RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17350
(528 letters)
>gnl|CDD|99848 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA
exonuclease 1, -3 and similar eukaryotic proteins. This
subfamily is composed of RNA exonuclease 1 (REX1 or
Rex1p), REX3 (or Rex3p), and similar eukaryotic
proteins. In yeast, REX1 and REX3 are required for 5S
rRNA and MRP (mitochondrial RNA processing) RNA
maturation, respectively. They are DEDDh-type DnaQ-like
3'-5' exonucleases containing three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. REX1 is the major
exonuclease responsible for pre-tRNA trail trimming and
may also be involved in nuclear CCA turnover. REX
proteins function in the processing and maturation of
many RNA species, similar to the function of Escherichia
coli RNase T.
Length = 150
Score = 232 bits (595), Expect = 1e-74
Identities = 82/151 (54%), Positives = 99/151 (65%), Gaps = 1/151 (0%)
Query: 365 YGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVA 424
+ LDCEMC T++ ELTRVT+VDE VV + LVKP I +Y T +SGIT +L V
Sbjct: 1 FALDCEMCYTTDGL-ELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVT 59
Query: 425 TRLEHVQKILSELLPPDAILVGQSLNCDLHALKMMHPYVIDTSVIFNTTGIRTHKPKLKM 484
T LE VQK L L+ PD ILVG SL DL ALK++HP VIDT+++F +KP LK
Sbjct: 60 TTLEDVQKKLLSLISPDTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKN 119
Query: 485 LTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515
L +LG DIQ +GGH S EDA AAL LVK
Sbjct: 120 LAKKYLGRDIQQGEGGHDSVEDARAALELVK 150
Score = 91.0 bits (227), Expect = 1e-21
Identities = 30/59 (50%), Positives = 39/59 (66%)
Query: 53 QMMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111
+++HP VIDT+++F +KP LK L +LG DIQ +GGH S EDA AAL LVK
Sbjct: 92 KLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150
>gnl|CDD|99840 cd06137, DEDDh_RNase, DEDDh 3'-5' exonuclease domain of the
eukaryotic exoribonucleases PAN2, RNA exonuclease
(REX)-1,-3, and -4, ISG20, and similar proteins. This
group is composed of eukaryotic exoribonucleases that
include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3
(Rex3p), REX4 (or Rex4p), ISG20, and similar proteins.
They are DEDDh-type DnaQ-like 3'-5' exonucleases
containing three conserved sequence motifs termed ExoI,
ExoII and ExoIII, with a specific Hx(4)D conserved
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. PAN2 is the catalytic subunit of poly(A)
nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease
which plays an important role in the posttranscriptional
maturation of pre-mRNAs. REX proteins are required for
the processing and maturation of many RNA species, and
ISG20 is an interferon-induced antiviral exonuclease
with a strong preference for single-stranded RNA.
Length = 161
Score = 133 bits (338), Expect = 5e-37
Identities = 59/160 (36%), Positives = 86/160 (53%), Gaps = 10/160 (6%)
Query: 365 YGLDCEMCKTSNDQNELTRVTLVDEQEN-VVYESLVKPYNPITNYLTAYSGITRALLAPV 423
LDCEM ++ +E+ R++ VD V+ +SLV+P +T++ T +SG+T A L
Sbjct: 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEA 60
Query: 424 ATR------LEHVQKILSELLPPDAILVGQSLNCDLHALKMMHPYVIDTSVIF-NTTGIR 476
A E + L + + PD ILVG SL DL AL+M+H V+DT+++
Sbjct: 61 AKAGKTIFGWEAARAALWKFIDPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGP 120
Query: 477 THKPK--LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLV 514
K + L+ L FLGL IQ GH S EDA+AA +V
Sbjct: 121 LAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160
Score = 51.9 bits (125), Expect = 6e-08
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 54 MMHPYVIDTSVIF-NTTGIRTHKPK--LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLV 110
M+H V+DT+++ K + L+ L FLGL IQ GH S EDA+AA +V
Sbjct: 101 MIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVV 160
>gnl|CDD|99847 cd06144, REX4_like, DEDDh 3'-5' exonuclease domain of RNA
exonuclease 4, XPMC2, Interferon Stimulated Gene product
of 20 kDa, and similar proteins. This subfamily is
composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2,
Interferon (IFN) Stimulated Gene product of 20 kDa
(ISG20), and similar proteins. REX4 is involved in
pre-rRNA processing. It controls the ratio between the
two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene
which was identified through its ability to correct a
mitotic defect in fission yeast. The human homolog of
XPMC2 (hPMC2) may be involved in angiotensin II-induced
adrenal cell cycle progression and cell proliferation.
ISG20 is an IFN-induced antiviral exonuclease with a
strong preference for single-stranded RNA and minor
activity towards single-stranded DNA. These proteins are
DEDDh-type DnaQ-like 3'-5' exonucleases containing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific Hx(4)D conserved pattern at ExoIII.
These motifs are clustered around the active site and
contain four conserved acidic residues that serve as
ligands for the two metal ions required for catalysis.
REX proteins function in the processing and maturation
of many RNA species, similar to the function of
Escherchia coli RNase T.
Length = 152
Score = 132 bits (335), Expect = 1e-36
Identities = 71/153 (46%), Positives = 87/153 (56%), Gaps = 11/153 (7%)
Query: 367 LDCEMCKTSNDQNE--LTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVA 424
LDCEM D +E L RV++V+E NVVY++ VKP P+T+Y TA SGI L A
Sbjct: 3 LDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKD-A 61
Query: 425 TRLEHVQKILSELLPPDAILVGQSLNCDLHALKMMHPYVI--DTSVI--FNTTGIRTHKP 480
E VQK ++ELL ILVG +L DL LK+ HP + DTS T + P
Sbjct: 62 PDFEEVQKKVAELL-KGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTA-KGKSP 119
Query: 481 KLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRL 513
LK L LGLDI Q+G H S EDA AA+RL
Sbjct: 120 SLKKLAKQLLGLDI--QEGEHSSVEDARAAMRL 150
Score = 52.5 bits (127), Expect = 3e-08
Identities = 20/38 (52%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 72 RTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRL 109
+ P LK L LGLDIQ +G H S EDA AA+RL
Sbjct: 115 KGKSPSLKKLAKQLLGLDIQ--EGEHSSVEDARAAMRL 150
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 101 bits (255), Expect = 3e-25
Identities = 53/171 (30%), Positives = 74/171 (43%), Gaps = 17/171 (9%)
Query: 364 LYGLDCEMCKTSNDQNELTRVTLVDE---QENVVYESLVKPYNPITNYLTAYSGITRALL 420
L +DCE ++E+ + VD + V+++ VKP PIT+Y T GIT +L
Sbjct: 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEML 61
Query: 421 APVATRLEHVQKILSELLPPDAILVGQSLNCDLHALKMMHP----------YVIDTSVIF 470
A E V + L E L ++ G S + DL LK+ HP VIDT +
Sbjct: 62 DD-APTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLA 120
Query: 471 NTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 521
T K LK L L IQ H + +DA A +L K L +
Sbjct: 121 RATNPGLPKYSLKKLAKRLLLEVIQR---AHRALDDARATAKLFKKLLERL 168
Score = 35.7 bits (83), Expect = 0.022
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 58 YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117
VIDT + T K LK L L IQ H + +DA A +L K L +
Sbjct: 112 PVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQR---AHRALDDARATAKLFKKLLERL 168
>gnl|CDD|99852 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of Interferon
Stimulated Gene product of 20 kDa, and similar proteins.
Interferon (IFN) Stimulated Gene product of 20 kDa
(ISG20) is an IFN-induced antiviral exonuclease with a
strong preference for single-stranded RNA and minor
activity towards single-stranded DNA. It was also
independently identified by its response to estrogen and
was called HEM45 (human estrogen regulated transcript).
ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease
containing three conserved sequence motifs termed ExoI,
ExoII and ExoIII with a specific Hx(4)D conserved
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. ISG20 may be a major effector of innate
immunity against pathogens including viruses, bacteria,
and parasites. It is located in promyelocytic leukemia
(PML) nuclear bodies, sites for oncogenic DNA viral
transcription and replication. It may carry out its
function by degrading viral RNAs as part of the
IFN-regulated antiviral response.
Length = 157
Score = 92.1 bits (229), Expect = 6e-22
Identities = 55/157 (35%), Positives = 80/157 (50%), Gaps = 10/157 (6%)
Query: 367 LDCEMCKT--SNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVA 424
+DCEM T ++EL R ++V+ +V+Y+ ++P P+T+Y T +SGI R L A
Sbjct: 3 IDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVN-A 61
Query: 425 TRLEHVQKILSELLPPDAILVGQSLNCDLHALKMMHP--YVIDTSVI--FNTTGIRTHKP 480
T QK + ++L ++VG +++ D ALK HP DTS I N
Sbjct: 62 TPFAVAQKEILKIL-KGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENC 120
Query: 481 K--LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515
+ LK+L L DIQ GH S EDA A + L K
Sbjct: 121 RVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
Score = 37.8 bits (88), Expect = 0.004
Identities = 16/34 (47%), Positives = 18/34 (52%)
Query: 78 LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111
LK+L L DIQ GH S EDA A + L K
Sbjct: 124 LKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease. This family includes a variety of
exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 161
Score = 75.9 bits (187), Expect = 3e-16
Identities = 40/162 (24%), Positives = 62/162 (38%), Gaps = 17/162 (10%)
Query: 367 LDCEMCKTSNDQN---ELTRVTLV-DEQENVVYESLVKPYNPITNYLTAYSGIT------ 416
+DCE +++ E+ V++V E V+++ VKP IT+ T + GIT
Sbjct: 3 IDCETTGLDPEKDEIIEIAAVSIVGGENIGPVFDTYVKPERLITDEATEFHGITPEMLRN 62
Query: 417 RALLAPVATRLEHVQKILSELLPP-DAILVGQSLNCDLHALK--MMHPYVIDTSVIFNTT 473
V K L L+ + VG L DL LK M + ++I +
Sbjct: 63 APSFEEVLEAFLEFLKKLKILVGHNASFDVGFLLYDDLRFLKLPMPKLNDVIDTLILDKA 122
Query: 474 GIRTHKPK-LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLV 514
+ K + L L IQ H + +DA A L
Sbjct: 123 TYKGFKRRSLDALAEKLGLEKIQR---AHRALDDARATAELF 161
>gnl|CDD|99846 cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain of the eukaryotic
exoribonuclease PAN2. PAN2 is the catalytic subunit of
poly(A) nuclease (PAN), a Pab1p-dependent 3'-5'
exoribonuclease which plays an important role in the
posttranscriptional maturation of pre-mRNAs. PAN
catalyzes the deadenylation of poly(A) tails, which are
initially synthesized to default lengths of 70 to 90, to
mRNA-specific lengths of 55 to 71. Pab1p and PAN also
play a role in the export and decay of mRNA. PAN2
contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain
with three conserved sequence motifs termed ExoI, ExoII
and ExoIII, with a specific Hx(4)D conserved pattern at
ExoIII. These motifs are clustered around the active
site and contain four conserved acidic residues that
serve as ligands for the two metal ions required for
catalysis.
Length = 174
Score = 71.1 bits (175), Expect = 2e-14
Identities = 41/120 (34%), Positives = 54/120 (45%), Gaps = 11/120 (9%)
Query: 403 NPITNYLTAYSGITRALLAPVA-----TRLEHVQKILSELLPPDAILVGQSLNCDLHALK 457
P+ +YLT +SGI L P T L+ L L+ I VG L D +
Sbjct: 59 EPVVDYLTRFSGIKPGDLDPKTSSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVIN 118
Query: 458 MMHP--YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515
+ P VIDT +F+ G R K L+ L + LG IQ H S EDA AL+L +
Sbjct: 119 IQVPKEQVIDTVELFHLPGQR--KLSLRFLAWYLLGEKIQ--SETHDSIEDARTALKLYR 174
Score = 46.8 bits (112), Expect = 4e-06
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 59 VIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111
VIDT +F+ G R K L+ L + LG IQ H S EDA AL+L +
Sbjct: 126 VIDTVELFHLPGQR--KLSLRFLAWYLLGEKIQ--SETHDSIEDARTALKLYR 174
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family. DEDDh
exonucleases, part of the DnaQ-like (or DEDD)
exonuclease superfamily, catalyze the excision of
nucleoside monophosphates at the DNA or RNA termini in
the 3'-5' direction. These proteins contain four
invariant acidic residues in three conserved sequence
motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases
are classified as such because of the presence of
specific Hx(4)D conserved pattern at the ExoIII motif.
The four conserved acidic residues are clustered around
the active site and serve as ligands for the two metal
ions required for catalysis. Most DEDDh exonucleases are
the proofreading subunits (epsilon) or domains of
bacterial DNA polymerase III, the main replicating
enzyme in bacteria, which functions as the chromosomal
replicase. Other members include other DNA and RNA
exonucleases such as RNase T, Oligoribonuclease, and RNA
exonuclease (REX), among others.
Length = 159
Score = 45.8 bits (109), Expect = 7e-06
Identities = 35/162 (21%), Positives = 58/162 (35%), Gaps = 18/162 (11%)
Query: 367 LDCEMCKTSNDQNELTRV--TLVDEQENVV--YESLVKPYNPITNYLTAYSGITRALLAP 422
D E ++ + + VD +V +E+LV P PI TA GIT +LA
Sbjct: 3 FDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLAD 62
Query: 423 VATRLEHVQKILSELLPPDAILVGQSLN---------CDLHALKMMHPYVIDTSVIFNTT 473
E + + L L +LV + + + IDT +
Sbjct: 63 APPFEEVLPEFLEFL--GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRL 120
Query: 474 GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515
+L +L + G+ +G H + DA+A L+
Sbjct: 121 LPGLRSHRLGLLLAERYGIP---LEGAHRALADALATAELLL 159
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 40.2 bits (94), Expect = 0.001
Identities = 39/196 (19%), Positives = 68/196 (34%), Gaps = 28/196 (14%)
Query: 341 LSAKFSKYINTKEVYAEVTPTSPLYGLDCEMCKTSNDQNELTRVTLV----DEQENVVYE 396
LS++F + T+ V +D E + ++ + + V +
Sbjct: 3 LSSRFRGLLPTRFV-----------VIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFH 51
Query: 397 SLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDAILVGQ--------- 447
+LV P PI + GIT +LA A + V + + +LV
Sbjct: 52 TLVNPERPIPPEIFKIHGITDEMLAD-APKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFL 110
Query: 448 SLNCDLHALKMMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDA 507
+ + +++ V+DT + + L L LG+D H + DA
Sbjct: 111 RVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAER-LGIDRNPF-HPHRALFDA 168
Query: 508 IAALRLVKLKLSKGDL 523
AL + L L G L
Sbjct: 169 -LALAELFLLLQTGLL 183
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 33.2 bits (76), Expect = 0.32
Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 8/93 (8%)
Query: 228 TSQNTK-----SQSQNIESAFQNTKSQSQYIESAFQNTKSQPQNIQLASQSTKSKSEIPL 282
+N++ S + S +T +QS + A N + ++ + + S P
Sbjct: 138 QPRNSEKSTNDSNKNSDSSIKNDTDTQSSKQDKADNQKAPSSNNTKPSTSNKQPNSPKPT 197
Query: 283 NDESKSATPQNTESQSVASAKRKSSESKSVEDK 315
++ P S A+ K S +++S+ D
Sbjct: 198 QPNQSNSQPA---SDDTANQKSSSKDNQSMSDS 227
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 33.3 bits (77), Expect = 0.36
Identities = 18/133 (13%), Positives = 42/133 (31%), Gaps = 11/133 (8%)
Query: 203 SQTIKSAFPIGTQPVRSANTESLSATSQNTKSQSQNIESAFQNTKSQSQYIESAFQNTKS 262
Q I+ A + A ++ + + + ++ ++
Sbjct: 318 VQAIQEALAQ-----SGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGSSPPASSPSSAP 372
Query: 263 QPQNIQLASQSTKSKSEIPLNDESKSATPQNTESQSVASAKRKSSESKSVE--DKFPRTM 320
Q+ + +S+ K+ + N A + + A+ +++ E D FP
Sbjct: 373 PEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAPEPAEAAEEADSFP--- 429
Query: 321 LLLSALQMIEEDY 333
L AL + Y
Sbjct: 430 -LGYALGQLHGTY 441
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 32.4 bits (73), Expect = 0.62
Identities = 27/132 (20%), Positives = 41/132 (31%), Gaps = 7/132 (5%)
Query: 172 VMSSRHMEAQDMTPSKETSLPSNVTNSTHSPSQTIKSAFPIGTQPVRSANTESLSATSQN 231
+S A TP+ T ++ T S + S PI +A + TS
Sbjct: 491 RTTSATPNATSPTPAVTTPNATSPTTQKTSDTPNATSPTPIVIGVTTTATSPPTGTTSVP 550
Query: 232 TKSQSQNIE-SAFQNTKSQSQYIESAFQNTKSQPQNIQLASQSTKSKSEIPLN------D 284
+ Q E S NT + + + S T + IP +
Sbjct: 551 NATSPQVTEESPVNNTNTPVVTSAPSVLTSAVTTGQHGTGSSPTSQQPGIPSSSHSTPRS 610
Query: 285 ESKSATPQNTES 296
S S TP T +
Sbjct: 611 NSTSTTPLLTSA 622
>gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon;
Provisional.
Length = 232
Score = 31.5 bits (72), Expect = 0.75
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 57 PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLV 110
PYVID +V R K L L H+ ++ D H + DA+AA R+
Sbjct: 128 PYVIDKAV----DRYRKGKRTLTALCEHY---GVR-LDNAHEATADALAAARVA 173
Score = 31.5 bits (72), Expect = 0.75
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 461 PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLV 514
PYVID +V R K L L H+ ++ D H + DA+AA R+
Sbjct: 128 PYVIDKAV----DRYRKGKRTLTALCEHY---GVR-LDNAHEATADALAAARVA 173
>gnl|CDD|215130 PLN02217, PLN02217, probable pectinesterase/pectinesterase
inhibitor.
Length = 670
Score = 31.6 bits (71), Expect = 1.2
Identities = 19/86 (22%), Positives = 34/86 (39%)
Query: 189 TSLPSNVTNSTHSPSQTIKSAFPIGTQPVRSANTESLSATSQNTKSQSQNIESAFQNTKS 248
++ SN T S+ SPS + + + S S +T + ++ S S
Sbjct: 576 SAASSNTTFSSDSPSTVVAPSTSPPAGHLGSPPATPSKIVSPSTSPPASHLGSPSTTPSS 635
Query: 249 QSQYIESAFQNTKSQPQNIQLASQST 274
I+ A T S +I++AS +
Sbjct: 636 PESSIKVASTETASPESSIKVASTES 661
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 31.6 bits (72), Expect = 1.4
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 5/94 (5%)
Query: 367 LDCEMCKTSNDQNELTRVTLVDEQENVV---YESLVKPYNPITNYLTAYSGITRALLAPV 423
D E S +E+ V + + ++ +KP+ P++ ++T +GIT+ +L
Sbjct: 195 FDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENA 254
Query: 424 ATRLEHVQKILSELLPPDAILVGQSLNCDLHALK 457
E ++K D+ILV + + D+ L
Sbjct: 255 PEIEEVLEKFKEFF--KDSILVAHNASFDIGFLN 286
>gnl|CDD|236123 PRK07883, PRK07883, hypothetical protein; Validated.
Length = 557
Score = 31.4 bits (72), Expect = 1.5
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 395 YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDAILV 445
+ +LV P PI ++T +GIT A++A A +E V E A+LV
Sbjct: 51 FATLVNPGRPIPPFITVLTGITTAMVAG-APPIEEVLPAFLEFA-RGAVLV 99
>gnl|CDD|191716 pfam07263, DMP1, Dentin matrix protein 1 (DMP1). This family
consists of several mammalian dentin matrix protein 1
(DMP1) sequences. The dentin matrix acidic
phosphoprotein 1 (DMP1) gene has been mapped to human
chromosome 4q21. DMP1 is a bone and teeth specific
protein initially identified from mineralised dentin.
DMP1 is primarily localised in the nuclear compartment
of undifferentiated osteoblasts. In the nucleus, DMP1
acts as a transcriptional component for activation of
osteoblast-specific genes like osteocalcin. During the
early phase of osteoblast maturation, Ca(2+) surges into
the nucleus from the cytoplasm, triggering the
phosphorylation of DMP1 by a nuclear isoform of casein
kinase II. This phosphorylated DMP1 is then exported out
into the extracellular matrix, where it regulates
nucleation of hydroxyapatite. DMP1 is a unique molecule
that initiates osteoblast differentiation by
transcription in the nucleus and orchestrates
mineralised matrix formation extracellularly, at later
stages of osteoblast maturation. The DMP1 gene has been
found to be ectopically expressed in lung cancer
although the reason for this is unknown.
Length = 514
Score = 31.2 bits (70), Expect = 1.5
Identities = 38/167 (22%), Positives = 68/167 (40%), Gaps = 27/167 (16%)
Query: 175 SRHMEAQDMTPSKETSLPSNVTNSTHSPSQTIKSAFPIGTQPVRSANTESLSATSQNTKS 234
S+ ++ S+E LPS S SQ + G P NT S S ++++S
Sbjct: 325 SQEVQDPSSESSQEADLPSQ---ENSSESQEEVVSESRGDNP---DNTTSHSEDQEDSES 378
Query: 235 QSQNIESAFQNTKSQS-----------------QYIESAFQNTKSQPQNIQLASQSTKSK 277
++ +++SQS + ES S + +Q S ST+S+
Sbjct: 379 SEEDSLDTPSSSESQSTEEQADSESNESLSSSEESPESTEDENSSSQEGLQSHSASTESR 438
Query: 278 SEIPLNDESKSATPQNTESQSVASAKRKS----SESKSVEDKFPRTM 320
S+ +++ + +++SQ + +K S S S S ED P+
Sbjct: 439 SQESQSEQDSRSEEDDSDSQDSSRSKEDSNSTESASSSEEDGQPKNT 485
>gnl|CDD|180434 PRK06158, PRK06158, thiolase; Provisional.
Length = 384
Score = 30.8 bits (70), Expect = 1.7
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 395 YESLVKPYNPITNYLTAYS------GITRALLAPVA 424
YE+ KP NP++ Y A + G TR LA VA
Sbjct: 131 YEAPYKPVNPVSAYALAAARHMHQYGTTREQLAEVA 166
>gnl|CDD|227430 COG5099, COG5099, RNA-binding protein of the Puf family,
translational repressor [Translation, ribosomal
structure and biogenesis].
Length = 777
Score = 30.9 bits (70), Expect = 2.2
Identities = 34/173 (19%), Positives = 56/173 (32%), Gaps = 20/173 (11%)
Query: 189 TSLPSNVTNS-----THSPSQTIKSAFPIGTQPVRSANTESLSATSQNTKSQSQNIESAF 243
+L + NS T S S K + S++T + S S N S
Sbjct: 56 FTLNLPINNSVNHKITSSSSSRRKPSGSWSVAI--SSSTSGSQSLLMELPSSSFN-PSTS 112
Query: 244 QNTKSQSQYIESAFQNTKSQPQNIQLASQSTKSKSEIPLNDESKSATPQNTESQSVASAK 303
KS S + N S + S + +++PL + + S + T +QS +S
Sbjct: 113 SRNKSNSALSSTQQGNANSSVTLSSSTASSMFNSNKLPLPNPNHSNS--ATTNQSGSSFI 170
Query: 304 RKSSESKSVEDKFPRTMLLLSALQMIEEDYPIPLRGELSAKFSKYINTKEVYA 356
+ S S ++ P LS F+ I+ A
Sbjct: 171 NTPASSSSQPLTNL----------VVSSIKRFPYLTSLSPFFNYLIDPSSDSA 213
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 29.7 bits (66), Expect = 3.9
Identities = 31/114 (27%), Positives = 44/114 (38%), Gaps = 17/114 (14%)
Query: 181 QDMTPSKETSLPSNVTNSTHSPSQTIK------------SAFPIGTQPVRSANTESLSAT 228
Q+ TP E + +N ++ S + I SA P Q TES +
Sbjct: 70 QERTPKLEKAPNTNEEKTSASKIEKISQPKQEEQKSLNISATPAPKQEQSQTTTESTTPK 129
Query: 229 SQNTKSQSQNIESAFQNTKS---QSQYIESAFQNTKSQPQNIQLASQSTKSKSE 279
++ T S N Q+TKS QS I+ A T P+ L + TK E
Sbjct: 130 TKVTTPPSTNTPQPMQSTKSDTPQSPTIKQA--QTDMTPKYEDLRAYYTKPSFE 181
>gnl|CDD|223520 COG0443, DnaK, Molecular chaperone [Posttranslational modification,
protein turnover, chaperones].
Length = 579
Score = 29.6 bits (67), Expect = 4.5
Identities = 30/141 (21%), Positives = 55/141 (39%), Gaps = 26/141 (18%)
Query: 352 KEVYAEVTPTSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTA 411
K + T TS + ELTR + E ++ + L + P+ L
Sbjct: 250 KIELSSATQTSINLPSIGG---DIDLLKELTR----AKFEELILDLLERTIEPVEQAL-K 301
Query: 412 YSGITRA-----LLAPVATRLEHVQKILSELLPPDAILVGQSLNCD--------LHALKM 458
+G+ ++ +L +TR+ VQ+++ E + +S+N D + A +
Sbjct: 302 DAGLEKSDIDLVILVGGSTRIPAVQELVKEFFGKEPE---KSINPDEAVALGAAIQAAVL 358
Query: 459 M--HPYVIDTSVIFNTTGIRT 477
P V+ VI + GI T
Sbjct: 359 SGEVPDVLLLDVIPLSLGIET 379
>gnl|CDD|214599 smart00283, MA, Methyl-accepting chemotaxis-like domains
(chemotaxis sensory transducer). Thought to undergo
reversible methylation in response to attractants or
repellants during bacterial chemotaxis.
Length = 262
Score = 29.2 bits (66), Expect = 5.0
Identities = 10/57 (17%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 219 SANTESLSATSQNTKSQSQNIESAFQNTKSQSQYIESAFQNTKSQPQNIQLASQSTK 275
+AN + ++AT+Q+ ++ A ++ + I + S + +L S +
Sbjct: 38 AANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAVE--ELEESSDE 92
>gnl|CDD|226406 COG3889, COG3889, Predicted solute binding protein [General
function prediction only].
Length = 872
Score = 29.4 bits (66), Expect = 6.4
Identities = 24/120 (20%), Positives = 40/120 (33%), Gaps = 9/120 (7%)
Query: 128 TVNLGFSLNDYLMFAHELPGLR------DRFVKMEVIPPSSYTTSLVHELVMSSRHMEAQ 181
TV +G +L Y G + VK+ ++ P+S T + + S
Sbjct: 720 TVKIGQALTVYGSLEVFPAGENWGFIPTTKRVKVRIMDPASGTGT---SITTSGTFTAEV 776
Query: 182 DMTPSKETSLPSNVTNSTHSPSQTIKSAFPIGTQPVRSANTESLSATSQNTKSQSQNIES 241
+P+K + S S S S T T S S T + +Q+ +
Sbjct: 777 PQSPTKTETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTT 836
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated.
Length = 232
Score = 28.6 bits (64), Expect = 7.1
Identities = 24/117 (20%), Positives = 44/117 (37%), Gaps = 12/117 (10%)
Query: 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRAL 419
+ ++ D E T D++ + + + + +++LV P PI + GIT
Sbjct: 1 MPALIF-YDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDE 59
Query: 420 LAPVATRLEHVQKILSELLPPDAILVGQSLN----------CDLHALKMMHPYVIDT 466
+A A + + E D ILV + + C H L+ ID+
Sbjct: 60 VAD-APKFPEAYQKFIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDS 115
>gnl|CDD|236653 PRK10137, PRK10137, alpha-glucosidase; Provisional.
Length = 786
Score = 29.0 bits (65), Expect = 7.5
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 6/80 (7%)
Query: 254 ESAFQNTKSQPQNIQLASQSTKSKSEIPLNDESKSATPQNTESQSVASAKRKSSESKSVE 313
ES +Q KS P ++ SK+ I +T T + +A+ S E +
Sbjct: 219 ESEYQVHKSLPVQTEINGNRFTSKAHI------NGSTTLYTTYSHLLTAQEVSKEQMQIR 272
Query: 314 DKFPRTMLLLSALQMIEEDY 333
D R L+A Q E+Y
Sbjct: 273 DILARPAFYLTASQQRWEEY 292
>gnl|CDD|233759 TIGR02170, thyX, thymidylate synthase, flavin-dependent. Two forms
of microbial thymidylate synthase are known: ThyA
(2.1.1.45) and ThyX (2.1.1.148). This model describes
ThyX, a homotetrameric flavoprotein. Both enzymes
convert dUMP to dTMP. Under oxygen-limiting conditions,
thyX can complement a thyA mutation [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 209
Score = 28.5 bits (64), Expect = 7.6
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 12 PGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEADKQMM---HPYV 59
P + + NAR + + + DA EI+ L EA ++ P+V
Sbjct: 155 PNALYTHIVVTGNARSLMHFLDLRASNDAQWEIRELAEAMLDIVKEVAPWV 205
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive
type) [DNA replication, recombination, and repair].
Length = 1444
Score = 28.8 bits (65), Expect = 8.5
Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 395 YESLVKPYNPITNYLTAYSGITRALLA---PVATRLEHVQKILSELLPPDAILVGQSLNC 451
++ +KP P++ +T +GIT +L + LE ++ + D+ILV + +
Sbjct: 457 FQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFREFIG-----DSILVAHNASF 511
Query: 452 DLHALKM 458
D+ L
Sbjct: 512 DMGFLNT 518
>gnl|CDD|145900 pfam02994, Transposase_22, L1 transposable element.
Length = 370
Score = 28.5 bits (63), Expect = 9.5
Identities = 24/143 (16%), Positives = 50/143 (34%), Gaps = 7/143 (4%)
Query: 174 SSRHMEAQDMTPSKETSLPSNVTNSTHSPSQTIKSAFPIGTQPVRSANTESLSATSQNTK 233
+ + + P K TS N+ + KS + + + N SL +
Sbjct: 11 NQDTQSSSE--PPKPTSSSPATPNTWENNDLDEKSYLIMMEEGFKKDNYSSLREDIETKG 68
Query: 234 SQSQNIESAFQN--TKSQSQYIESAFQNTKSQPQNIQLASQSTKSKSEIPLNDESKSATP 291
+ QN + TK +IE K + ++L ++ + K E + T
Sbjct: 69 KEVQNFLKELEECITKQVEAHIE---NTEKCLKELMELKKKARELKEECRSIKKEHMETT 125
Query: 292 QNTESQSVASAKRKSSESKSVED 314
+ E+Q +S + +++
Sbjct: 126 LDIENQKKRQGVVDTSFTNRIQE 148
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 28.5 bits (64), Expect = 9.5
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 336 PLRGELSAKFSKYINTKEVYAEVTPTSPLYGLDCEMCKTSND 377
P RG +S K SK +V V LY L ++ K N
Sbjct: 630 PPRGPVSIKKSKEGPFNQVVPNVETLKDLYDLLWDLAKKGNK 671
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
0.313 0.128 0.351
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,676,255
Number of extensions: 2266941
Number of successful extensions: 1643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1604
Number of HSP's successfully gapped: 76
Length of query: 528
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 427
Effective length of database: 6,457,848
Effective search space: 2757501096
Effective search space used: 2757501096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (27.3 bits)