RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18106
(76 letters)
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 41.2 bits (97), Expect = 1e-06
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 23 LVVVTLERSHTGLGISLAGHKDRTKMAVFVCGLNPSGSASKTGSVLVGDELLEI 76
+V LE+ GLG SL G KD V V + P A+K G + VGD +LE+
Sbjct: 2 PRLVELEKGGGGLGFSLVGGKD-EGGGVVVSSVVPGSPAAKAG-LRVGDVILEV 53
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of
Eumetazoan signaling molecules, often in tandem
arrangements. May be responsible for specific
protein-protein interactions, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of PDZ domains an
N-terminal beta-strand forms the peptide-binding groove
base, a circular permutation with respect to PDZ
domains found in proteases.
Length = 82
Score = 41.0 bits (97), Expect = 2e-06
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 23 LVVVTLERSHT-GLGISLAGHKDRTKMAVFVCGLNPSGSASKTGSVLVGDELLEI 76
+ VTL + GLG SL G KD +FV + P G A + G + VGD +LE+
Sbjct: 1 VRTVTLRKDPGGGLGFSLRGGKDS-GGGIFVSRVEPGGPAERGG-LRVGDRILEV 53
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 30.7 bits (70), Expect = 0.019
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 26 VTLER-SHTGLGISLAGHKDRTKMAVFVCGLNPSGSASKTGSVLVGDELLEI 76
VTLE+ GLG SL G D +FV + P G A++ G + GD +L I
Sbjct: 2 VTLEKSGRGGLGFSLVGGSD-GDPGIFVSEVLP-GGAAEAGGLQEGDRILSI 51
>gnl|CDD|131111 TIGR02056, ChlG, chlorophyll synthase, ChlG. This model represents
the strictly cyanobacterial and plant-specific
chlorophyll synthase ChlG. ChlG is the enzyme (esterase)
which attaches the side chain moiety onto chlorophyllide
a. Both geranylgeranyl and phytyl pyrophosphates are
substrates to varying degrees in enzymes from different
sources. Thus, ChlG may act as the final or penultimate
step in chlorophyll biosynthesis (along with the
geranylgeranyl reductase, ChlP) [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 306
Score = 28.8 bits (64), Expect = 0.20
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 16 YGSLGPDLVVVTLERSHTGLGISL 39
+G L PD+ V+TL S GLGI++
Sbjct: 178 FGELNPDIAVLTLIYSIAGLGIAI 201
>gnl|CDD|215028 PLN00012, PLN00012, chlorophyll synthetase; Provisional.
Length = 375
Score = 28.3 bits (63), Expect = 0.27
Identities = 13/24 (54%), Positives = 19/24 (79%)
Query: 16 YGSLGPDLVVVTLERSHTGLGISL 39
+G+L PD+VV+TL S GLGI++
Sbjct: 247 FGTLTPDVVVLTLLYSIAGLGIAI 270
>gnl|CDD|132565 TIGR03526, selenium_YgeY, putative selenium metabolism hydrolase.
SelD, selenophosphate synthase, is the selenium donor
protein for both selenocysteine and selenouridine
biosynthesis systems, but it occurs also in a few
prokaryotes that have neither of those pathways. The
method of partial phylogenetic profiling , starting from
such orphan-selD genomes, identifies this protein as one
of those most strongly correlated to SelD occurrence.
Its distribution is also well correlated with that of
family TIGR03309, a putative accessory protein of labile
selenium (non-selenocysteine) enzyme maturation. This
family includes the uncharacterized YgeY of Escherichia
coli, and belongs to a larger family of metalloenzymes
in which some are known peptidases, others enzymes of
different types.
Length = 395
Score = 28.2 bits (63), Expect = 0.33
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 21 PDLVVVTLERSHTGLGISLAGHKDRTKMAVFVCGLNPSGSASKTG 65
P+ VV+T T + I G + R ++ V V G++ GSA + G
Sbjct: 161 PEFVVIT---EPTDMNIYR-GQRGRMEIKVTVKGVSCHGSAPERG 201
>gnl|CDD|214455 MTH00202, ND3, NADH dehydrogenase subunit 3; Provisional.
Length = 117
Score = 27.6 bits (62), Expect = 0.41
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 37 ISLAGHKDRTKMAVFVCGLNPSGSA 61
+S DR K + F CG +P SA
Sbjct: 25 LSFRSLMDREKSSPFECGFDPKESA 49
>gnl|CDD|214359 CHL00085, ycf24, putative ABC transporter.
Length = 485
Score = 27.3 bits (61), Expect = 0.60
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 7 FSSDKVKKKYGSLGPDLVVVTLERSHTGLGISLAGHKDRTKMAV 50
+S+ K+KKK SL D V L + LGISL K +AV
Sbjct: 90 YSAPKLKKKLNSL--DEVDPELLDTFEKLGISLNEQKRLANVAV 131
>gnl|CDD|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 26.7 bits (60), Expect = 0.89
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 30/73 (41%)
Query: 11 KVKKKYGSLGPDLVVVTLERSHTGL--------------------GIS-LAGHKDRTKMA 49
KV+K + GP + + R+H GL I+ AG RTK+A
Sbjct: 184 KVEK--TTKGP---QIFVSRTHPGLVKRLFELEVPEIYDGTVEIKSIAREAGD--RTKIA 236
Query: 50 VFVC--GLNPSGS 60
V ++ G+
Sbjct: 237 VRSNNPNVDAKGA 249
>gnl|CDD|217398 pfam03166, MH2, MH2 domain. This is the MH2 (MAD homology 2)
domain found at the carboxy terminus of MAD related
proteins such as Smads. This domain is separated from
the MH1 domain by a non-conserved linker region. The
MH2 domain mediates interaction with a wide variety of
proteins and provides specificity and selectivity to
Smad function and also is critical for mediating
interactions in Smad oligomers. Unlike MH1, MH2 does
not bind DNA. The well-studied MH2 domain of Smad4 is
composed of five alpha helices and three loops
enclosing a beta sandwich. Smads are involved in the
propagation of TGF-beta signals by direct association
with the TGF-beta receptor kinase which phosphorylates
the last two Ser of a conserved 'SSXS' motif located at
the C-terminus of MH2.
Length = 179
Score = 25.4 bits (56), Expect = 2.8
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 7/30 (23%)
Query: 30 RSHTGLGISLAGHKD-------RTKMAVFV 52
R H G G+ L+ D R+ +FV
Sbjct: 62 RRHIGKGVQLSYKADGEVWVYNRSDSPIFV 91
>gnl|CDD|168128 PRK05613, PRK05613, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 437
Score = 25.2 bits (55), Expect = 3.2
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 19 LGPDLVVVTLERSHTGLGISLAG 41
LG D+VV +L + +TG G L G
Sbjct: 205 LGADVVVASLTKFYTGNGSGLGG 227
>gnl|CDD|240417 PTZ00435, PTZ00435, isocitrate dehydrogenase; Provisional.
Length = 413
Score = 24.9 bits (55), Expect = 4.0
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 8/36 (22%)
Query: 5 GNFSSDKVKKKYGSLG--------PDLVVVTLERSH 32
G+ SD V + YGSLG PD V E +H
Sbjct: 275 GDVQSDIVAQGYGSLGLMTSVLVCPDGKTVEAEAAH 310
>gnl|CDD|162981 TIGR02707, butyr_kinase, butyrate kinase. This model represents an
enzyme family in which members are designated either
butryate kinase or branched-chain carboxylic acid
kinase. The EC designation 2.7.2.7 describes an enzyme
with relatively broad specificity; gene products whose
context suggests a role in metabolism of aliphatic amino
acids are likely to act as branched-chain carboxylic
acid kinase. The gene typically found adjacent, ptb
(phosphate butyryltransferase), likewise encodes an
enzyme that may have a broad specificity that includes a
role in aliphatic amino acid cabolism [Energy
metabolism, Fermentation].
Length = 351
Score = 24.7 bits (54), Expect = 4.8
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 10/60 (16%)
Query: 14 KKYGSLGPDLVVVTLERSHTGLGISLAGHKDRTKMAVFVCGLNPSG--SASKTGSVLVGD 71
K+Y + +L+V H G GIS+A H+ + ++ L+ G S ++G++ +GD
Sbjct: 169 KRYEEM--NLIVA-----HMGGGISVAAHR-KGRVIDVNNALDGEGPFSPERSGTLPLGD 220
>gnl|CDD|214433 MTH00148, ND3, NADH dehydrogenase subunit 3; Provisional.
Length = 117
Score = 24.4 bits (54), Expect = 5.0
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 34 GLGISLAGHKDRTKMAVFVCGLNPSGSA 61
GL +S + DR K + F CG +P SA
Sbjct: 22 GLVLSKRSYSDREKSSPFECGFDPISSA 49
>gnl|CDD|177217 MTH00161, ND3, NADH dehydrogenase subunit 3; Provisional.
Length = 113
Score = 24.4 bits (54), Expect = 6.0
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 44 DRTKMAVFVCGLNPSGSA 61
DR K + F CG +P SA
Sbjct: 30 DREKSSPFECGFDPKSSA 47
>gnl|CDD|221725 pfam12704, MacB_PCD, MacB-like periplasmic core domain. This
family represents the periplasmic core domain found in
a variety of ABC transporters. The structure of this
family has been solved for the MacB protein. Some
structural similarity was found to the periplasmic
domain of the AcrB multidrug efflux transporter.
Length = 226
Score = 24.6 bits (54), Expect = 6.4
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 1 MSSFGNFSSDKVKKKYGSLGPDLVVVT 27
+ S GN V ++ SLG +L+VV+
Sbjct: 29 ILSLGNGLQASVLEQISSLGANLIVVS 55
>gnl|CDD|164592 MTH00018, ND3, NADH dehydrogenase subunit 3; Validated.
Length = 113
Score = 24.3 bits (53), Expect = 7.2
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 44 DRTKMAVFVCGLNPSGSASKTGSV---LVG 70
DR K++ + CG +P G + S+ L+G
Sbjct: 30 DREKVSAYECGFDPFGFPGRPFSIRFFLIG 59
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 0.133 0.371
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,686,965
Number of extensions: 277427
Number of successful extensions: 182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 181
Number of HSP's successfully gapped: 25
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
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 (21.9 bits)
S2: 53 (24.3 bits)