RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4641
(229 letters)
>gnl|CDD|183846 PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional.
Length = 206
Score = 282 bits (725), Expect = 1e-97
Identities = 106/206 (51%), Positives = 142/206 (68%), Gaps = 1/206 (0%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGIVQ +V A+ + ++ I FP +LL+G+ I SVA+NGVCL+VTKIEG+ +
Sbjct: 1 MFTGIVQATAEVVAIHKKDGLNTLEIAFPPELLEGLEIGASVAVNGVCLTVTKIEGDRVF 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
FDV+ ETL++TNL + V VN+ERSAK E+GGH LSGH+ A V I E+NY
Sbjct: 61 FDVMEETLRLTNLADLRVGDRVNIERSAKFGAEIGGHILSGHVDTTATVVEISDTEENYD 120
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ ++ + MKY+F KG++ ++G SLT+G+V E F VHLIPET+ T + K VGD +
Sbjct: 121 IRFRVPPE-WMKYIFAKGFIGVNGCSLTVGEVDESEFEVHLIPETLRATNLGAKKVGDLV 179
Query: 181 NIEVDSQTQVIVNTVERVLKENYGNL 206
NIE+DSQTQVIV+TVERVL E L
Sbjct: 180 NIEIDSQTQVIVDTVERVLAERLAEL 205
>gnl|CDD|236455 PRK09289, PRK09289, riboflavin synthase subunit alpha; Provisional.
Length = 194
Score = 238 bits (609), Expect = 3e-80
Identities = 75/196 (38%), Positives = 117/196 (59%), Gaps = 2/196 (1%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGIV+ +G V ++ D +TI L D + + S+A+NGVCL+VT+I+G+ +
Sbjct: 1 MFTGIVEEVGTVESIEPKGDGLRLTIEAGKLLSD-LKLGDSIAVNGVCLTVTEIDGDSFT 59
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
DV ETL+ TNL + V VNLER+ ++ +GGH +SGH+ + +I+ +
Sbjct: 60 VDVSPETLRRTNLGDLKVGDRVNLERALRLGDRLGGHIVSGHVDGTGEIVSIEKEGNSVE 119
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ L KY+ KG +A+DG+SLT+ +V D F V+LIP T+E TT+ +K VGD +
Sbjct: 120 FRFKAP-AELAKYIVEKGSIAVDGVSLTVNEVDGDRFSVNLIPHTLENTTLGEKKVGDRV 178
Query: 181 NIEVDSQTQVIVNTVE 196
N+E+D + + E
Sbjct: 179 NLEIDLLAKYVERLTE 194
>gnl|CDD|223384 COG0307, RibC, Riboflavin synthase alpha chain [Coenzyme
metabolism].
Length = 204
Score = 234 bits (600), Expect = 1e-78
Identities = 82/206 (39%), Positives = 122/206 (59%), Gaps = 7/206 (3%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGIV+ IGKV V + ++TI +L+ + + S+A+NGVCL+VT+ + S
Sbjct: 1 MFTGIVEEIGKVKKV---ENGITLTIESAKLILEDVKLGDSIAVNGVCLTVTEFNEDGFS 57
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
DV+ ETL+ TNL + V VNLER+ K+ +GGH +SGH+ + I+ R
Sbjct: 58 VDVMPETLRRTNLGDLKVGDKVNLERALKLGDRLGGHLVSGHVDGTGEIVKIEKDGNAVR 117
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
+ + L KY+ KG +A+DGISLT+ +V +D F V LIP T+E+TT+ +K VGD +
Sbjct: 118 FWFKAPPEELAKYIVEKGSIAVDGISLTVNEVEDDTFSVSLIPHTLERTTLGEKKVGDRV 177
Query: 181 NIEVDSQTQVIVNTVERVLKENYGNL 206
NIE+D + VER+L +
Sbjct: 178 NIEIDVLAK----YVERLLAAGKASQ 199
>gnl|CDD|232864 TIGR00187, ribE, riboflavin synthase, alpha subunit. This protein
family consists almost entirely of two lumazine-binding
domains, described in the Lum_binding model from PFAM.
The model generates lower scores against other proteins
that also have two lumazine-binding domains, including
some involved in bioluminescence.The name ribE was
selected, from among alternatives including ribB and
ribC, to match the usage in EcoCyc [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 200
Score = 208 bits (531), Expect = 2e-68
Identities = 88/199 (44%), Positives = 128/199 (64%)
Query: 1 MFTGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYIS 60
MFTGI+QG K+ ++ F S+ + +LD + + S+A+NGVCL+VT+I N+ S
Sbjct: 1 MFTGIIQGTAKLVSIKEKPLFISLVVNLADHMLDDLELGDSIAVNGVCLTVTEINKNHFS 60
Query: 61 FDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYR 120
D+ ETLK TNL + V +VN+ER+ K + E+GGHF+SGHI A + I+ E N +
Sbjct: 61 VDLSPETLKRTNLGDLKVGTWVNIERALKADGEIGGHFVSGHIDTTAEIAKIETSENNVQ 120
Query: 121 MEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDAL 180
++ + LMKY+ KG +A+DGISLTIGKV E F V LIP T+E T + K +GD +
Sbjct: 121 FWFKLQDSELMKYIVEKGSIAVDGISLTIGKVTETRFCVSLIPHTLENTILGLKKLGDRV 180
Query: 181 NIEVDSQTQVIVNTVERVL 199
NIE+D + + +T+ER L
Sbjct: 181 NIEIDMLGKAVADTLERTL 199
>gnl|CDD|178342 PLN02741, PLN02741, riboflavin synthase.
Length = 194
Score = 174 bits (442), Expect = 6e-55
Identities = 67/200 (33%), Positives = 116/200 (58%), Gaps = 9/200 (4%)
Query: 1 MFTGIVQGIGKVSAVFSYND-FKSMTIWFPSDLLDGISISCSVAINGVCLSVTKIEGNYI 59
+FTGIV+ +G+V ++ +D + I S +LDG+ + S+A+NG CL+VT+ +G+
Sbjct: 1 LFTGIVEEMGEVKSLGVTDDGGFDLKIE-ASTVLDGVKLGDSIAVNGTCLTVTEFDGDEF 59
Query: 60 SFDVINETLKITNLKAVAVDQFVNLERSAKMNTEVGGHFLSGHIIDVANVRAIQALEKNY 119
+ + ETL+ T+L + VNLER+ + + +GGHF+ GH+ + + +
Sbjct: 60 TVGLAPETLRKTSLGELKTGSLVNLERALRPGSRMGGHFVQGHVDGTGTIVEQEPEGDSL 119
Query: 120 RMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVF--EDYFYVHLIPETMEKTTMSKKAVG 177
++++ + L+KY+ KG++A+DG SLT+ V E F L+P T +K + K VG
Sbjct: 120 WVKVKADPE-LLKYIVPKGFIAVDGTSLTVVDVDDEEGCFNFMLVPYTQQKVVIPLKKVG 178
Query: 178 DALNIEVDSQTQVIVNTVER 197
D +N+EVD ++ VER
Sbjct: 179 DKVNLEVD----ILGKYVER 194
>gnl|CDD|201387 pfam00677, Lum_binding, Lumazine binding domain. This domain binds
to derivatives of lumazine in some proteins. Some
proteins have lost the residues involved in binding
lumazine.
Length = 86
Score = 77.6 bits (192), Expect = 7e-19
Identities = 28/86 (32%), Positives = 50/86 (58%)
Query: 100 SGHIIDVANVRAIQALEKNYRMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYV 159
+G + A + +I + I++ +K L K + K +A++GISLT+ +V + F
Sbjct: 1 TGIVEGTAEIASITENGNARSIWIKIPDKMLTKVIIGKDSIAVNGISLTVTEVTGNIFTF 60
Query: 160 HLIPETMEKTTMSKKAVGDALNIEVD 185
LIPET+++T + VGD +N+E+D
Sbjct: 61 DLIPETLKRTNLGSLKVGDKVNLEID 86
Score = 75.3 bits (186), Expect = 6e-18
Identities = 34/85 (40%), Positives = 55/85 (64%), Gaps = 1/85 (1%)
Query: 3 TGIVQGIGKVSAVFSYNDFKSMTIWFPSDLLDGISISC-SVAINGVCLSVTKIEGNYISF 61
TGIV+G +++++ + +S+ I P +L + I S+A+NG+ L+VT++ GN +F
Sbjct: 1 TGIVEGTAEIASITENGNARSIWIKIPDKMLTKVIIGKDSIAVNGISLTVTEVTGNIFTF 60
Query: 62 DVINETLKITNLKAVAVDQFVNLER 86
D+I ETLK TNL ++ V VNLE
Sbjct: 61 DLIPETLKRTNLGSLKVGDKVNLEI 85
>gnl|CDD|236214 PRK08274, PRK08274, tricarballylate dehydrogenase; Validated.
Length = 466
Score = 30.6 bits (70), Expect = 0.63
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 134 VFYKGYVAIDGISLTIGKVF 153
V KGY A G+ LTIG VF
Sbjct: 432 VLGKGYPA--GVGLTIGAVF 449
>gnl|CDD|132767 cd07306, Porin3_VDAC, Voltage-dependent anion channel of the outer
mitochondrial membrane. The voltage-dependent anion
channel (VDAC) regulates the flux of mostly anionic
metabolites through the outer mitochondrial membrane,
which is highly permeable to small molecules. VDAC is
the most abundant protein in the outer membrane, and
membrane potentials can toggle VDAC between open or
high-conducting and closed or low-conducting forms. VDAC
binds to and is regulated in part by hexokinase, an
interaction that renders mitochondria less susceptible
to pro-apoptotic signals, most likely by intefering with
VDAC's capability to respond to Bcl-2 family proteins.
While VDAC appears to play a key role in mitochondrially
induced cell death, a proposed involvement in forming
the mitochondrial permeability transition pore, which is
characteristic for damaged mitochondria and apoptosis,
has been challenged by more recent studies.
Length = 276
Score = 29.1 bits (66), Expect = 1.9
Identities = 16/107 (14%), Positives = 32/107 (29%), Gaps = 5/107 (4%)
Query: 87 SAKMNTEVGGHFLSGHIIDVANVRAIQALEKNYRMEIQMTNKSLMKYVFYKGYVAID--- 143
+N +V G ++ + V + + KY F GY D
Sbjct: 117 PININADVD--LNKGPLVGASAVLGYKGFLLGAEVVYDTAKSKFTKYNFALGYTNGDFEL 174
Query: 144 GISLTIGKVFEDYFYVHLIPETMEKTTMSKKAVGDALNIEVDSQTQV 190
+ L GK ++ + P ++ + + V Q +
Sbjct: 175 SLKLNNGKTLRGSYFHKVSPRLAVGAKVTWYSGTNETTFAVGGQYAL 221
>gnl|CDD|197212 cd09113, PLDc_ymdC_like_2, Putative catalytic domain, repeat 2, of
Escherichia coli uncharacterized protein ymdC and
similar proteins. Putative catalytic domain, repeat 2,
of Escherichia coli uncharacterized protein ymdC and
similar proteins. In Escherichia coli, there are two
genes, f413 (ybhO) and o493 (ymdC), which are homologous
to gene cls that encodes the Escherichia coli
cardiolipin (CL) synthase. The prototype of this
subfamily is an uncharacterized protein ymdC specified
by the o493 (ymdC) gene. Although the functional
characterization of ymdC and similar proteins remains
unknown, members of this subfamily show high sequence
homology to bacterial CL synthases, which catalyze the
reversible phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Moreover, ymdC and its similar proteins contain two HKD
motifs (H-x-K-x(4)-D, where x represents any amino acid
residue) that characteriszes the phospholipase D (PLD)
superfamily. The two motifs may be part of the active
site and may be involved in phosphatidyl group transfer.
Length = 218
Score = 28.7 bits (65), Expect = 2.2
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 7/29 (24%)
Query: 74 KAVAVDQ---FV---NLE-RSAKMNTEVG 95
K+ +D FV NL+ RSA +NTE+G
Sbjct: 120 KSFVIDDRLVFVGSFNLDPRSAYLNTEMG 148
>gnl|CDD|236418 PRK09225, PRK09225, threonine synthase; Validated.
Length = 462
Score = 28.6 bits (65), Expect = 2.7
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 105 DVANVRAI-QALEKNYRMEIQMTNKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYV 159
D A V + + LE+ ++ + ++ F G V+ + TI +V+E+Y Y+
Sbjct: 326 DAAAVEELMEDLEEKGEYDLSDEELAALREDFSAGSVSDEETLATIREVYEEYGYL 381
>gnl|CDD|227252 COG4915, XpaC, 5-bromo-4-chloroindolyl phosphate hydrolysis protein
[General function prediction only].
Length = 204
Score = 26.7 bits (59), Expect = 8.0
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 154 EDYFYVHL--IPETMEKTTMSKKAVGDALNIEVD-SQTQVIVNTVERVLKENY 203
E++FY HL + E EK KK + I D S+T++++ + R ++++
Sbjct: 128 EEFFYSHLDNMVELTEKYAFLKKQPVKSKEINQDLSETRILLKELSRSIEKDL 180
>gnl|CDD|205348 pfam13167, GTP-bdg_N, GTP-binding GTPase N-terminal. This is the
N-terminal region of GTP-binding HflX-like proteins. The
full-length members bind and interact with the 50S
ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP.
This N-terminal region is necessary for stability of the
whole protein.
Length = 95
Score = 25.9 bits (57), Expect = 8.7
Identities = 21/84 (25%), Positives = 45/84 (53%), Gaps = 8/84 (9%)
Query: 112 IQALEKNYRMEI--QMT-NKSLMKYVFYKGYVAIDGISLTIGKVFEDYFYVHLIPETMEK 168
+++L + ++E+ Q+T N+ + +Y G ID I K F ++ + ++ E
Sbjct: 13 LKSLSQTCQLEVKGQITQNRDRVDNKYYVGKGKIDEI-----KAFIEFHDIDVVVVNDEL 67
Query: 169 TTMSKKAVGDALNIEVDSQTQVIV 192
TT K++ D L +++ +TQ+I+
Sbjct: 68 TTAQSKSLNDNLGVKIIDRTQLIL 91
>gnl|CDD|218746 pfam05784, Herpes_UL82_83, Betaherpesvirus UL82/83 protein N
terminus. This family represents the N terminal region
of the Betaherpesvirus UL82 and UL83 proteins. As
viruses are reliant upon their host cell to serve as
proper environments for their replication, many have
evolved mechanisms to alter intracellular conditions to
suit their own needs. Human cytomegalovirus induces
quiescent cells to enter the cell cycle and then arrests
them in late G(1), before they enter the S phase, a cell
cycle compartment that is presumably favourable for
viral replication. The protein product of the human
cytomegalovirus UL82 gene, pp71, can accelerate the
movement of cells through the G(1) phase of the cell
cycle. This activity would help infected cells reach the
late G(1) arrest point sooner and thus may stimulate the
infectious cycle. pp71 also induces DNA synthesis in
quiescent cells, but a pp71 mutant protein that is
unable to induce quiescent cells to enter the cell cycle
still retains the ability to accelerate the G(1) phase.
Thus, the mechanism through which pp71 accelerates G(1)
cell cycle progression appears to be distinct from the
one that it employs to induce quiescent cells to exit
G(0) and subsequently enter the S phase.
Length = 346
Score = 26.9 bits (60), Expect = 8.8
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 10 GKVSAVFSYNDFKS----MTIWFPSDLLDGISISCSVAINGVCLSVT 52
G+ S V N F+S ++FP D+ G+SISC + L +
Sbjct: 272 GQTSHVMIDNAFESDQTHAGLFFPKDIP-GLSISCGPWMERQPLFIE 317
>gnl|CDD|216212 pfam00955, HCO3_cotransp, HCO3- transporter family. This family
contains Band 3 anion exchange proteins that exchange
CL-/HCO3-. This family also includes cotransporters of
Na+/HCO3-.
Length = 501
Score = 27.3 bits (61), Expect = 9.1
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 19 NDFKSMTIWFPSDLLDGISISCSVAI 44
D K W+ SD D ++ C AI
Sbjct: 14 RDIKRRYPWYLSDFRDALNPQCLAAI 39
>gnl|CDD|200521 cd11260, Sema_4E, The Sema domain, a protein interacting module, of
semaphorin 4E (Sema4E). Sema4E is expressed in the
epithelial cells that line the pharyngeal arches in
zebrafish. It may act as a guidance molecule to restrict
the branchiomotor axons to the mesenchymal cells.
Gain-of-function and loss-of-function studies
demonstrate that Sema4E is essential for the guidance of
facial axons from the hindbrain into their pharyngeal
arch targets and is sufficient for guidance of gill
motor axons. Sema4E guides facial motor axons by a
repulsive action. Sema4E belongs to the class 4
transmembrane semaphorin family of proteins. Semaphorins
are regulatory molecules involved in the development of
the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 456
Score = 27.2 bits (60), Expect = 9.2
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 182 IEVDSQTQVIVNTVERVLKENYGNLRCL 209
+E D +++V+ V RV K + G R L
Sbjct: 200 VEYDFYNKLVVSRVARVCKGDLGGQRTL 227
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 0.134 0.382
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,159,601
Number of extensions: 1030117
Number of successful extensions: 865
Number of sequences better than 10.0: 1
Number of HSP's gapped: 846
Number of HSP's successfully gapped: 25
Length of query: 229
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 135
Effective length of database: 6,768,326
Effective search space: 913724010
Effective search space used: 913724010
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: 57 (25.9 bits)