RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6385
(137 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 = 125 bits (317), Expect = 2e-38
Identities = 43/84 (51%), Positives = 61/84 (72%)
Query: 1 MISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYR 60
++ GLQ +DKL Q+ D+++PLEV YID GRNP LYT++ +E L KN+ VKGK+ A++
Sbjct: 37 LVRGLQSLDKLAQQLSDVNIPLEVIQYIDDGRNPDLYTREFVELVLRKNQYVKGKMHAFK 96
Query: 61 KFKAHMLVELSGAFPNELAKYRAI 84
KF+ + ELS AFP +A+YR I
Sbjct: 97 KFRDVLAEELSEAFPELVAEYRDI 120
>gnl|CDD|185748 cd09235, V_Alix, Middle V-domain of mammalian Alix and related
domains are dimerization and protein interaction
modules. This family contains the middle V-shaped (V)
domain of mammalian Alix (apoptosis-linked gene-2
interacting protein X) and related domains. It belongs
to the V_Alix_like superfamily which includes the
V-domains of Bro1 and Rim20 (also known as PalA) from
Saccharomyces cerevisiae, mammalian His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), and related domains. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1), is
part of the ESCRT (Endosomal Sorting Complexes Required
for Transport) system, and participates in membrane
remodeling processes, including the budding of enveloped
viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), the abscission reactions
of mammalian cell division, and in apoptosis. The Alix
V-domain is a dimerization domain, and contains a
binding site, partially conserved in the V_Alix_like
superfamily, for the retroviral late assembly (L) domain
YPXnL motif. In addition to the V-domain, Alix also has
an N-terminal Bro1-like domain, which binds components
of the ESCRT-III complex, in particular CHMP4. The
Bro1-like domain of Alix can also bind to human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix
also has a C-terminal proline-rich region (PRR) that
binds multiple partners including Tsg101 (tumor
susceptibility gene 101, a component of ESCRT-1), and
the apoptotic protein ALG-2.
Length = 339
Score = 29.6 bits (67), Expect = 0.41
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 69 ELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKY 124
+L+ E +KYR I + A+ ++ V+ K +++R+ +EL ELA
Sbjct: 124 KLTKPLRAEGSKYRTILDNAVQADKIVREKYESHREG-----IELLSKPEEELANA 174
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 29.7 bits (68), Expect = 0.46
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 42 IEKALTKNEQVKGKIDAYRKFKAHMLVELSG--AF-PNELAKYRAIREKALTKNEQVKGK 98
+EKA E V+G I K K V+L+G AF P R +R+ + ++++ K
Sbjct: 108 LEKAFENGEIVEGVI--NGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELEFK 165
Query: 99 I 99
+
Sbjct: 166 V 166
>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 = 28.3 bits (64), Expect = 1.2
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 4 GLQEIDKLKSQVQDIHVPLEVFDYIDQGRN 33
G QE L Q+ D+ L +D+I GR+
Sbjct: 39 GTQEA--LPHQLADLEELLPEYDWIGVGRD 66
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 28.5 bits (64), Expect = 1.2
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 47 TKNEQVKGKIDAYRKFKAHMLVELSGAF-PNELAKYRAIREKALTKNEQVKGKIDAYRKF 105
N++ + ++ R+ K EL F + + R +E+A EQV+ K+D R+
Sbjct: 620 ELNDERRERLAEKRERKR----ELEAEFDEARIEEAREDKERAEEYLEQVEEKLDELREE 675
Query: 106 KAHMLVELSGAFPNELAKYRAIR 128
+ + E+ GA NEL + +R
Sbjct: 676 RDDLQAEI-GAVENELEELEELR 697
>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 = 27.4 bits (61), Expect = 3.0
Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 1/63 (1%)
Query: 1 MISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYR 60
+ G Q + +V+ + VP+ V Y++ G QL + +E
Sbjct: 137 LTVGTQRGPAVNQKVKSLRVPIRVLPYVNAG-GEQLQHDLMKPIIILDDEARVEVKSEES 195
Query: 61 KFK 63
+
Sbjct: 196 RAP 198
>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 = 26.6 bits (59), Expect = 5.5
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 17/81 (20%)
Query: 20 VPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVE----LSGAFP 75
VP EV+D+ + K E+ ++ AY+K + E LSG P
Sbjct: 282 VPQEVYDH---------FQKTVKERGAKAEQEWNELFAAYKKKYPELAAEFTRRLSGELP 332
Query: 76 ----NELAKYRAIREKALTKN 92
+L +++A + T+
Sbjct: 333 ADWDKKLPEFKAKLQALATRK 353
>gnl|CDD|182181 PRK09983, pflD, putative formate acetyltransferase 2; Provisional.
Length = 765
Score = 26.3 bits (58), Expect = 6.5
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 84 IREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIRGGDETPPSY 137
+R + + + E+ ID A +L + E+ KY+ RGG TP SY
Sbjct: 568 VRARLINRFEKYGNDIDEVDNISAELL----RHYCKEVEKYQNPRGGYFTPGSY 617
>gnl|CDD|237027 PRK12266, glpD, glycerol-3-phosphate dehydrogenase; Reviewed.
Length = 508
Score = 26.3 bits (59), Expect = 6.8
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 54 GKIDAYRKFKAHMLVELSGAFPN 76
GKI YRK H L +L+ P
Sbjct: 359 GKITTYRKLAEHALEKLAPYLPQ 381
Score = 26.3 bits (59), Expect = 6.8
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 97 GKIDAYRKFKAHMLVELSGAFPN 119
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 = 25.9 bits (58), Expect = 8.1
Identities = 8/28 (28%), Positives = 18/28 (64%)
Query: 2 ISGLQEIDKLKSQVQDIHVPLEVFDYID 29
+G +++++K +++ V EVF +ID
Sbjct: 217 QTGKGDLEEVKKAYEELGVNYEVFPFID 244
>gnl|CDD|223651 COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 532
Score = 26.1 bits (58), Expect = 8.1
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 11/79 (13%)
Query: 54 GKIDAYRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKG--KIDAYRKFKAHMLV 111
GK+ YRK L + + + IR T + + G + A + A +
Sbjct: 367 GKLTTYRKMAEDAL--------DAVCEKLGIRPPCTTADLPLPGGDENAALAELAAALGA 418
Query: 112 ELSGAFPNELAKYRAIRGG 130
G P+ LA++ A G
Sbjct: 419 AYPG-LPSALARHLARLYG 436
>gnl|CDD|112245 pfam03420, Peptidase_U9, Prohead core protein protease.
Length = 220
Score = 25.8 bits (56), Expect = 8.6
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 32 RNPQLYTKDCIEKALTK--NEQVKGK 55
RN +LY K +EKA+ NEQVK K
Sbjct: 53 RNGRLYPKKILEKAVKDYINEQVKTK 78
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 25.8 bits (57), Expect = 8.9
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 55 KIDAYRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLVEL 113
++D Y K K +L L EL K KA VKG+I + +A +L EL
Sbjct: 988 RLDLYVKRKEVLLENLE----YELKKLD---NKARFILAVVKGEIVVNNRKRAELLAEL 1039
>gnl|CDD|216121 pfam00790, VHS, VHS domain. Domain present in VPS-27, Hrs and
STAM.
Length = 136
Score = 25.3 bits (56), Expect = 9.8
Identities = 30/134 (22%), Positives = 48/134 (35%), Gaps = 26/134 (19%)
Query: 8 IDKLKSQV---QDIHVPLEVFDYIDQGRNPQLYTKDCIEKAL-TKNEQVKGKIDAYRKFK 63
IDK +D + L++ D I++ I+K + + N V A
Sbjct: 6 IDKATDPSLREEDWSLILDICDLINETETGPKEAVRLIKKRINSPNPHV-----ALLALT 60
Query: 64 A-HMLVELSG-AFPNELAKY-------RAIREKALTKNEQVKGKIDAYRKFKAHMLVELS 114
V+ G F E+A + I K K +VK KI ++ E +
Sbjct: 61 LLDACVKNCGSKFHLEIASKEFLNELVKLIPNKPYGKPAKVKKKI-------LELIQEWA 113
Query: 115 GAFPNELAKYRAIR 128
AF N+ + IR
Sbjct: 114 DAFKND-PDLKYIR 126
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 0.135 0.380
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,066,525
Number of extensions: 625278
Number of successful extensions: 609
Number of sequences better than 10.0: 1
Number of HSP's gapped: 605
Number of HSP's successfully gapped: 36
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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: 54 (24.6 bits)