Score = 86.3 bits (212), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 38/55 (69%), Positives = 45/55 (81%)
Query: 56 LQAGGHGIAICQCKSAKIVTTKTIPMQVDGEACRVNPSIILLNHLNKAPMLAKRK 110
LQAG HG ICQC+ A+I+T +TIPMQVDGEACRV PS+I + LNKA ML+KRK
Sbjct: 1087 LQAGMHGTCICQCRKARIITKRTIPMQVDGEACRVKPSVIEIELLNKALMLSKRK 1141
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.292 0.119 0.301
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 54,396,681
Number of Sequences: 539616
Number of extensions: 3536326
Number of successful extensions: 630447
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 9283
Number of HSP's successfully gapped in prelim test: 467
Number of HSP's that attempted gapping in prelim test: 127591
Number of HSP's gapped (non-prelim): 198886
length of query: 117
length of database: 191,569,459
effective HSP length: 84
effective length of query: 33
effective length of database: 146,241,715
effective search space: 4825976595
effective search space used: 4825976595
T: 11
A: 40
X1: 17 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 44 (21.6 bits)
S2: 55 (25.8 bits)
Required for the maintenance of phospholipid turnover within the photoreceptor. Drosophila melanogaster (taxid: 7227) EC: 2EC: .EC: 7EC: .EC: 1EC: .EC: 1EC: 0EC: 7
Close Homologs in the Non-Redundant Database Detected by BLAST
CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional
CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain might either be an accessory domain or else contribute to the catalytic domain. Bacterial homologues are known. Length = 160
Score = 46.4 bits (111), Expect = 2e-07
Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 56 LQAGGH-GIAICQCKSAKIVTTKTIPMQVDGEA 87
+Q G I Q +I T K IPMQVDGE
Sbjct: 125 VQVGLGSAKRIAQGGPIRIETKKKIPMQVDGEP 157
Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown. Length = 157
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
Score = 44.7 bits (106), Expect = 2e-06
Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 4 REEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
E E+ E +EEEE+EEEEEEEDE+E E ++EE EE++ E + E+
Sbjct: 378 ALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYED 429
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Score = 44.1 bits (104), Expect = 3e-06
Identities = 37/59 (62%), Positives = 42/59 (71%)
Query: 1 MGKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAG 59
M +E EEE+ EE+EEEEEEEEEEE+E EEEE EDEEEEEE E + EEE E G
Sbjct: 434 MASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEG 492
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
Score = 44.0 bits (104), Expect = 3e-06
Identities = 24/60 (40%), Positives = 39/60 (65%)
Query: 6 EEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGGHGIAI 65
E E E+++EEEE+EEEEEE++E+E +E ++EE EE++ E + E G +A+
Sbjct: 379 LEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSSLAV 438
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Score = 43.7 bits (103), Expect = 4e-06
Identities = 34/60 (56%), Positives = 43/60 (71%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGGHG 62
+E EE+E E+EEEEEEEEEEEE++ EEEE ++EEEEEE E + EEE E + G G
Sbjct: 435 ASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDG 494
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation factor RRN3
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit
Score = 43.2 bits (102), Expect = 5e-06
Identities = 23/49 (46%), Positives = 30/49 (61%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEE 50
GK ++ E EE E++ +E+EEDE EEDE E EEEE+EE E
Sbjct: 24 GKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72
The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein
Score = 43.1 bits (102), Expect = 7e-06
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 1 MGKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ + E EE+EEE E E E + + E+E +E+ EE+E+ ++ E+
Sbjct: 226 LKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDL 280
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit
The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein
CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
Score = 42.2 bits (99), Expect = 2e-05
Identities = 31/59 (52%), Positives = 39/59 (66%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGG 60
+ EE E+EEEE+EEEEEEE+E EEE+ E+EEE+EE E + EEE E E G
Sbjct: 439 SEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGE 497
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
Score = 41.9 bits (99), Expect = 2e-05
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 4 REEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQ 57
EE E+E + + E E + ++E E EED EE+E+ ++ E+ ++L+
Sbjct: 231 ETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLE 284
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 41.9 bits (99), Expect = 2e-05
Identities = 18/48 (37%), Positives = 24/48 (50%)
Query: 10 KEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQ 57
KE E EE EEE + E E E + +E+E EE+ EE+E
Sbjct: 227 KETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDP 274
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 41.5 bits (98), Expect = 2e-05
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEL 56
K E E+ EEE + E E E + +E+E EE+ EE+E+ ++ E+L
Sbjct: 227 KETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDL 280
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Human SGLT1 (hSGLT1) is a high-affinity/low-capacity glucose transporter, which can also transport galactose. In the transport mechanism, two Na+ ions first bind to the extracellular side of the transporter and induce a conformational change in the glucose binding site. This results in an increased affinity for glucose. A second conformational change in the transporter follows, bringing the Na+ and glucose binding sites to the inner surface of the membrane. Glucose is then released, followed by the Na+ ions. In the process, hSGLT1 is also able to transport water and urea and may be a major pathway for transport of these across the intestinal brush-border membrane. hSGLT1 is encoded by the SLC5A1 gene and expressed mostly in the intestine, but also in the trachea, kidney, heart, brain, testis, and prostate. The WHO/UNICEF oral rehydration solution (ORS) for the treatment of secretory diarrhea contains salt and glucose. The glucose, along with sodium ions, is transported by hSGLT1 and water is either co-transported along with these or follows by osmosis. Mutations in SGLT1 are associated with intestinal glucose galactose malabsorption (GGM). Up-regulation of intestinal SGLT1 may protect against enteric infections. SGLT1 is expressed in colorectal, head and neck, and prostate tumors. Epidermal growth factor receptor (EGFR) functions in cell survival by stabilizing SGLT1, and thereby maintaining intracellular glucose levels. SGLT1 is predicted to have 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5)transporter family. Length = 635
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi
Score = 41.8 bits (98), Expect = 2e-05
Identities = 21/53 (39%), Positives = 34/53 (64%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEE 54
E EEE E++ +E +++E+E E ED E E E + E+ EE+E+E++ E E
Sbjct: 643 QLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANE 695
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Score = 41.5 bits (98), Expect = 3e-05
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 1 MGKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQ 57
+ EEE E E E + ++E+E EE+ EE+E+ ++ E+ ++ E L+
Sbjct: 231 ETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEILK 287
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 41.1 bits (97), Expect = 3e-05
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEE 53
K +E E EE E+E + E E E + ++E+E EE+ EE+E+ +
Sbjct: 225 KLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPD 275
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 41.3 bits (97), Expect = 3e-05
Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQA 58
E+E+E+EE+ +E EEEE E+ EE+ + ED E + + E + ++ A
Sbjct: 370 VDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKESA 425
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
Score = 40.9 bits (96), Expect = 3e-05
Identities = 20/51 (39%), Positives = 28/51 (54%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
EE +E E+EE+E+ +E EEEE ED EEE E+ E + + E
Sbjct: 368 EEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSES 418
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
Score = 40.6 bits (95), Expect = 5e-05
Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 1 MGKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEE 52
+ + EEE+E + EE +++E+E E E+ + E E + E+ EE+E+E++ E E
Sbjct: 644 LFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANE 695
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi
Score = 40.6 bits (95), Expect = 6e-05
Identities = 19/56 (33%), Positives = 38/56 (67%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQA 58
K ++ E EE++E++ EE +++E++ E E+ E E E + E+ EE+E+E++ +A
Sbjct: 638 KSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEA 693
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi
Score = 40.2 bits (94), Expect = 6e-05
Identities = 20/53 (37%), Positives = 35/53 (66%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ ++ E E+E+E++ EE +++EDE E ED E E E + E+ EE+E+E+
Sbjct: 637 NKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQED 689
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
Score = 40.0 bits (94), Expect = 7e-05
Identities = 14/46 (30%), Positives = 30/46 (65%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEE 50
E + E ++ + EEEE +E+++DE++ + ++++EEE + E E
Sbjct: 217 EIQNELDDIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPEVER 262
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein
CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit
The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi
Score = 39.5 bits (92), Expect = 1e-04
Identities = 18/53 (33%), Positives = 36/53 (67%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ E EE++E++ EE +++E+E E ++ E E + + E+ EE+E+E++ E E
Sbjct: 643 QLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANE 695
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
Score = 39.5 bits (93), Expect = 1e-04
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 3/30 (10%)
Query: 3 KREE---EEEKEEEEKEEEEEEEEEEEEED 29
KR E + +EEEE E E EE E D
Sbjct: 266 KRAEILAQRAEEEEESSEGAAETIEEPELD 295
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. Length = 339
>gnl|CDD|221775 pfam12794, MscS_TM, Mechanosensitive ion channel inner membrane domain 1
Score = 39.1 bits (92), Expect = 1e-04
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 14 EKEEEEEEEEEEEEEDEEEEEEDEEEEEE 42
K E + EEEE+ E + EE E
Sbjct: 265 AKRAEILAQRAEEEEESSEGAAETIEEPE 293
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. Length = 339
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation factor RRN3
Score = 39.2 bits (92), Expect = 2e-04
Identities = 14/46 (30%), Positives = 31/46 (67%)
Query: 7 EEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEE 52
E + E ++ ++EEEE +E+D++E++ + ++++EEE + E E
Sbjct: 217 EIQNELDDIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPEVER 262
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
Score = 39.2 bits (92), Expect = 2e-04
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEE 54
K+ +E + EE +EE + E E E ++E++ EE+ EE+E+ +
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPD 275
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 38.9 bits (90), Expect = 2e-04
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEE-----EEEEEEEEEEEELQ 57
KREE EK + E E++ EE E E+E E+E E + E E E E E +L
Sbjct: 580 KREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKASSSSHESRMSEPQLS 639
Query: 58 AGGH 61
H
Sbjct: 640 GPAH 643
Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979
Score = 38.4 bits (89), Expect = 3e-04
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEE-EEEEEELQAGG 60
G+ E E E E K E+E E E E +E + + E + EE E E E E E E+E E++ G
Sbjct: 677 GENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGE 736
Query: 61 HG 62
G
Sbjct: 737 EG 738
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation factor RRN3
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
Score = 38.4 bits (90), Expect = 3e-04
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 15 KEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEL 56
K +E E EE EEE + E E E + ++E+E EE+ L
Sbjct: 225 KLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSL 266
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 38.6 bits (90), Expect = 3e-04
Identities = 20/53 (37%), Positives = 31/53 (58%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
K + +K + + EE +E+E++EEE+ DE EEEE E+ EEE + E
Sbjct: 350 KESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSRE 402
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
Score = 38.0 bits (88), Expect = 4e-04
Identities = 28/51 (54%), Positives = 36/51 (70%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
EEEEE+EEE++ EEEE E+EEEEE+ E + EEE E E + + EE EE
Sbjct: 451 EEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEE 501
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation factor RRN3
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
Score = 37.7 bits (87), Expect = 5e-04
Identities = 27/58 (46%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 6 EEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEE-EEEEEEEEEEEEEEEELQAGGHG 62
E E KE + K E E EE E E E E E EDE E E EE EE E+E E E +
Sbjct: 698 EIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEV 755
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
Score = 38.0 bits (88), Expect = 5e-04
Identities = 30/54 (55%), Positives = 38/54 (70%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ EEEEE+EEEE+E+E EEEE E+EE+EEE E D EEE E E + + EE
Sbjct: 445 VEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEE 498
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Score = 37.7 bits (88), Expect = 5e-04
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 10 KEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
K +E E EE EEE + E + E + ++E+E EE+ EE
Sbjct: 225 KLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEE 270
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Score = 37.7 bits (88), Expect = 5e-04
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 10 KEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEE----EEEEEEL 56
K+ +E E EE EEE + E E E ++E+E EE+ EE+E+
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDP 274
The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D
Score = 37.5 bits (87), Expect = 7e-04
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 13 EEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEL 56
E E + E E EEE DE ++ + ++ EE ++ EEL
Sbjct: 267 PEPEPQPPPPPPPPEPPEPEEEPDEPDQTDPDDGEETDQIPEEL 310
This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll]. Length = 589
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
Score = 37.2 bits (86), Expect = 8e-04
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 1 MGKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
MG E E++E+ + ++ E E+EE+ E E E +E +E E + E E EEE
Sbjct: 203 MGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEE 257
This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332
Score = 36.9 bits (85), Expect = 0.001
Identities = 24/54 (44%), Positives = 32/54 (59%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
G++E E E E +E + + E E EE E + E E E E+E E E EE EE E+E
Sbjct: 691 GEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDE 744
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
Score = 36.9 bits (85), Expect = 0.001
Identities = 27/59 (45%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEE-ELQAGGHG 62
E E +E EE E+E E E E + E E E + E E E E E E +E+E+E E+QAG G
Sbjct: 731 EIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDG 789
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
Score = 36.7 bits (85), Expect = 0.001
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 9 EKEEEEKEEEEEEEEEEEEED--EEEEEEDEEEEEEEEEEEEEEEEEEELQAGGHG 62
E ++K + +E E++ D E ED E ++EEEE+EEEEEEE + G
Sbjct: 354 ETLNKQKWTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPS 409
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi
Score = 36.8 bits (85), Expect = 0.001
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 2 GKREEEEEKEEEEKEEEEEEE----EEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQ 57
G+ E+E++ EE + +E+E E E E E D E+ EEDE+E++ E E ++ +
Sbjct: 647 GEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKAVRR 706
Query: 58 A 58
A
Sbjct: 707 A 707
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
Score = 36.8 bits (86), Expect = 0.001
Identities = 12/29 (41%), Positives = 13/29 (44%)
Query: 9 EKEEEEKEEEEEEEEEEEEEDEEEEEEDE 37
K E + EEEEE E E EE E
Sbjct: 265 AKRAEILAQRAEEEEESSEGAAETIEEPE 293
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. Length = 339
>gnl|CDD|221775 pfam12794, MscS_TM, Mechanosensitive ion channel inner membrane domain 1
Score = 36.8 bits (86), Expect = 0.001
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 30 EEEEEEDEEEEEEEEEEEEEEEEEEEL 56
E + EEEEE E E EE EL
Sbjct: 268 AEILAQRAEEEEESSEGAAETIEEPEL 294
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. Length = 339
Score = 36.5 bits (84), Expect = 0.001
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQA 58
++ E ++EE+ ++++ E E+EE+ E E E E +E E + E E E +
Sbjct: 205 DDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEM 258
This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600
>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional
Score = 37.0 bits (85), Expect = 0.001
Identities = 25/60 (41%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 13 EEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGGHGIAICQCKSAK 72
E EE EEE+ + E D E EEEDEEEE E + E + E L G+A C + K
Sbjct: 81 EAGEEAEEEDNDRECPDTEAEEEDEEEEIEAPDPEVNPLDAEGLS----GLAREACDALK 136
Length = 499
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)
Score = 36.1 bits (83), Expect = 0.002
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEE----EEEEEELQ 57
G+ EE E E++ E E + E E E + E + E+E E E E +E E E EE++
Sbjct: 657 GENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVE 716
Query: 58 AGGHG 62
G
Sbjct: 717 HEGET 721
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein
This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794
Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)
Score = 36.0 bits (84), Expect = 0.002
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 20 EEEEEEEEEDEEEEEEDEEEEEEEEEEEE 48
+ E + EEEEE E E EE E
Sbjct: 265 AKRAEILAQRAEEEEESSEGAAETIEEPE 293
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. Length = 339
Score = 36.0 bits (83), Expect = 0.002
Identities = 19/49 (38%), Positives = 27/49 (55%)
Query: 6 EEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEE 54
E+ E EE E +E EE+E E + E EE E + E E+ E +E +E
Sbjct: 245 EDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDE 293
Score = 36.0 bits (83), Expect = 0.002
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ E +EE E +E EE+E E + E EE E + E E+ E +E +E+ E
Sbjct: 246 DSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTE 296
Length = 620
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family
Score = 36.2 bits (84), Expect = 0.002
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 6 EEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGG 60
+E ++ E E+ E EEE+ E D +EE D+ + E + EE +E E + A G
Sbjct: 12 AKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASG 66
This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family
Score = 36.2 bits (84), Expect = 0.002
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 4 REEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQA 58
+E E E KE + E+E+ E EEE+ E + +EE ++ + E + EEL
Sbjct: 2 KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLD 56
This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis
Score = 35.7 bits (83), Expect = 0.002
Identities = 17/46 (36%), Positives = 24/46 (52%)
Query: 9 EKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEE 54
K KEEEEE E +E E E + +E +EE +EEE++
Sbjct: 15 PKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDRF 60
It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192
>gnl|CDD|240331 PTZ00254, PTZ00254, 40S ribosomal protein SA; Provisional
Score = 35.7 bits (82), Expect = 0.003
Identities = 20/55 (36%), Positives = 27/55 (49%)
Query: 6 EEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGG 60
E E + EE E E+E E E + E E E + E + E+E E E E +E G
Sbjct: 654 EAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKG 708
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family
Score = 35.5 bits (82), Expect = 0.003
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
E +++ E+ K E + EEEE + E EE E E+ E EE+ E
Sbjct: 374 AEYDQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELY 424
Score = 35.6 bits (82), Expect = 0.003
Identities = 14/55 (25%), Positives = 27/55 (49%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAG 59
+E+E + E+ E E E + E+ EEDE+E++ + E ++ + L
Sbjct: 661 DEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKAVRRALPKVLNLP 715
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi
Score = 35.6 bits (82), Expect = 0.003
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 7 EEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
E + ++ E EEE+E++ EE +++E+E E E+ E E E + E+ EE
Sbjct: 636 ENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEE 684
This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784
>gnl|CDD|221775 pfam12794, MscS_TM, Mechanosensitive ion channel inner membrane domain 1
Score = 35.3 bits (82), Expect = 0.003
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 4 REEEEEKEEEEKEEEEEEEEEEEEEDEEEE 33
+ + E + EEEEE E E EE E
Sbjct: 264 KAKRAEILAQRAEEEEESSEGAAETIEEPE 293
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. Length = 339
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]
Score = 34.7 bits (80), Expect = 0.003
Identities = 16/48 (33%), Positives = 31/48 (64%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEE 52
++EEE+ EEE +E E+E+ E + E +E++ E + + E+E+ + E
Sbjct: 95 DDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTE 142
The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein
The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Score = 35.6 bits (82), Expect = 0.003
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ E +E E +E EE+E E + + EE E D E E+ E +E +E+ E
Sbjct: 244 NEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTET 297
Score = 35.2 bits (82), Expect = 0.003
Identities = 22/54 (40%), Positives = 27/54 (50%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQA 58
EEEE ++EE K E EEE + E EE E E+E + E EE E A
Sbjct: 39 EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAA 92
Length = 746
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional
The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]
Score = 35.4 bits (82), Expect = 0.003
Identities = 20/33 (60%), Positives = 25/33 (75%)
Query: 17 EEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEE 49
E+++EEEE+EDEEEEEE+EE EE E EE
Sbjct: 343 NPEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPP 375
This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481
>gnl|CDD|220605 pfam10156, Med17, Subunit 17 of Mediator complex
Score = 35.4 bits (82), Expect = 0.003
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 12 EEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQ 57
EE EE +E + + EE +EE+++EE++ ++ EE ++ EE
Sbjct: 51 EESLREEIAKEAAKIDFSEESDEEEDDEEDDNDDSEENKDTVEEFP 96
This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures. Length = 454
Score = 35.0 bits (80), Expect = 0.004
Identities = 24/59 (40%), Positives = 32/59 (54%)
Query: 2 GKREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGG 60
K + + + E E+ E E E E E EDE E E EE EE E+E E E E + E++ G
Sbjct: 701 AKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEG 759
[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096
Human SGLT1 (hSGLT1) is a high-affinity/low-capacity glucose transporter, which can also transport galactose. In the transport mechanism, two Na+ ions first bind to the extracellular side of the transporter and induce a conformational change in the glucose binding site. This results in an increased affinity for glucose. A second conformational change in the transporter follows, bringing the Na+ and glucose binding sites to the inner surface of the membrane. Glucose is then released, followed by the Na+ ions. In the process, hSGLT1 is also able to transport water and urea and may be a major pathway for transport of these across the intestinal brush-border membrane. hSGLT1 is encoded by the SLC5A1 gene and expressed mostly in the intestine, but also in the trachea, kidney, heart, brain, testis, and prostate. The WHO/UNICEF oral rehydration solution (ORS) for the treatment of secretory diarrhea contains salt and glucose. The glucose, along with sodium ions, is transported by hSGLT1 and water is either co-transported along with these or follows by osmosis. Mutations in SGLT1 are associated with intestinal glucose galactose malabsorption (GGM). Up-regulation of intestinal SGLT1 may protect against enteric infections. SGLT1 is expressed in colorectal, head and neck, and prostate tumors. Epidermal growth factor receptor (EGFR) functions in cell survival by stabilizing SGLT1, and thereby maintaining intracellular glucose levels. SGLT1 is predicted to have 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5)transporter family. Length = 635
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31
RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family
Score = 35.4 bits (81), Expect = 0.004
Identities = 19/49 (38%), Positives = 29/49 (59%)
Query: 10 KEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQA 58
K +++EE E+ + E E+ EE E E+E+E+E E E E E E +A
Sbjct: 576 KLAKKREEAVEKAKREAEQKAREEREREKEKEKEREREREREAERAAKA 624
Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979
Score = 35.2 bits (81), Expect = 0.004
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 8 EEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEE 50
E E + E E EE+ +E ++ + ++ EE ++ EE
Sbjct: 267 PEPEPQPPPPPPPPEPPEPEEEPDEPDQTDPDDGEETDQIPEE 309
This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll]. Length = 589
>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740)
Score = 35.3 bits (81), Expect = 0.004
Identities = 17/56 (30%), Positives = 30/56 (53%)
Query: 5 EEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEELQAGG 60
E+EE+ ++++ E E+EE+ E E + +E +E E + E E EEE +
Sbjct: 210 EDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDD 265
This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600
>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional
The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein
Score = 35.0 bits (81), Expect = 0.004
Identities = 32/86 (37%), Positives = 42/86 (48%), Gaps = 30/86 (34%)
Query: 4 REEEEEKEEEEKEEEEEEEEEEEEED------------------------------EEEE 33
EEEEE+EEEE E +E EE + E E++
Sbjct: 288 EEEEEEEEEEEPAERDELEENPDFEGLEVRELADSLDNWVHHVQHILPQGRCTWVNPEQK 347
Query: 34 EEDEEEEEEEEEEEEEEEEEEELQAG 59
+E+EE+E+EEEEEEEEE EE E + G
Sbjct: 348 DEEEEQEDEEEEEEEEEPEEPEPEEG 373
This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481
>gnl|CDD|220605 pfam10156, Med17, Subunit 17 of Mediator complex
Score = 35.0 bits (81), Expect = 0.004
Identities = 17/44 (38%), Positives = 29/44 (65%)
Query: 6 EEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEE 49
EE +EE KE + + EE +E+E++EE+D ++ EE ++ EE
Sbjct: 51 EESLREEIAKEAAKIDFSEESDEEEDDEEDDNDDSEENKDTVEE 94
This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures. Length = 454
Score = 35.0 bits (81), Expect = 0.004
Identities = 21/53 (39%), Positives = 36/53 (67%)
Query: 3 KREEEEEKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEE 55
+ E+ E ++++ EEEE E EE+E+ D+E E D E ++E E + E+EEE++
Sbjct: 87 EAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKD 139
This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6
Score = 35.2 bits (81), Expect = 0.004
Identities = 20/48 (41%), Positives = 31/48 (64%)
Query: 9 EKEEEEKEEEEEEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEL 56
E +E +KEEE +E EE E E+++ + E E +EE+E+ E EE + L
Sbjct: 71 ELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENEELQYL 118
In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. Length = 356
>PF00609 DAGK_acc: Diacylglycerol kinase accessory domain; InterPro: IPR000756 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases
Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The DAG kinase domain is assumed to be an accessory domain. Upon cell stimulation, DAG kinase converts DAG into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It catalyses the reaction: ATP + 1,2-diacylglycerol = ADP + 1,2-diacylglycerol 3-phosphate. The enzyme is stimulated by calcium and phosphatidylserine and phosphorylated by protein kinase C. This domain is always associated with IPR001206 from INTERPRO.; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway
The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized.
Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain might either be an accessory domain or else contribute to the catalytic domain. Bacterial homologues are known.
Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. Bakali, et al. report phosphatidylglycerol kinase activity for the member from Escherichia coli, but refrain from calling that activity synonymous with its biological role. Note that a broader, subfamily-type model (TIGR00147), includes this family but also multiple paralogs in some species and varied functions.
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box
CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
>COG1597 LCB5 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]
Lipid kinase; DAG kinase, transferase; 1.90A {Esch
96.78
>3s40_A Diacylglycerol kinase; structural genomics, the center for structural genomics of infectious diseases, csgid, transfer; 2.10A {Bacillus anthracis} PDB: 3t5p_A
