RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17788
(365 letters)
>gnl|CDD|218774 pfam05843, Suf, Suppressor of forked protein (Suf). This family
consists of several eukaryotic suppressor of forked
(Suf) like proteins. The Drosophila melanogaster
Suppressor of forked [Su(f)] protein shares homology
with the yeast RNA14 protein and the 77-kDa subunit of
human cleavage stimulation factor, which are proteins
involved in mRNA 3' end formation. This suggests a role
for Su(f) in mRNA 3' end formation in Drosophila. The
su(f) gene produces three transcripts; two of them are
polyadenylated at the end of the transcription unit, and
one is a truncated transcript, polyadenylated in intron
4. It is thought that su(f) plays a role in the
regulation of poly(A) site utilisation and an important
role of the GU-rich sequence for this regulation to
occur.
Length = 271
Score = 40.3 bits (95), Expect = 0.001
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 297 YVDMLVKSDRVDLGRQVIQRAVTQKLPPKK-LKPLYMKWLKLEEQYGDAEAVENVKKEIE 355
Y+D L+ + R + + VT KL P+ LKPL+ K++K E ++GD ++ ++K +
Sbjct: 76 YLDYLISLNDDTNARVLFETVVT-KLTPEPELKPLWKKFIKYESKFGDLSSILKLEKRMF 134
Query: 356 QY 357
+
Sbjct: 135 EL 136
>gnl|CDD|227438 COG5107, RNA14, Pre-mRNA 3'-end processing (cleavage and
polyadenylation) factor [RNA processing and
modification].
Length = 660
Score = 34.6 bits (79), Expect = 0.085
Identities = 50/252 (19%), Positives = 101/252 (40%), Gaps = 16/252 (6%)
Query: 101 FDRMLLGQPNNSELWVKYMAYHLQATEIEKARSIARRALTVINIRNEEDRLNVWTSLLNL 160
+++L E+W Y Y + ++ +KA R + L ++ S
Sbjct: 291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGI------EMSPSLTMFLSEY-- 342
Query: 161 EHLYGTKESLQECLHEAVRCNDETKVYMNMMEIYAASAQIRDLESTVKLLLKKAGQTHSS 220
L +E++ C +C + K +M E +AS + E + +LLLK+ +
Sbjct: 343 YELVNDEEAVYGCFD---KCTQDLKRKYSMGESESASKVDNNFEYSKELLLKRINKLTFV 399
Query: 221 VNIYLQCATLLLRLGQKDTARHILQRGLNNLPPAVHVTLITRFALAENKFGDASRAQALL 280
++L +LR + AR + + L H I + GD + A +
Sbjct: 400 FCVHLNY---VLRKRGLEAARKLFIK-LRKEGIVGHHVYIYCAFIEYYATGDRATAYNIF 455
Query: 281 EHTLTSYPARVDVWGVYVDMLVKSDRVDLGRQVIQRAVTQKLPPKKLKPLYMKWLKLEEQ 340
E L +P Y+ L++ + + R + + +V ++L +LK +Y K ++ E
Sbjct: 456 ELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSV-ERLEKTQLKRIYDKMIEYESM 514
Query: 341 YGDAEAVENVKK 352
G V ++++
Sbjct: 515 VGSLNNVYSLEE 526
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 30.4 bits (69), Expect = 1.4
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 49 DSEDEEEEVEIKKVKPKLTKAEKLAAAKAEEARIRQAEDE 88
DSEDEEE+ E K + + E + E A +AE E
Sbjct: 131 DSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAE 170
>gnl|CDD|214526 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
Microtubule-dependent molecular motors that play
important roles in intracellular transport of organelles
and in cell division.
Length = 335
Score = 30.2 bits (69), Expect = 1.5
Identities = 19/93 (20%), Positives = 43/93 (46%), Gaps = 17/93 (18%)
Query: 160 LEHLYGTKESLQECLHEAVRCNDETKVYMNMMEIYAASAQIRDL--ESTVKLLLKKAGQT 217
L+ L+ + +E + V ++ +EIY + +IRDL S+ KL +++
Sbjct: 111 LKDLFEKIDKREE--------GWQFSVKVSYLEIY--NEKIRDLLNPSSKKLEIRE---- 156
Query: 218 HSSVNIYLQCATLLLRLGQKDTARHILQRGLNN 250
+Y++ T + + + ++L++G N
Sbjct: 157 DEKGGVYVKGLT-EISVSSFEEVYNLLEKGNKN 188
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 30.0 bits (68), Expect = 1.6
Identities = 12/53 (22%), Positives = 26/53 (49%)
Query: 47 QDDSEDEEEEVEIKKVKPKLTKAEKLAAAKAEEARIRQAEDELLQNGEPVSPD 99
++ ++E+EE + K K A + +E R+ E++ L+ E +P+
Sbjct: 38 DEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPE 90
Score = 28.1 bits (63), Expect = 6.6
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 14/57 (24%)
Query: 49 DSEDEEEEVEIKKVKP--------------KLTKAEKLAAAKAEEARIRQAEDELLQ 91
DS DEEE+ E ++ K K+ + EK K E+ ED
Sbjct: 35 DSWDEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPED 91
>gnl|CDD|143500 cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Proteobacterial Alanine
Racemases. This subfamily is composed mainly of
proteobacterial alanine racemases (EC 5.1.1.1), fold
type III PLP-dependent enzymes that catalyze the
interconversion between L- and D-alanine, which is an
essential component of the peptidoglycan layer of
bacterial cell walls. hese proteins are similar to other
bacterial ARs and are fold type III PLP-dependent
enzymes containing contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
They exist as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Homodimer formation and the presence of the PLP
cofactor are required for catalytic activity.
Length = 354
Score = 30.2 bits (69), Expect = 1.6
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 218 HSSVNIYLQCATLLLRLG-QKDTARHILQRGLNNLPPAVHVTLITRFALAEN 268
+N++L+ + + RLG + QR L P + L+T FA A+
Sbjct: 112 SKPLNVWLKLDSGMHRLGFSPEEYAAAYQR-LKASPNVASIVLMTHFACADE 162
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 30.6 bits (69), Expect = 1.9
Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 2/81 (2%)
Query: 2 DVEEQQSEELLAKSTTQSNSIPDSLPQVGFTWGMA--MEDLNLLKPNQDDSEDEEEEVEI 59
D++++ + L + QS + +++ V A ++ + D +D++ VE+
Sbjct: 1265 DLKDRLAAYNLDSAPAQSAKMEETVKAVPARRAAARKKPLASVSVISDSDDDDDDFAVEV 1324
Query: 60 KKVKPKLTKAEKLAAAKAEEA 80
+ K + AA ++A
Sbjct: 1325 SLAERLKKKGGRKPAAANKKA 1345
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 328
Score = 29.9 bits (68), Expect = 2.0
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 18/95 (18%)
Query: 160 LEHLYGTKESLQECLHEAVRCNDETKVYMNMMEIYAASAQIRDL----ESTVKLLLKKAG 215
LE L+ + +E N V ++ +EIY + ++ DL + L L++
Sbjct: 110 LEDLFNLIDERKEK-------NKSFSVSVSYLEIY--NEKVYDLLSPEPPSKPLSLREDP 160
Query: 216 QTHSSVNIYLQCATLLLRLGQKDTARHILQRGLNN 250
+ V + + +G + A +LQ+GL N
Sbjct: 161 KGGVYVKGLTE-----VEVGSAEDALSLLQKGLKN 190
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 30.2 bits (68), Expect = 2.1
Identities = 22/105 (20%), Positives = 37/105 (35%), Gaps = 6/105 (5%)
Query: 49 DSEDEEEEVEIKKVKPKLTKAEKLAAAKAE-EARIRQAEDELLQNGEPVSPDGFDR---- 103
+ + E + E + + A K AAA A + R+ E + P PD +
Sbjct: 794 RAAEAERQAESAERELA-RAARKAAAAAAAWKQARRELERDAADLDLPTDPDALEAVGLA 852
Query: 104 MLLGQPNNSELWVKYMAYHLQATEIEKARSIARRALTVINIRNEE 148
+ + L V AT + R+ A RA + E+
Sbjct: 853 LKRFGDHLHTLEVAVRELRHAATRAAEQRARAARAESDAREAAED 897
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 29.3 bits (66), Expect = 3.1
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 15/80 (18%)
Query: 51 EDEEEEVEIK----KVKPKLTKAEKLAAAKAEE-----ARIRQAEDELLQNGEPVSPDGF 101
+D+++ E++ +++ + +AE+ A A+AE AR+R + + + G P
Sbjct: 230 KDQQQLSELRANESRLRDSIARAEREAKARAEREAREAARVRDKQKQAKRKGSTYKPTES 289
Query: 102 DRML------LGQPNNSELW 115
+R L LG+P W
Sbjct: 290 ERSLMSRTGGLGRPRGQAFW 309
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 26.5 bits (59), Expect = 4.3
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 228 ATLLLRLGQKDTARHILQRGLNNLPPAVHVTLITRFALAENKFGDASRAQALLEHTLTSY 287
A LR G D A L+ L P A L+ A + G + A ALL L +
Sbjct: 4 ARAALRAGDYDEALAALEAALARYPLAAEALLLL--GEALLRQGRLAEAAALLRAALAAD 61
Query: 288 P 288
P
Sbjct: 62 P 62
Score = 25.7 bits (57), Expect = 9.4
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 263 FALAENKF--GDASRAQALLEHTLTSYPARVDVWGVYVDMLVKSDRVDLGRQVIQRAV 318
ALA GD A A LE L YP + + + L++ R+ +++ A+
Sbjct: 1 LALARAALRAGDYDEALAALEAALARYPLAAEALLLLGEALLRQGRLAEAAALLRAAL 58
>gnl|CDD|218358 pfam04979, IPP-2, Protein phosphatase inhibitor 2 (IPP-2).
Protein phosphotase inhibitor 2 (IPP-2) is a
phosphoprotein conserved among all eukaryotes, and it
appears in both the nucleus and cytoplasm of tissue
culture cells.
Length = 123
Score = 27.4 bits (61), Expect = 5.3
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 46 NQDDSEDEEEEVEIKKVKPKLTKAEKLAAAKAEEARIRQAEDE 88
++ D ED + E E + + AEKLAAA++ + E E
Sbjct: 35 HRMDDEDSDSESEGNESLTPESLAEKLAAAESSDPSFSIEESE 77
>gnl|CDD|226014 COG3483, TDO2, Tryptophan 2,3-dioxygenase (vermilion) [Amino acid
transport and metabolism].
Length = 262
Score = 28.2 bits (63), Expect = 5.8
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 87 DELLQNGEPVSPDGFDRMLLGQPNNSELWVKYMAYHLQA 125
DELL P+S D + + + Q SELW+K + + L+A
Sbjct: 13 DELLSAQGPLSDDHDEMLFIVQHQTSELWMKLILHELRA 51
>gnl|CDD|188272 TIGR03036, trp_2_3_diox, tryptophan 2,3-dioxygenase. Members of
this family are tryptophan 2,3-dioxygenase, as confirmed
by several experimental characterizations, and by
conserved operon structure for many of the other
members. This enzyme represents the first of a two-step
degradation to L-kynurenine, and a three-step pathway
(via kynurenine) to anthranilate plus alanine [Energy
metabolism, Amino acids and amines].
Length = 264
Score = 28.4 bits (64), Expect = 6.1
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 11/54 (20%)
Query: 87 DELLQNGEPVSPDGFDRML-LGQPNNSELWVKYMAYHLQATEIEKARSIARRAL 139
D LL P+S D D ML + Q SELW+K + + L+A ARRA+
Sbjct: 15 DTLLSAQHPLSDD-HDEMLFIVQHQTSELWMKLILHELRA---------ARRAI 58
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 1480
Score = 28.7 bits (64), Expect = 6.2
Identities = 11/61 (18%), Positives = 33/61 (54%)
Query: 301 LVKSDRVDLGRQVIQRAVTQKLPPKKLKPLYMKWLKLEEQYGDAEAVENVKKEIEQYVRN 360
L +S+ D+ R++++ Q+ ++++PL M+ +LE++ ++ E + + +
Sbjct: 489 LARSEAWDVARELLREGPDQRHLAEQVQPLRMRLSELEQRLRQQQSAERLLADFCKRQGK 548
Query: 361 S 361
+
Sbjct: 549 N 549
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 28.5 bits (64), Expect = 7.1
Identities = 29/101 (28%), Positives = 52/101 (51%), Gaps = 6/101 (5%)
Query: 232 LRLGQKDTARHILQRGLNNLPPAVHVTL-ITRFALAENKFGDASRAQALLEHTLTSYPAR 290
L LGQ + A+ ++ L P +++ L + + ALAEN+F A+AL++ LT+ P
Sbjct: 136 LGLGQLELAQKSYEQALAIDPRSLYAKLGLAQLALAENRF---DEARALIDEVLTADPGN 192
Query: 291 VDVWGVYVDMLVKSDRVDLGRQVIQRAVTQKLPPKKLKPLY 331
VD + D+L+ ++L ++A+ L P + L
Sbjct: 193 VDALLLKGDLLLSLGNIELALAAYRKAI--ALRPNNIAVLL 231
>gnl|CDD|227518 COG5191, COG5191, Uncharacterized conserved protein, contains HAT
(Half-A-TPR) repeat [General function prediction only].
Length = 435
Score = 28.4 bits (63), Expect = 7.4
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 101 FDRMLLGQPNNSELWVKYMAYHLQA-TEIEKARSIARRALTVINIRNEEDRLNVWTSLLN 159
F L P N +LW+ A+ L IE +R++ + L R +W
Sbjct: 130 FAECLTKHPLNVDLWIYCCAFELFEIANIESSRAMFLKGL-----RMNSRSPRIWIEYFR 184
Query: 160 LEHLYGTK 167
+E +Y TK
Sbjct: 185 MELMYITK 192
>gnl|CDD|222984 PHA03100, PHA03100, ankyrin repeat protein; Provisional.
Length = 422
Score = 28.1 bits (63), Expect = 8.4
Identities = 22/107 (20%), Positives = 36/107 (33%), Gaps = 16/107 (14%)
Query: 185 KVYMNMMEIYAASAQIRDLESTVKLLLKKAGQTHSSVNIYLQCATLLLRLGQ-------- 236
++ +Y A VK+LL +SS T L L
Sbjct: 31 SYKKPVLPLYLAKEARN--IDVVKILLDNGADINSSTKNNS---TPLHYLSNIKYNLTDV 85
Query: 237 KDTARHILQRGLN-NLPPAVHVTLITRFALAENKFGDASRAQALLEH 282
K+ + +L+ G N N P +T + K S + LL++
Sbjct: 86 KEIVKLLLEYGANVNAPDNNGITPL--LYAISKKSNSYSIVEYLLDN 130
>gnl|CDD|180745 PRK06915, PRK06915, acetylornithine deacetylase; Validated.
Length = 422
Score = 28.1 bits (63), Expect = 8.5
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 257 VTLITRFALAENKFGDASRAQALLEHTLTSYPARVDVWGVYVDMLV-----KSDRVDL 309
V L+ R ++ GD S AQA++ L +D+W L S R
Sbjct: 20 VKLLKRLIQEKSVSGDESGAQAIVIEKLRELGLDLDIWEPSFKKLKDHPYFVSPRTSF 77
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 27.8 bits (62), Expect = 9.4
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 68 KAEKLAAAKAEEARIRQAEDELLQNGEPVSPDGFDRMLLGQPN 110
E AAA+A AR R AE + GE P ++ML+
Sbjct: 250 AREAAAAAEAAAARARAAEAKR--TGETYKPTAPEKMLISSTG 290
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
0.314 0.129 0.363
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,434,083
Number of extensions: 1792082
Number of successful extensions: 2042
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2010
Number of HSP's successfully gapped: 88
Length of query: 365
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 267
Effective length of database: 6,590,910
Effective search space: 1759772970
Effective search space used: 1759772970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (26.8 bits)