSISVVSCNKNQVLCAT-GCDVYYLEVHGSEIKQLAHRALEY----EVA 350
W + I+ S N + VL A G ++ L ++ + +L E+
Sbjct: 450 KITDEWS---DEIITAASVNGSLVLVAVAGRNLVSLRIYLGLLVIEDDGSLTLLDLGEIL 506
Query: 351 CLDISPL 357
CLD P+
Sbjct: 507 CLDYEPI 513
Score = 98.6 bits (246), Expect = 3e-21
Identities = 49/255 (19%), Positives = 101/255 (39%), Gaps = 43/255 (16%)
Query: 735 DLLFIITQRYNAMILECRGDIDNLE-ILTKAHGNVSDRIGKPSENGIIAIIDPEARVIGL 793
D+L + + L + L + ++ + + ++G +DP R + +
Sbjct: 1 DILVLSLDSGELLFLYYDEEPRQLFPEFYHSRRDLPSDVSRLEQSGRHIAVDPSGRAMAV 60
Query: 794 RLYNGLFKIIPLEKDNFELKASS--------------IRMEELEIQDVQFLHGCQ----N 835
Y+G F + PL++DN + S R+ + +I D+ FL+ +
Sbjct: 61 SAYSGFFGVYPLQRDNKTQELQSQMAEGPLSPIEEERFRLVDGDILDMCFLYPKSEDDDH 120
Query: 836 PTIICIHQDVNGR-HVKTHEISLKE-------KEFTKTPWKQDNIEMEASLVIPVPEPLG 887
++ + D R H+K +E S E KE + + SL+IP+P+P G
Sbjct: 121 VILLLLVFDEQRRLHLKLYEWSAGEGLNQVISKETRLPLPNEFEL---PSLLIPLPKP-G 176
Query: 888 GAIIIGQESILYHSGKSYVAVAPQII------KSSTIVCYAKVDANG------ERYLLGD 935
+++G S++Y++ + + S +A+ D N + LL
Sbjct: 177 SFLVVGPTSLVYYTVHLIESAEYPFLRLEIGSDKSIWTAWARPDRNWSYNEKHDDILLAR 236
Query: 936 LAGRLFMLLLEKEEK 950
GR++ L + + +
Sbjct: 237 EDGRIYYLEISNDGE 251
Score = 53.5 bits (129), Expect = 6e-07
Identities = 26/58 (44%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 1 EGSLRIIRNGIGIEEHACI--DLPGIKGIWALSIGSPKNLDNTLVLSFVGHTRVLTLS 56
GSLR +R+GI E I +L GI+G+W L GS N L++SF TRVL L
Sbjct: 345 RGSLRELRHGIEAEIGLVIEEELRGIRGLWLLPSGS--NGGYYLLVSFPFETRVLQLP 400
>gnl|CDD|227490 COG5161, SFT1, Pre-mRNA cleavage and polyadenylation specificity
factor [RNA processing and modification].
Length = 1319
Score = 46.1 bits (109), Expect = 1e-04
Identities = 58/314 (18%), Positives = 99/314 (31%), Gaps = 70/314 (22%)
Query: 80 ERYLLGDLAGRLFMLLLEKEEKMDGTFSVKEPKVE--LLGEISIPECLTYLDNGVVFVGS 137
E LGDL G + L + + K F + + E LL + S C+ +++N + F G
Sbjct: 349 ETLFLGDLNGDRYYLRISMDGKRIIGFDIASLEFEGDLLKKGSAVSCVGHVNNLLFFGGV 408
Query: 138 RLGDSQLVKLNR-------------SPDENGT---------------------------- 156
+S+++++ P E G
Sbjct: 409 GDSNSRVLRIKSLLPTIETRASEGVGPLEGGNDEEMDDEYSAPENKLFGNKEQEVRRQDE 468
Query: 157 --YVSVMESFTNLAPIIDMVV--VDLER------QGQGQLVTCSGGFKEGSLRIIRNGIG 206
+ + +N PI D V VD+E+ G LV G E +L + +
Sbjct: 469 PYDAELFNALSNAGPITDFAVGKVDVEKGLPIPNIGLLNLVVTKGSDSEAALAVEGTSLE 528
Query: 207 IEEHACIDLPGIKGIWALSIGS---PKNLDNTLVLSFVGHTRVLTLSGAEVEETEMGGFT 263
++ +W+ I + +LS V +R+ E G +T
Sbjct: 529 PCICTVSSFIPLEIVWSQKIRGYLRCSRALDFYILSRVSDSRIF-RWSEEFLLEVSGEYT 587
Query: 264 SDQQTFYCGNV-DPRTVLQVTPSAAILISTESKARVSSWEPPNGKSISVVSCNKNQVLCA 322
D T + V+QVTPS + + + + V V
Sbjct: 588 RDVNTLLFVEFGEENRVVQVTPSYLLRYDQ------------DLRMLGRVEFASRAVEAR 635
Query: 323 TGCDVYYLEVHGSE 336
+ D L V S
Sbjct: 636 SVRDPLILVVRDSG 649
Score = 39.2 bits (91), Expect = 0.018
Identities = 38/204 (18%), Positives = 81/204 (39%), Gaps = 22/204 (10%)
Query: 1007 LLIIDQNTFEILHAHQLFPGEYALSLISSKFGEDPNT-----YFVLGTAVVHPEENEPKQ 1061
+ + ++E++ ++ EY + + T Y ++GT + E+ P +
Sbjct: 960 VDLYSPKSWEVIDTYEFDENEYVFHIKYLILDDMQGTKGKSPYILVGTTFIEGEDR-PAR 1018
Query: 1062 GRIIIFH-----------YDDGKLQQIAEKEIKGACYSMCEFNGKLLASINSTVRLFEWT 1110
GR+ + + D KL+ + +E KG +CE GK+ V + +
Sbjct: 1019 GRLHVLEIISVVPSPGSPFTDCKLKVLGIEETKGTVVRVCEVRGKIALCQGQKVMVRKID 1078
Query: 1111 NEKELRLECSHFN-NIIALFLKVKGDFILVGDLMRSLTLLQYKTMEGSFEEISRDYNPNW 1169
+ + ++ +I +KV + +L GD+ + L+ +++ IS
Sbjct: 1079 RSSGI-IPVGFYDLHIFTSSIKVVKNLLLAGDIYQGLSFFGFQSEPYRMHLISSSEPLRN 1137
Query: 1170 MTSIEIL---DDELFLGAENSYNL 1190
TS E L ++ FL + N+
Sbjct: 1138 ATSTEFLVTGNELYFLCCDAKGNI 1161
Score = 38.0 bits (88), Expect = 0.042
Identities = 59/307 (19%), Positives = 103/307 (33%), Gaps = 46/307 (14%)
Query: 626 FTSSTDLNLVVAKNNRIEIHTVT-PEGLRPVKEIFLYGKIAVMKFFRGPTDKKDLLFIIT 684
FT S +L+V N + + GL V E L K+ ++ + + ++D L ++T
Sbjct: 22 FTPSRTCSLLVYNGNILAVRLWKYDSGLVLVDEHMLLEKVTQIEKYPQISSEQDGLLLLT 81
Query: 685 QRTDLNLVVAKNNRIEIHTVTP---EGLRPVKEIFLYGKIAVMKFFRGPTDKKDLLF--- 738
R ++L+ + E T++ EG K + K + ++F LLF
Sbjct: 82 HRAKISLLRFDSQANEFRTISLHYYEGKFKGKSLVELAKFSTLEF--DIRSSCALLFNED 139
Query: 739 ----IITQRYNAMILECRGDID-NLEILTKAHGNVSDRIGKPSENGIIAIIDPEARVIGL 793
+ E R D+D + ++K H ++ G + N + P
Sbjct: 140 IGNFLPFHVNKNDDDEVRIDVDLGMFQMSKRHFSIFPSQGTNTFNKRKRTLFPGK----- 194
Query: 794 RLYNGLFKIIPLEKDNFELKASSIRMEELEIQDVQFLHGCQNPTIICIHQDVNGRHVKTH 853
+ LK S + + I D FL PT + + D + +
Sbjct: 195 -----------FSAPSKVLKFSELDGKIKNIIDFVFLENYSIPT-VALLYDPKLSLPRKY 242
Query: 854 EISLKEKEFTKTPWKQDNIEMEASLVIP------------VPEPLGGAIIIGQESILYHS 901
I K ++ S VI V P+G + E IL S
Sbjct: 243 TIL---KNPYNAIVFTLDLGAGRSAVIDEFLVLPRDFRVTVAGPVGALLFGSNELILIDS 299
Query: 902 GKSYVAV 908
S +
Sbjct: 300 TGSSYTI 306
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 32.8 bits (74), Expect = 1.4
Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 958 KEPKVELLGEHCKGPVVEMSSLSYIKPGSTKQSTANQPAD-FNMEVEVHNLLIID-QNTF 1015
KE K L G++ K P L + GS +T N+PAD + E EV + D T
Sbjct: 375 KEIKQYLAGDYGKTPAPVNEDLKRSQIGSAPVTT-NRPADQLSPEFEVLKAEVADLAQTD 433
Query: 1016 EILHAHQLFPGEYALSLISSKFGED 1040
E + + LFP A +++K+ D
Sbjct: 434 EDVLTYALFP-SVAKPFLTTKYQTD 457
>gnl|CDD|129585 TIGR00494, crcB, protein CrcB. The role of this protein is
uncharacterized, but phenotypes associated with
overproduction include resistance to camphor,
suppression of a mukB chromosomal partition mutant, and
chromosome condensation, together suggesting a function
related to chromosome folding [Unknown function,
General].
Length = 117
Score = 30.8 bits (70), Expect = 1.6
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 15/75 (20%)
Query: 37 NLDNTLVLSFVGHTRVLTLSGAEWGFHLLRG-------FSSLG----SLWN----GWSER 81
N+ + FV + + + G FS+ SL G +
Sbjct: 38 NIIGCFGIGFVTLFTQPAVISPDLKLLIGTGFLGGFTTFSTFSLETTSLLQEGQLGEAVL 97
Query: 82 YLLGDLAGRLFMLLL 96
Y+LG L G L + L
Sbjct: 98 YILGTLGGGLIGVAL 112
>gnl|CDD|219923 pfam08596, Lgl_C, Lethal giant larvae(Lgl) like, C-terminal. The
Lethal giant larvae (Lgl) tumour suppressor family is
conserved from yeast to mammals. The Lgl family
functions in cell polarity, at least in part, by
regulating SNARE-mediated membrane delivery events at
the cell surface. The N-terminal half of Lgl members
contains WD40 repeats (see pfam00400), while the
C-terminal half appears specific to the family.
Length = 393
Score = 32.3 bits (74), Expect = 1.6
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 339 QLAHRALEYEVACLDISPLSNEETSSEPAKAQLAAVGLWTDISARLLSLPSLEEVCKEPL 398
+ H++ +Y + C S + + + V L+ + S ++ SLPSL+E+ K L
Sbjct: 246 KGTHKSFDYPILCSGASVVPTNQRKH-----GIVLVALFINGSIKVYSLPSLKEIKKMKL 300
Query: 399 GGEIIPRSI 407
I R +
Sbjct: 301 PFPIDARYL 309
>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 814
Score = 31.7 bits (72), Expect = 2.8
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 4/93 (4%)
Query: 545 SSQTFGVITTRIDIQEADGSTPVRPSASTQAQNTTSSTISSLSYIKPGSTKQSTANQPAD 604
S++ D E +T +A+T A+ +SS + S P S T A
Sbjct: 39 STEAEQTTPVESDATEEADNTETPVAATTAAEAPSSSETAETS--DPTSEATDTTTSEAR 96
Query: 605 FNMEVEVHNLLIIDQNTFERNFTSSTDL--NLV 635
++ T + S+TDL NLV
Sbjct: 97 TVTPAATETSKPVEGQTVDVRILSTTDLHTNLV 129
>gnl|CDD|235765 PRK06274, PRK06274, indolepyruvate oxidoreductase subunit B;
Reviewed.
Length = 197
Score = 30.8 bits (70), Expect = 3.0
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 187 VTCSGGFKEGSLRIIRNGIG-IEEHACIDLPGIKGIWALSIGSPKNLDNTLVLSFVGHTR 245
T G K + I+ I + CID + A IG+P++L N ++L
Sbjct: 102 ATTVGSEKYDPEKEIKFAKEKICDVICIDFTKL----ADEIGNPRSL-NVIMLGAAFGAG 156
Query: 246 VLTLSGAEVEET 257
+L LS V ET
Sbjct: 157 LLPLSKESVLET 168
>gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional.
Length = 343
Score = 30.9 bits (70), Expect = 4.1
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 983 KPGSTKQSTANQPADFNMEVEVHNLLIIDQNTFEILHAHQLFPGEYALSLISSKFGED 1040
P + ++ + +PA + + +VH LL+++Q +E + +FP ++ K GED
Sbjct: 54 GPCAEWENGSCRPAVLSPDRKVHGLLVLEQGEYETIRLDVVFP------VLHGKLGED 105
>gnl|CDD|239640 cd03585, NTR_TIMP, NTR domain, TIMP subfamily; TIMPs, or tissue
inibitors of metalloproteases, are essential regulators
of extracellular matrix turnover and remodeling. They
form complexes with matrix metalloproteases (MMPs) and
inactivate them irreversibly by non-covalently binding
their active zinc-binding sites. The levels of activated
membrane-type MMPs, MMPs, and free TIMPs determine the
balance between matrix degradation and matrix formation
or stabilization. Consequently, TIMPs play roles in
processes that require the remodeling and degradation of
connective tissue, such as development, morphogenesis,
wound healing, as well as in various diseases and
pathological states such as tumor cell metastasis,
arthritis, and artherosclerosis. Most TIMPs bind to a
variety of MMPs. TIMP-1 and TIMP-2 appear to be
multifunctional proteins with diverse biological action.
They may exhibit growth factor-like activity and can
inhibit angiogenesis. TIMP-3 has been implicated in
apoptosis.
Length = 183
Score = 29.3 bits (66), Expect = 8.6
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 664 IAVMKFFRGPTDKKDLLFIIT 684
I +K F+G KD+ +I T
Sbjct: 46 IKQIKMFKGFDKDKDIQYIYT 66
Score = 29.3 bits (66), Expect = 8.6
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 721 IAVMKFFRGPTDKKDLLFIIT 741
I +K F+G KD+ +I T
Sbjct: 46 IKQIKMFKGFDKDKDIQYIYT 66
>gnl|CDD|183377 PRK11910, PRK11910, amidase; Provisional.
Length = 615
Score = 30.0 bits (67), Expect = 8.8
Identities = 22/100 (22%), Positives = 40/100 (40%), Gaps = 20/100 (20%)
Query: 573 TQAQNTTSSTISSLSYIKPGSTKQSTANQPA----------DFNMEVEVHNLLIIDQNTF 622
T Q TTS S++S K + K+ Q + +F++E N + +
Sbjct: 26 TSQQTTTSENKSAVSKKKKPTVKKEKPKQSSNNLTLGKNKENFHLEKGFGNKQLQVERII 85
Query: 623 ERNFTSSTDLNLVVAKNNRIEI----HTVTPEGLRPVKEI 658
+R F SS + I++ + + ++PVK I
Sbjct: 86 DRIFQSS------LKNRTEIKVKPKNNPQKKQNIKPVKPI 119
>gnl|CDD|205304 pfam13123, DUF3978, Protein of unknown function (DUF3978). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 150 amino acids in length.
Length = 145
Score = 28.7 bits (64), Expect = 9.7
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 7/47 (14%)
Query: 606 NMEVEVH------NLLIIDQNTFERNFTSSTDLNLVVAKNNRIEIHT 646
N +E NL I + N F+ N T ST L+ +V K N I+I+T
Sbjct: 11 NTNIESIPDETNFNLHICESNEFDPNLTKSTTLSFIVTKEN-IKIYT 56
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 0.136 0.396
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 61,970,037
Number of extensions: 6221219
Number of successful extensions: 4280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4260
Number of HSP's successfully gapped: 20
Length of query: 1225
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1117
Effective length of database: 6,147,370
Effective search space: 6866612290
Effective search space used: 6866612290
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: 65 (29.1 bits)