RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6386
(116 letters)
>gnl|CDD|150423 pfam09748, Med10, Transcription factor subunit Med10 of Mediator
complex. Med10 is one of the protein subunits of the
Mediator complex, tethered to Rgr1 protein. The Mediator
complex is required for the transcription of most RNA
polymerase II (Pol II)-transcribed genes. Med10
specifically mediates basal-level HIS4 transcription via
Gcn4, and, additionally, there is a putative requirement
for Med10 in Bas2-mediated transcription. Med10 is part
of the middle region of Mediator.
Length = 120
Score = 128 bits (324), Expect = 8e-40
Identities = 44/86 (51%), Positives = 62/86 (72%)
Query: 21 QTMISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDA 80
T++ GLQ +DKL Q+ D+++PLEV YID GRNP LYT++ +E L KN+ VKGK+ A
Sbjct: 35 NTLVRGLQSLDKLAQQLSDVNIPLEVIQYIDDGRNPDLYTREFVELVLRKNQYVKGKMHA 94
Query: 81 YRKFKAHMLVELSGAFPNELAKYRAI 106
++KF+ + ELS AFP +A+YR I
Sbjct: 95 FKKFRDVLAEELSEAFPELVAEYRDI 120
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 28.6 bits (65), Expect = 0.61
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 64 IEKALTKNEQVKGKIDAYRKFKAHMLVELSG--AF-PNELAKYRAIRGGDETP 113
+EKA E V+G I K K V+L+G AF P R +R D P
Sbjct: 108 LEKAFENGEIVEGVI--NGKVKGGFTVDLNGVEAFLPGSQVDVRPVR--DTDP 156
>gnl|CDD|219995 pfam08737, Rgp1, Rgp1. Rgp1 forms heterodimer with Ric1
(pfam07064) which associates with Golgi membranes and
functions as a guanyl-nucleotide exchange factor.
Length = 402
Score = 28.5 bits (64), Expect = 0.73
Identities = 11/68 (16%), Positives = 22/68 (32%), Gaps = 1/68 (1%)
Query: 18 SFRQTMISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGK 77
+ G Q + +V+ + VP+ V Y++ G QL + +E
Sbjct: 132 KISYKLTVGTQRGPAVNQKVKSLRVPIRVLPYVNAG-GEQLQHDLMKPIIILDDEARVEV 190
Query: 78 IDAYRKFK 85
+
Sbjct: 191 KSEESRAP 198
>gnl|CDD|197317 cd09083, EEP-1, Exonuclease-Endonuclease-Phosphatase domain;
uncharacterized family 1. This family of
uncharacterized proteins belongs to a superfamily that
includes the catalytic domain
(exonuclease/endonuclease/phosphatase, EEP, domain) of
a diverse set of proteins including the ExoIII family
of apurinic/apyrimidinic (AP) endonucleases, inositol
polyphosphate 5-phosphatases (INPP5), neutral
sphingomyelinases (nSMases), deadenylases (such as the
vertebrate circadian-clock regulated nocturnin),
bacterial cytolethal distending toxin B (CdtB),
deoxyribonuclease 1 (DNase1), the endonuclease domain
of the non-LTR retrotransposon LINE-1, and related
domains. These diverse enzymes share a common catalytic
mechanism of cleaving phosphodiester bonds. Their
substrates range from nucleic acids to phospholipids
and perhaps, proteins.
Length = 252
Score = 28.0 bits (63), Expect = 1.1
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 26 GLQEIDKLKSQVQDIHVPLEVFDYIDQGRN 55
G QE L Q+ D+ L +D+I GR+
Sbjct: 39 GTQEA--LPHQLADLEELLPEYDWIGVGRD 66
>gnl|CDD|112245 pfam03420, Peptidase_U9, Prohead core protein protease.
Length = 220
Score = 26.6 bits (58), Expect = 3.2
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 54 RNPQLYTKDCIEKALTK--NEQVKGK 77
RN +LY K +EKA+ NEQVK K
Sbjct: 53 RNGRLYPKKILEKAVKDYINEQVKTK 78
>gnl|CDD|237027 PRK12266, glpD, glycerol-3-phosphate dehydrogenase; Reviewed.
Length = 508
Score = 26.6 bits (60), Expect = 3.6
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 76 GKIDAYRKFKAHMLVELSGAFPN 98
GKI YRK H L +L+ P
Sbjct: 359 GKITTYRKLAEHALEKLAPYLPQ 381
>gnl|CDD|99961 cd03785, GT1_MurG, MurG is an N-acetylglucosaminyltransferase, the
last enzyme involved in the intracellular phase of
peptidoglycan biosynthesis. It transfers
N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the
C4 hydroxyl of a lipid-linked N-acetylmuramoyl
pentapeptide (NAM). The resulting disaccharide is then
transported across the cell membrane, where it is
polymerized into NAG-NAM cell-wall repeat structure.
MurG belongs to the GT-B structural superfamily of
glycoslytransferases, which have characteristic N- and
C-terminal domains, each containing a typical Rossmann
fold. The two domains have high structural homology
despite minimal sequence homology. The large cleft that
separates the two domains includes the catalytic center
and permits a high degree of flexibility.
Length = 350
Score = 26.3 bits (59), Expect = 3.7
Identities = 8/28 (28%), Positives = 18/28 (64%)
Query: 24 ISGLQEIDKLKSQVQDIHVPLEVFDYID 51
+G +++++K +++ V EVF +ID
Sbjct: 217 QTGKGDLEEVKKAYEELGVNYEVFPFID 244
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 26.4 bits (59), Expect = 4.4
Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 16 ISSFRQTMISGLQEIDKLKSQVQDIHVPLEV-FDYIDQGRNPQLYTKDCIEKALT 69
+ S+ + GLQE+ + ++ + E+ + G P+ Y ++C + LT
Sbjct: 32 LDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPKFYPEECRLRGLT 86
>gnl|CDD|223651 COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 532
Score = 26.1 bits (58), Expect = 4.6
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 3/39 (7%)
Query: 76 GKIDAYRKFKAHMLVELSGAFPNE---LAKYRAIRGGDE 111
GK+ YRK L + + GGDE
Sbjct: 367 GKLTTYRKMAEDALDAVCEKLGIRPPCTTADLPLPGGDE 405
>gnl|CDD|222816 PHA00911, 21, prohead core scaffolding protein and protease.
Length = 212
Score = 25.4 bits (56), Expect = 6.4
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 54 RNPQLYTKDCIEKALTK--NEQVKGK 77
RN +LY K +EKA+ EQV+
Sbjct: 46 RNGRLYPKKVLEKAVEDYIEEQVETG 71
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 25.6 bits (57), Expect = 8.2
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 14/54 (25%)
Query: 33 LKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDA---YRK 83
L + Q E+++ I +G Y ++ I+K G++D YRK
Sbjct: 647 LAKEFQ-----QELYERIFRGEPYVDYVREVIDKLR------AGELDEKLVYRK 689
>gnl|CDD|232887 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous
[Energy metabolism, Pentose phosphate pathway].
Length = 653
Score = 25.4 bits (56), Expect = 9.4
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 17/72 (23%)
Query: 42 VPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVE----LSGAFP 97
VP EV+D+ + K E+ ++ AY+K + E LSG P
Sbjct: 282 VPQEVYDH---------FQKTVKERGAKAEQEWNELFAAYKKKYPELAAEFTRRLSGELP 332
Query: 98 ----NELAKYRA 105
+L +++A
Sbjct: 333 ADWDKKLPEFKA 344
>gnl|CDD|163611 pfam10046, BLOC1_2, Biogenesis of lysosome-related organelles
complex-1 subunit 2. Members of this family of
proteins play a role in cellular proliferation, as well
as in the biogenesis of specialized organelles of the
endosomal-lysosomal system.
Length = 99
Score = 24.6 bits (54), Expect = 9.5
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 28 QEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRK 83
+ K++ + + V +E + + P L D IE+ +T E+ ++D Y K
Sbjct: 35 LKYKKMRQSAKGLRVEIEALNQKYEELKPYLQQIDAIEQQVTTLEEAVYELDEYSK 90
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 0.137 0.394
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,941,761
Number of extensions: 503884
Number of successful extensions: 499
Number of sequences better than 10.0: 1
Number of HSP's gapped: 499
Number of HSP's successfully gapped: 29
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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 (21.7 bits)
S2: 53 (24.2 bits)