RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5978
(159 letters)
>gnl|CDD|190664 pfam03501, S10_plectin, Plectin/S10 domain. This presumed domain
is found at the N-terminus of some isoforms of the
cytoskeletal muscle protein plectin as well as the
ribosomal S10 protein. This domain may be involved in
RNA binding.
Length = 96
Score = 188 bits (480), Expect = 4e-63
Identities = 70/96 (72%), Positives = 83/96 (86%)
Query: 3 MPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFAWR 62
+PK NR IYEYLFKEGVLVAKKDF+ PKHPE+DVPNLQVIK +QSLKS+G+V EQFAWR
Sbjct: 1 IPKANRRAIYEYLFKEGVLVAKKDFNLPKHPEIDVPNLQVIKAMQSLKSRGYVKEQFAWR 60
Query: 63 HYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQARTT 98
HYYWY+TN+GIE LR L++P E+VP+TLK+ AR
Sbjct: 61 HYYWYLTNEGIEYLREYLHLPAEVVPATLKKPARPF 96
>gnl|CDD|173331 PTZ00034, PTZ00034, 40S ribosomal protein S10; Provisional.
Length = 124
Score = 146 bits (371), Expect = 3e-46
Identities = 60/126 (47%), Positives = 85/126 (67%), Gaps = 3/126 (2%)
Query: 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFA 60
+ +PK NR IY YLFKEGV+V KKD P HPEL+VPNL V+ ++SLKS+G V EQFA
Sbjct: 2 VYVPKANRKAIYRYLFKEGVIVCKKDPKGPWHPELNVPNLHVMMLMRSLKSRGLVKEQFA 61
Query: 61 WRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQARTTDASKVPRQMTQRPDGGRGADDR 120
W+HYY+Y+T++GIE LR L++P ++ P+T K+++ K + ++ GGRG
Sbjct: 62 WQHYYYYLTDEGIEYLRTYLHLPPDVFPATHKKKSVNF-ERKTEEEGSRGGRGGRGRGR- 119
Query: 121 MSYRKG 126
Y +G
Sbjct: 120 -GYGRG 124
>gnl|CDD|227378 COG5045, COG5045, Ribosomal protein S10E [Translation, ribosomal
structure and biogenesis].
Length = 105
Score = 128 bits (322), Expect = 3e-39
Identities = 51/96 (53%), Positives = 67/96 (69%)
Query: 1 MLMPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQFA 60
ML+PK+NRY I++ LF++GV VAKKDF+ KH EL++PNL VIK +QSL S G+V
Sbjct: 1 MLVPKENRYKIHQRLFQKGVAVAKKDFNLGKHRELEIPNLHVIKAMQSLISYGYVKTIHV 60
Query: 61 WRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQAR 96
WRH Y+ +T +G+E LR L +PDE VPST
Sbjct: 61 WRHSYYTLTPEGVEYLREYLVLPDEGVPSTEAPAVS 96
>gnl|CDD|224296 COG1378, COG1378, Predicted transcriptional regulators
[Transcription].
Length = 247
Score = 30.5 bits (69), Expect = 0.30
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 11 IYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWVNEQ 58
+Y L G AK+ A VP +V L+SL+ KG V
Sbjct: 21 VYLALLCLGEATAKEISEA-----SGVPRPKVYDVLRSLEKKGLVEVI 63
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 28.3 bits (64), Expect = 1.8
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 9/44 (20%)
Query: 58 QFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQARTTDAS 101
Q R IE + L IP+E V T+ + T+ AS
Sbjct: 250 QANLRI---------IEAIAKKLGIPEEKVVVTVDKYGNTSAAS 284
>gnl|CDD|216824 pfam01978, TrmB, Sugar-specific transcriptional regulator TrmB.
One member of this family, TrmB, has been shown to be a
sugar-specific transcriptional regulator of the
trehalose/maltose ABC transporter in Thermococcus
litoralis.
Length = 68
Score = 26.3 bits (59), Expect = 1.9
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 11 IYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLKSKGWV 55
+Y L K G A + E VP +V + L+SL+ KG V
Sbjct: 13 VYLALLKLGPATADEIAE-----ESGVPRSKVYEVLRSLEKKGLV 52
>gnl|CDD|216839 pfam02002, TFIIE_alpha, TFIIE alpha subunit. The general
transcription factor TFIIE has an essential role in
eukaryotic transcription initiation together with RNA
polymerase II and other general factors. Human TFIIE
consists of two subunits TFIIE-alpha and TFIIE-beta,
and joins the pre-initiation complex after RNA
polymerase II and TFIIF. This family consists of the
conserved amino terminal region of eukaryotic
TFIIE-alpha and proteins from archaebacteria that are
presumed to be TFIIE-alpha subunits also Archaeoglobus
fulgidus tfe.
Length = 105
Score = 26.9 bits (60), Expect = 2.8
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 6/35 (17%)
Query: 41 QVIKTLQSLKSKG------WVNEQFAWRHYYWYIT 69
++ K L L +++ W YYWYI
Sbjct: 43 ELRKLLYRLYDARLVKYRRRRDDETGWYRYYWYIN 77
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 27.2 bits (61), Expect = 3.5
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 8 RYIIYEYLFKEGVLVAKKDFHAPKHPELDVPN 39
RYI ++ L A A K+P+ ++P
Sbjct: 241 RYICSSHVVTRPELAA---LLAKKYPQYNIPT 269
>gnl|CDD|240129 cd04859, Prim_Pol, Prim_Pol: Primase-polymerase (primpol) domain of
the type found in bifunctional replicases from archaeal
plasmids, including ORF904 protein of the crenarchaeal
plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol).
These primpol domains belong to the archaeal/eukaryal
primase (AEP) superfamily. This group includes archaeal
plasmids and bacteriophage AEPs. The ORF904 protein is a
multifunctional protein having ATPase, primase and DNA
polymerase activity, and may play a role in the
replication of the archaeal plasmid. The pRN1 primpol
domain exhibits DNA polymerase and primase activities; a
cluster of active site residues (three acidic residues,
and a histidine) is required for both these activities.
For pRN1 primpol, the primase activity prefers dNTPs to
rNTPs; incorporation of dNTPs requires rNTP as cofactor.
The pRN1 primpol contains an unusual zinc-binding stem,
which is not conserved in other members of this group.
Length = 152
Score = 27.0 bits (60), Expect = 3.6
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 123 YRKGPQGVDKKADVGAGSTEVEFKGYGGF 151
Y + P GV K+ G G ++ +G GG+
Sbjct: 92 YFRVPDGVPVKSVKGKGGPGIDIRGGGGY 120
>gnl|CDD|148473 pfam06874, FBPase_2, Firmicute fructose-1,6-bisphosphatase. This
family consists of several bacterial
fructose-1,6-bisphosphatase proteins (EC:3.1.3.11) which
seem to be specific to phylum Firmicutes.
Fructose-1,6-bisphosphatase (FBPase) is a well known
enzyme involved in gluconeogenesis. This family does not
seem to be structurally related to pfam00316.
Length = 641
Score = 27.6 bits (62), Expect = 3.8
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 3 MPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLK 50
+PK YII E L+++ KK ++ ++I T+ L
Sbjct: 131 LPKDFAYIIEELLYEDDEEPNKKSYYE-----------EIISTIIELG 167
>gnl|CDD|222813 PHA00730, int, integrase.
Length = 337
Score = 26.7 bits (59), Expect = 6.3
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 56 NEQFAWRHYY-WYITNDGIEKLRGVLNIPDEIVPS 89
N AWR++Y + D + L+ + PD VP+
Sbjct: 147 NSIKAWRNFYRFLGNRDPPKSLKTKKSKPDLRVPT 181
>gnl|CDD|215817 pfam00248, Aldo_ket_red, Aldo/keto reductase family. This family
includes a number of K+ ion channel beta chain
regulatory domains - these are reported to have
oxidoreductase activity.
Length = 277
Score = 26.5 bits (59), Expect = 7.3
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 33 PELDVPNLQVIKTLQSLKSKGWV 55
P+ +P + ++ L+ LK +G +
Sbjct: 107 PDPSLPIEETLEALEELKKEGKI 129
>gnl|CDD|236475 PRK09352, PRK09352, 3-oxoacyl-(acyl carrier protein) synthase III;
Reviewed.
Length = 319
Score = 26.2 bits (59), Expect = 9.2
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 73 IEKLRGVLNIPDEIVPSTLKRQARTTDASKVP 104
I+ L +P E V T+ + T+ AS +P
Sbjct: 252 IDATAKKLGLPMEKVVVTVDKYGNTSAAS-IP 282
>gnl|CDD|226373 COG3855, Fbp, Uncharacterized protein conserved in bacteria
[Carbohydrate transport and metabolism].
Length = 648
Score = 26.2 bits (58), Expect = 9.3
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 3 MPKKNRYIIYEYLFKEGVLVAKKDFHAPKHPELDVPNLQVIKTLQSLK 50
+PK YI+ E L++ KK+++ +++ + SL
Sbjct: 137 LPKDFAYILEELLYEVDETTDKKEYYD-----------EILDQIISLD 173
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
0.317 0.137 0.419
Gapped
Lambda K H
0.267 0.0611 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,269,241
Number of extensions: 732779
Number of successful extensions: 570
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 21
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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 (21.6 bits)
S2: 55 (25.2 bits)