RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2623
(707 letters)
>gnl|CDD|217857 pfam04042, DNA_pol_E_B, DNA polymerase alpha/epsilon subunit B.
This family contains a number of DNA polymerase
subunits. The B subunit of the DNA polymerase alpha
plays an essential role at the initial stage of DNA
replication in S. cerevisiae and is phosphorylated in a
cell cycle-dependent manner. DNA polymerase epsilon is
essential for cell viability and chromosomal DNA
replication in budding yeast. In addition, DNA
polymerase epsilon may be involved in DNA repair and
cell-cycle checkpoint control. The enzyme consists of at
least four subunits in mammalian cells as well as in
yeast. The largest subunit of DNA polymerase epsilon is
responsible for polymerase epsilon is responsible for
polymerase activity. In mouse, the DNA polymerase
epsilon subunit B is the second largest subunit of the
DNA polymerase. A part of the N-terminal was found to be
responsible for the interaction with SAP18. Experimental
evidence suggests that this subunit may recruit histone
deacetylase to the replication fork to modify the
chromatin structure.
Length = 189
Score = 91.2 bits (227), Expect = 4e-21
Identities = 30/106 (28%), Positives = 49/106 (46%), Gaps = 2/106 (1%)
Query: 537 PALPKFITSEFQGFVPNSTMATNPCRVQYCSQEILVVREELLSKMCRNCIKFPEEGDISK 596
P P+ + + + + + TNPCR EI+V + + + R +KF +
Sbjct: 80 PPFPRCLFPKSKKYN-SLQFVTNPCRFSINGVEIVVTSGDNVKDLLRYSLKFSSSEERLL 138
Query: 597 HFVRTLVSQGTLVSL-PLNLCPVYWSQYGALSLYPLPDLVILGDQL 641
V T++ Q L L P L P + + L PLPD+ I+GD+L
Sbjct: 139 RLVETILRQRHLYPLAPDTLGPYPYDKDDPFVLDPLPDVFIVGDKL 184
Score = 54.2 bits (131), Expect = 2e-08
Identities = 11/51 (21%), Positives = 20/51 (39%)
Query: 460 VPNSTMATNPCRVQYCSQEILVVREELLSKMCRNCIKFPEEGDISKHVSKN 510
+ TNPCR EI+V + + + R +KF + + +
Sbjct: 93 YNSLQFVTNPCRFSINGVEIVVTSGDNVKDLLRYSLKFSSSEERLLRLVET 143
>gnl|CDD|185521 PTZ00235, PTZ00235, DNA polymerase epsilon subunit B; Provisional.
Length = 291
Score = 36.5 bits (84), Expect = 0.033
Identities = 40/152 (26%), Positives = 66/152 (43%), Gaps = 27/152 (17%)
Query: 537 PALPKFI---TSEFQGFVP---NSTMATNPCRVQYCSQEILVVREELLSKM--------C 582
P LP +I + F N ATNPCR+++ S++++ R ++L+ +
Sbjct: 132 PILPYYIRKFKQNIESFFSSKRNIIFATNPCRIRHLSKKMIFFRHDILNDLIWSSTINAT 191
Query: 583 RNCIKFPEEGDISKHFVRTLVSQGTLVSLPL-NLCPVYWSQYGALSLYPLPDLVILGDQ- 640
N E ++ V T+V Q + +P N +S + L LYPLP + + D
Sbjct: 192 NN-----ERNNLQNILVSTIVGQSHIYPIPHDNRILKRYSPF--LFLYPLPHFICVCDNS 244
Query: 641 ---LNAYTIQNT-DCIFINPVFHNTVRNAFEV 668
+Y ++T DCI N T + F V
Sbjct: 245 CNSFISYASEDTSDCIISNSDMSFTRKKTFTV 276
>gnl|CDD|147688 pfam05666, Fels1, Fels-1 Prophage Protein-like.
Length = 45
Score = 30.0 bits (68), Expect = 0.28
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 46 DYDPDLKKFK---LVDKKRKLCADSDAKSKLFRERY 78
D DP L L D+K +LCADS S+ ++Y
Sbjct: 6 DQDPTLFSPANGVLCDRKERLCADSGGISRALTKKY 41
Score = 30.0 bits (68), Expect = 0.28
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 252 DYDPDLKKFK---LVDKKRKLCADSDAKSKLFRERY 284
D DP L L D+K +LCADS S+ ++Y
Sbjct: 6 DQDPTLFSPANGVLCDRKERLCADSGGISRALTKKY 41
>gnl|CDD|224826 COG1914, MntH, Mn2+ and Fe2+ transporters of the NRAMP family
[Inorganic ion transport and metabolism].
Length = 416
Score = 33.8 bits (78), Expect = 0.32
Identities = 25/111 (22%), Positives = 31/111 (27%), Gaps = 22/111 (19%)
Query: 119 TVVLGMISQLKENITTSGLLGKHQSPHLNLLCLIWVKIFICTLIFIFIILIISLCSFSFN 178
TVV Q I G L L I I I L F
Sbjct: 302 TVVATYAGQ----IVMEGFLNWRIPLWRRRLITRTFAIVPGLAIIILFGDPARLLVF--- 354
Query: 179 SSQVPTDVQGPVTAFETYHNLVPLILHPVIPVSNREQN---NIMNWLKLSS 226
SQV V P L+PL+L S+++ WL +
Sbjct: 355 -SQVLLSVILPFA-------LIPLLLL----TSDKKLMGDYKNPRWLTVLG 393
>gnl|CDD|238895 cd01914, HCP, Hybrid cluster protein (HCP), formerly known as
prismane, is thought to play a role in nitrogen
metabolism but its specific function is unknown. HCP has
three structural domains, an N-terminal alpha-helical
domain, and two similar domains comprising a central
beta-sheet flanked by alpha-helices. HCP contains two
iron-sulfur clusters, one of which is a [Fe4-S4] cubane
cluster similar to that of carbon monoxide dehydrogenase
(CODH). The second cluster, referred to as the hybrid
cluster, is a hybrid [Fe4-S2-O2] center located at the
interface of the three domains. Although the hybrid
cluster is buried within the protein, it is accessible
through a large hydrophobic cavity.
Length = 423
Score = 30.7 bits (70), Expect = 2.7
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 359 PGLYTENCIVLVEGHYKDQILHVDALGFP 387
P L T NCI+ YKD+I +G+P
Sbjct: 186 PILMTTNCIIPPRESYKDRIFTTGIVGWP 214
>gnl|CDD|130764 TIGR01703, hybrid_clust, hydroxylamine reductase. This model
represents a family of proteins containing an unusual
4Fe-2S-2O hydrid cluster. Earlier reports had proposed a
6Fe-6S prismane cluster. This subfamily is heterogeneous
with respect to the presence or absence of a region of
about 100 amino acids not far from the N-terminus of the
protein. Members have been described as monomeric. The
general function is unknown, although members from E.
coli and several other species have hydroxylamine
reductase activity. Members are found in various
bacteria, in Archaea, and in several parasitic
eukaryotes: Giardia intestinalis, Trichomonas vaginalis,
and Entamoeba histolytica [Cellular processes,
Detoxification, Energy metabolism, Amino acids and
amines].
Length = 522
Score = 30.6 bits (69), Expect = 3.2
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 359 PGLYTENCIVLVEGHYKDQILHVDALGFP 387
P L T NCI+ YKD+I +G+P
Sbjct: 285 PILMTSNCIIPPRKSYKDRIFTTGIVGWP 313
>gnl|CDD|222970 PHA03072, PHA03072, putative viral membrane protein; Provisional.
Length = 190
Score = 29.2 bits (66), Expect = 5.6
Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 22/77 (28%)
Query: 160 TLIFIFIILIISLCSFSFNSSQVPTDVQGPVTAFETYHNLVPLILHPVIPVSNREQNNIM 219
TLIF IIL IS+ F +S + Y R +NN+
Sbjct: 31 TLIFFVIILAISVLLLWFQTSDNS-----VFSELTKY---------------ARIKNNVK 70
Query: 220 NWLKLSSECCRTEINSE 236
+W L +T++ S+
Sbjct: 71 SWRPLVES--KTKLESD 85
>gnl|CDD|236009 PRK07392, PRK07392, threonine-phosphate decarboxylase; Validated.
Length = 360
Score = 29.6 bits (67), Expect = 6.4
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 565 YCSQEILVVREELLSK---MCRNCIKFPEEGDISKHF---VRTLVSQGTLVS 610
L ++E+LL + + R+C+ FPE GD ++F VRT L+
Sbjct: 302 QSQGSALQLQEKLLQQHRILIRDCLSFPELGD--RYFRVAVRTEAENQRLLE 351
>gnl|CDD|224098 COG1177, PotC, ABC-type spermidine/putrescine transport system,
permease component II [Amino acid transport and
metabolism].
Length = 267
Score = 29.1 bits (66), Expect = 8.0
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 153 WVKIFICTLIFIFIIL-IISLCSFSFNSSQVPT 184
L+ +F+ L ++ L +SFNSS++
Sbjct: 11 IFLKLYLALVLLFLYLPLLVLVLYSFNSSRLGL 43
>gnl|CDD|131100 TIGR02045, P_fruct_ADP, ADP-specific phosphofructokinase.
Phosphofructokinase is a key enzyme of glycolysis. The
phosphate group donor for different subtypes of
phosphofructokinase can be ATP, ADP, or pyrophosphate.
This family consists of ADP-dependent
phosphofructokinases. Members are more similar to
ADP-dependent glucokinases (excluded from this family)
than to other phosphofructokinases [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 446
Score = 29.4 bits (66), Expect = 8.4
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 81 IRQRTLRHSLFNNINPNADSVKLDWVE 107
I+ R +R + NI P+ DSV +D E
Sbjct: 260 IQNREIRKKVVTNIFPHVDSVGMDEAE 286
Score = 29.4 bits (66), Expect = 8.4
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 287 IRQRTLRHSLFNNINPNADSVKLDWVE 313
I+ R +R + NI P+ DSV +D E
Sbjct: 260 IQNREIRKKVVTNIFPHVDSVGMDEAE 286
>gnl|CDD|215864 pfam00335, Tetraspannin, Tetraspanin family.
Length = 221
Score = 28.9 bits (65), Expect = 8.7
Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 14/80 (17%)
Query: 150 CLIWVKIFICTLIFIFIILIISLCSFSFNSSQVPTDVQGPVTAFETYHNLVPLILHPVIP 209
CL+ + L+ +FI+ I + ++ + ++ + + +N
Sbjct: 74 CLLL--TYFILLLILFILEIAAGILAFVYRDKLESSLKEGLNYKDKSYN----------- 120
Query: 210 VSNREQNNIMNWLKLSSECC 229
+ ++ L+ S ECC
Sbjct: 121 -DDPNLTEAIDELQKSLECC 139
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
0.321 0.137 0.415
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 35,634,787
Number of extensions: 3457293
Number of successful extensions: 3411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3392
Number of HSP's successfully gapped: 36
Length of query: 707
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 603
Effective length of database: 6,324,786
Effective search space: 3813845958
Effective search space used: 3813845958
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 (21.9 bits)
S2: 63 (28.1 bits)