RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1775
(304 letters)
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 138 bits (348), Expect = 3e-39
Identities = 73/185 (39%), Positives = 95/185 (51%), Gaps = 19/185 (10%)
Query: 114 LGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLI 173
+G P + R SPSP P Y G+R+NTRE R KKLE+ER L
Sbjct: 81 TPDGVPSKRELR--------------SPSPPPRYDEIGRRLNTREARYNKKLEDERLWLK 126
Query: 174 QKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGA 233
++ K+ P F P DY P K +K+ IP E+P+ NFVGLLIGPRG+TLK +E+ + A
Sbjct: 127 ERAQKILPRFVLPNDYIRPS-KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRA 185
Query: 234 KIIIRGKGSVKEGKVGRKDGQPLPGE-NEPLHAYVTAHNPENVKKAVDRLVCLVSARPRA 292
KI IRG GSVKEGK D LH + A + + + + L + R
Sbjct: 186 KIAIRGSGSVKEGK-ISSDTPESLKNAEAVLHCLIEADSEDKICRL--IKSQLNAIREAR 242
Query: 293 RFPPG 297
R P G
Sbjct: 243 RNPEG 247
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point sequence
(BPS) UACUAAC in the pre-mRNA transcripts during
spliceosome assembly. We show that the KH-QUA2 region of
SF1 defines an enlarged KH (hnRNP K) fold which is
necessary and sufficient for BPS binding. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 120
Score = 123 bits (312), Expect = 2e-35
Identities = 47/85 (55%), Positives = 59/85 (69%), Gaps = 3/85 (3%)
Query: 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK-DGQPL 256
+KV IP ++P NFVGL++GPRGNTLK +EK+TGAKI IRGKGS+K+GK + G
Sbjct: 2 EKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKY 61
Query: 257 PGENEPLHAYVTAHNP--ENVKKAV 279
NEPLH +TA P E + KAV
Sbjct: 62 AHLNEPLHVLITAETPPEEALAKAV 86
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 49.1 bits (118), Expect = 4e-08
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 23/84 (27%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
+V++P + VG +IG G+T+K + ++TGAKI I GS
Sbjct: 3 RVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---------------- 40
Query: 259 ENEPLHAYVTAHNPENVKKAVDRL 282
+E +T PE V+KA + +
Sbjct: 41 GSEERIVTITG-TPEAVEKAKELI 63
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 48.3 bits (115), Expect = 5e-07
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 44 CTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGG 91
C NCG + H S CP+ P + C +CG GHI+R+C + G
Sbjct: 55 CYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAA 102
Score = 42.5 bits (100), Expect = 4e-05
Identities = 19/48 (39%), Positives = 23/48 (47%)
Query: 44 CTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGG 91
C CG H S CP P C +CG GH++R+C E PG G
Sbjct: 30 CYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGP 77
Score = 39.4 bits (92), Expect = 5e-04
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 40 EGPRCTNCGASDHKSWLCPDKPNITNSTL-CSSCGGAGHIARDCREKRPGMGGP 92
C NCG + H S CP++ + C +CGG GHI+RDC GG
Sbjct: 76 GPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGD 129
Score = 39.0 bits (91), Expect = 7e-04
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 44 CTNCGASDHKSWLCPDKPN--ITNSTLCSSCGGAGHIARDCREKRPGMGGPP 93
C CG H+S CP+ + C CG GH++R+C G G
Sbjct: 3 CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERS 54
Score = 34.8 bits (80), Expect = 0.018
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 44 CTNCGASDHKSWLCPDKPNIT-NSTLCSSCGGAGHIARDCREK 85
C NCG H S CP+ C +CG GH++RDC +K
Sbjct: 106 CYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
Score = 26.7 bits (59), Expect = 10.0
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 67 TLCSSCGGAGHIARDCREKRPGM 89
+C CGG GH +R+C P
Sbjct: 1 MVCYRCGGVGHQSRECPNSAPAG 23
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 45.4 bits (108), Expect = 8e-07
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 6/48 (12%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242
V +V+IP + VGL+IG G+T+K +E++TG KI I G GS
Sbjct: 2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 40.6 bits (96), Expect = 3e-05
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242
+ VG +IG G+ +K + ++TG KI I
Sbjct: 9 DKVGRIIGKGGSNIKEIREETGVKIRIPDDRD 40
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the daughter
cell. ASH1 is a specific repressor of transcription that
localizes asymmetrically to the daughter cell nucleus.
RNA localisation is a widespread mechanism for achieving
localised protein synthesis.
Length = 42
Score = 39.5 bits (93), Expect = 5e-05
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 212 FVGLLIGPRGNTLKSMEKDTGAKIII 237
VG +IG G T+K + ++TGAKI I
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQI 26
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 40.6 bits (95), Expect = 3e-04
Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 12/60 (20%)
Query: 39 NEGPRCTNCGASDHKSWLCPDKPNITNST------------LCSSCGGAGHIARDCREKR 86
E P C NCG + H CP S C +CG GH++RDC +
Sbjct: 58 EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSK 117
Score = 35.2 bits (81), Expect = 0.023
Identities = 20/64 (31%), Positives = 24/64 (37%), Gaps = 14/64 (21%)
Query: 41 GPRCTNCGASDHKSWLCP-----------DKPNITNSTLCSSCGGAGHIARDCREKRPGM 89
C +C ++ H S CP D I C SCG AGH DC+E R
Sbjct: 120 QKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKF--CYSCGSAGHFGDDCKEPRS-S 176
Query: 90 GGPP 93
P
Sbjct: 177 RVPY 180
Score = 32.5 bits (74), Expect = 0.14
Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 2/58 (3%)
Query: 44 CTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGGPPANTHRNRA 101
C NCG + H S C P+ C C H + DC + H +
Sbjct: 100 CYNCGETGHLSRDCN--PSKDQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKK 155
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 42.0 bits (100), Expect = 3e-04
Identities = 28/109 (25%), Positives = 44/109 (40%), Gaps = 35/109 (32%)
Query: 175 KMFKVNPEFKPPPDYKP--PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTG 232
KM + E P + P P I+ + IP D + +IGP G T++ + ++TG
Sbjct: 536 KMNEAISE--PRAELSPYAPRIET---IKIPPD------KIRDVIGPGGKTIREITEETG 584
Query: 233 AKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDR 281
AKI I G+VK + A + E + A +R
Sbjct: 585 AKIDIEDDGTVK----------------------IAATDGEAAEAAKER 611
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 39.8 bits (93), Expect = 0.002
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 13/86 (15%)
Query: 188 DYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGK 247
Y P +I V IP D+ +G +IGP+G + ++ +TGA+I I G+V
Sbjct: 574 PYAPRIITVK----IPVDK------IGEVIGPKGKMINQIQDETGAEISIEDDGTV---Y 620
Query: 248 VGRKDGQPLPGENEPLHAYVTAHNPE 273
+G DG ++A PE
Sbjct: 621 IGAADGPSAEAARAMINAIANPTMPE 646
>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA in prokaryotes and plant chloroplasts. The
C-terminal region of PNPase contains domains homologous
to those in other RNA binding proteins: a KH domain and
an S1 domain. KH domains bind single-stranded RNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 61
Score = 35.6 bits (83), Expect = 0.002
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 22/73 (30%)
Query: 209 DINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVT 268
+ + +IGP G T+K + ++TG KI I G+V Y+
Sbjct: 9 PPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTV----------------------YIA 46
Query: 269 AHNPENVKKAVDR 281
A + E +KA
Sbjct: 47 ASDKEAAEKAKKM 59
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 65
Score = 34.4 bits (80), Expect = 0.006
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 213 VGLLIGPRGNTLKSMEKDTGAKIII 237
G +IG G+T+K + ++TGAKI +
Sbjct: 11 AGSIIGKGGSTIKEIREETGAKIRV 35
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 32.8 bits (76), Expect = 0.009
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 69 CSSCGGAGHIARDCRE 84
C +CG GHIARDC
Sbjct: 2 CYNCGKEGHIARDCPS 17
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 62
Score = 33.6 bits (78), Expect = 0.010
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKE 245
+V IP+ H I IG +G+ ++ + ++TG KI GS +
Sbjct: 3 EVEIPKKLHRFI------IGKKGSNIRKIMEETGVKIRFPDPGSKSD 43
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 35.6 bits (83), Expect = 0.011
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 10/58 (17%)
Query: 200 VMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK-GSVKEGKVGRKDGQPL 256
V IP+D +G+LIG G T K +E+ TG K+ I + G V K+ +D PL
Sbjct: 2 VKIPKDR------IGVLIGKGGETKKEIEERTGVKLDIDSETGEV---KIEEEDEDPL 50
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 35.6 bits (83), Expect = 0.015
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 7/46 (15%)
Query: 200 VMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK-GSVK 244
V IP+D +G+LIG +G T K +E+ TG K+ I + G V
Sbjct: 7 VKIPKDR------IGVLIGKKGETKKEIEERTGVKLEIDSETGEVI 46
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved
in eukaryotic gene regulation, such as C. elegans
GLH-1. Structure is an 18-residue zinc finger.
Length = 18
Score = 31.7 bits (73), Expect = 0.023
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 69 CSSCGGAGHIARDCRE 84
C +CG GH+ARDC E
Sbjct: 3 CYNCGKEGHLARDCPE 18
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 33.3 bits (77), Expect = 0.16
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 213 VGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVK 244
+ +IGP G T+K++ ++TG KI I G+VK
Sbjct: 563 IRDVIGPGGKTIKAITEETGVKIDIEDDGTVK 594
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 32.9 bits (76), Expect = 0.21
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 24/75 (32%)
Query: 207 HPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAY 266
+PD + +IGP G ++ + ++TGAKI I G+VK
Sbjct: 558 NPD--KIRDVIGPGGKVIREITEETGAKIDIEDDGTVK---------------------- 593
Query: 267 VTAHNPENVKKAVDR 281
+ A + E + A+
Sbjct: 594 IAASDGEAAEAAIKM 608
>gnl|CDD|222791 PHA00431, PHA00431, internal virion protein C.
Length = 746
Score = 32.5 bits (74), Expect = 0.29
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 153 RMNTREYRTRKKLEEERHDLIQ-------KMFKVNPE 182
++ E+RTR+++EE RH +Q + F +NP
Sbjct: 125 KIKNGEFRTRQEMEEYRHSRLQESAKSYAEQFGINPT 161
>gnl|CDD|216902 pfam02146, SIR2, Sir2 family. This region is characteristic of
Silent information regulator 2 (Sir2) proteins, or
sirtuins. These are protein deacetylases that depend on
nicotine adenine dinucleotide (NAD). They are found in
many subcellular locations, including the nucleus,
cytoplasm and mitochondria. Eukaryotic forms play in
important role in the regulation of transcriptional
repression. Moreover, they are involved in microtubule
organisation and DNA damage repair processes.
Length = 177
Score = 31.4 bits (72), Expect = 0.32
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGGA 75
RC +C L P++ + C CGG
Sbjct: 106 RCVSCHKKYTGETL-PERIDAAKVPKCDKCGGL 137
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 31.1 bits (71), Expect = 0.45
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 193 VIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240
VI + D V + D I G +IG G T +++E+ TG I + GK
Sbjct: 95 VIDLKDVVTLSGDHLRRI--KGRIIGREGKTRRAIEELTGVYISVYGK 140
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 30.8 bits (70), Expect = 0.90
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 13/90 (14%)
Query: 157 REYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLL 216
E K EEE I++ + E + D + V+KV +K IP+ +
Sbjct: 454 EESPALKLAEEEIEREIKRYLPGDVEVEVVGDGRA-VVKVPEK-YIPK-----------V 500
Query: 217 IGPRGNTLKSMEKDTGAKIIIRGKGSVKEG 246
IG G +K +EK G KI ++ +EG
Sbjct: 501 IGKGGKRIKEIEKKLGIKIDVKPLEEEEEG 530
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 30.8 bits (70), Expect = 1.0
Identities = 18/75 (24%), Positives = 25/75 (33%), Gaps = 12/75 (16%)
Query: 42 PRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGGPPANTHRNRA 101
RC +CG ++CPD CG R + P R
Sbjct: 680 NRCPDCGTHTEPVYVCPD------------CGAEVPPDESGRVECPRCDVELTPYQRRTI 727
Query: 102 KIDEEYMSLMAELGE 116
+ EEY S + +GE
Sbjct: 728 NVKEEYRSALENVGE 742
>gnl|CDD|218461 pfam05139, Erythro_esteras, Erythromycin esterase. This family
includes erythromycin esterase enzymes that confer
resistance to the erythromycin antibiotic.
Length = 344
Score = 30.4 bits (69), Expect = 1.2
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 252 DGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCL 285
D L G + + Y+ +PE +A +R CL
Sbjct: 69 DLYSLGGSMDAVLDYLDRVDPEAAARARERYACL 102
>gnl|CDD|238218 cd00368, Molybdopterin-Binding, Molybdopterin-Binding (MopB) domain
of the MopB superfamily of proteins, a large, diverse,
heterogeneous superfamily of enzymes that, in general,
bind molybdopterin as a cofactor. The MopB domain is
found in a wide variety of molybdenum- and
tungsten-containing enzymes, including formate
dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of
nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide
reductase (DMSOR), thiosulfate reductase,
formylmethanofuran dehydrogenase, and arsenite oxidase.
Molybdenum is present in most of these enzymes in the
form of molybdopterin, a modified pterin ring with a
dithiolene side chain, which is responsible for ligating
the Mo. In many bacterial and archaeal species,
molybdopterin is in the form of a dinucleotide, with two
molybdopterin dinucleotide units per molybdenum. These
proteins can function as monomers, heterodimers, or
heterotrimers, depending on the protein and organism.
Also included in the MopB superfamily is the
eukaryotic/eubacterial protein domain family of the
75-kDa subunit/Nad11/NuoG (second domain) of respiratory
complex 1/NADH-quinone oxidoreductase which is
postulated to have lost an ancestral formate
dehydrogenase activity and only vestigial sequence
evidence remains of a molybdopterin binding site.
Length = 374
Score = 30.4 bits (69), Expect = 1.2
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 11/61 (18%)
Query: 246 GKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPR----ARFPPGADFI 301
G +GR G PG N PL +A + V+ A+ +L +V A + AD +
Sbjct: 275 GNIGRPGGGLGPGGN-PLV---SAPDANRVRAALKKLDFVVVIDIFMTETAAY---ADVV 327
Query: 302 L 302
L
Sbjct: 328 L 328
>gnl|CDD|221343 pfam11962, Peptidase_G2, Peptidase_G2, IMC autoproteolytic cleavage
domain. This domain is found at the very C-terminus of
bacteriophage parallel beta-helical tailspike proteins.
It carries the enzymic residues that induce
autoproteolytic cleavage to bring about maturation of
the folding process of the helix in a chaperone-like
manner. The domain thus mediates the assembly of a large
tailspike protein and then releases itself after
maturation. These C-terminal regions that
autoproteolytically release themselves after maturation
are exchangeable between functionally unrelated
N-terminal proteins and have been identified in a number
of bacteriophage tailspike proteins.
Length = 222
Score = 29.2 bits (66), Expect = 1.9
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 161 TRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLL 216
+ +E+ + K K NP++ P +Y IP++E P+ N VGL+
Sbjct: 124 YEEVTDEDGNVETVKEPKENPDYDPNLEY------------IPREERPEWNPVGLI 167
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 29.5 bits (67), Expect = 3.0
Identities = 9/32 (28%), Positives = 10/32 (31%)
Query: 42 PRCTNCGASDHKSWLCPDKPNITNSTLCSSCG 73
RC CG + CP C CG
Sbjct: 639 RRCPFCGTHTEPVYRCPRCGIEVEEDECEKCG 670
>gnl|CDD|109380 pfam00320, GATA, GATA zinc finger. This domain uses four
cysteine residues to coordinate a zinc ion. This domain
binds to DNA. Two GATA zinc fingers are found in the
GATA transcription factors. However there are several
proteins which only contains a single copy of the
domain.
Length = 36
Score = 25.7 bits (57), Expect = 3.8
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 44 CTNCGASDHKSW-LCPDKPNITNSTLCSSCG 73
C+NCG + W PD N TLC++CG
Sbjct: 1 CSNCGTTKTPLWRRGPDG----NRTLCNACG 27
>gnl|CDD|226693 COG4242, CphB, Cyanophycinase and related exopeptidases [Secondary
metabolites biosynthesis, transport, and catabolism /
Inorganic ion transport and metabolism].
Length = 293
Score = 28.6 bits (64), Expect = 4.1
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 207 HPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPL 263
HP L IG NT +++D AK++ +G + + + +PL + PL
Sbjct: 206 HPSR----LGIGIDENTCAVVDRDGKAKVLGQGAVTFVDAREITYTNEPLVLRDAPL 258
>gnl|CDD|237663 PRK14293, PRK14293, chaperone protein DnaJ; Provisional.
Length = 374
Score = 28.8 bits (65), Expect = 4.2
Identities = 15/40 (37%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 44 CTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCR 83
C C S K T T CS+CGGAG + R R
Sbjct: 146 CETCRGSGAKPG--------TGPTTCSTCGGAGQVRRATR 177
>gnl|CDD|206088 pfam13917, zf-CCHC_3, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved
in eukaryotic gene regulation, such as C. elegans
GLH-1. Structure is an 18-residue zinc finger.
Length = 40
Score = 25.8 bits (57), Expect = 4.5
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 64 TNSTLCSSCGGAGHIARDCREKRP 87
S C C GH +C+ +R
Sbjct: 2 NASARCQKCLKKGHWTYECKNERK 25
>gnl|CDD|225504 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 28.5 bits (64), Expect = 4.7
Identities = 11/24 (45%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 36 LRENEGPRCTNCGASDHK-SWLCP 58
LR RC NCG + H W CP
Sbjct: 349 LRRKPRYRCQNCGFTAHTLYWHCP 372
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 28.7 bits (65), Expect = 4.7
Identities = 22/121 (18%), Positives = 44/121 (36%), Gaps = 22/121 (18%)
Query: 163 KKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDK--VMIPQDEHPDINFVGLLIGPR 220
+ E+E I++ E + + ++K V +P+ + + +IG
Sbjct: 455 RLAEKEIEREIKRYLPGPVEVE---------VVSDNKAVVYVPEKD------IPKVIGKG 499
Query: 221 GNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGE-NEPLHAYVTAHNPENVKKAV 279
G +K +EK G I +R + + G + + E + P+ K V
Sbjct: 500 GKRIKKIEKKLGIDIDVR----PLDEEPGEEAEEGEEVTVEETKKHVILIVGPDYAGKTV 555
Query: 280 D 280
D
Sbjct: 556 D 556
>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 28.2 bits (64), Expect = 4.9
Identities = 8/17 (47%), Positives = 9/17 (52%), Gaps = 1/17 (5%)
Query: 43 RCTNCGASDHK-SWLCP 58
RC NCG + W CP
Sbjct: 356 RCRNCGFTARTLYWHCP 372
>gnl|CDD|214648 smart00401, ZnF_GATA, zinc finger binding to DNA consensus
sequence [AT]GATA[AG].
Length = 52
Score = 25.8 bits (57), Expect = 5.4
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 39 NEGPRCTNCGASDHKSWL-CPDKPNITNSTLCSSCG 73
G C+NCG ++ W P N TLC++CG
Sbjct: 1 GSGRSCSNCGTTETPLWRRGPSG----NKTLCNACG 32
>gnl|CDD|146809 pfam04362, Iron_traffic, Bacterial Fe(2+) trafficking. This is a
family of bacterial Fe(2+) trafficking proteins.
Length = 87
Score = 26.4 bits (59), Expect = 5.9
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 5/41 (12%)
Query: 152 KRMNTREYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPP 192
KR+N + RK LEE+ + F P Y PP
Sbjct: 52 KRLNMMDPEARKFLEEQM-----EKFFFGEGADKPEGYVPP 87
>gnl|CDD|128708 smart00431, SCAN, leucine rich region.
Length = 113
Score = 26.9 bits (60), Expect = 6.4
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 3/24 (12%)
Query: 256 LPGENEPLHAYVTAHNPENVKKAV 279
LPGE L A+V H+PE+ ++AV
Sbjct: 57 LPGE---LQAWVREHHPESGEEAV 77
>gnl|CDD|188130 TIGR01323, nitrile_alph, nitrile hydratase, alpha subunit. This
model describes both iron- and cobalt-containing nitrile
hydratase alpha chains. It excludes the thiocyanate
hydrolase gamma subunit of Thiobacillus thioparus, a
sequence that appears to have evolved from within the
family of nitrile hydratase alpha subunits but which
differs by several indels and a more rapid accumulation
of point mutations [Energy metabolism, Amino acids and
amines].
Length = 189
Score = 27.3 bits (61), Expect = 6.9
Identities = 21/74 (28%), Positives = 29/74 (39%), Gaps = 14/74 (18%)
Query: 58 PDKPNITNSTLCSSCGGAGHIARDCREKRPGMGGPPA--NTHRNRAKIDEEYMSLMAELG 115
P+ N+ TLCS C P +G PP + R++ E ++AE G
Sbjct: 86 PEVHNVIVCTLCS-----------CY-PWPVLGLPPYWYKSPEYRSRAVREPRGVLAEFG 133
Query: 116 EGPPPDKRQRDNDS 129
P D R DS
Sbjct: 134 VELPEDVEVRVWDS 147
>gnl|CDD|240367 PTZ00338, PTZ00338, dimethyladenosine transferase-like protein;
Provisional.
Length = 294
Score = 27.7 bits (62), Expect = 8.1
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 9/48 (18%)
Query: 173 IQKMFKVNP-EFKPPPDYKPPVIKVNDKVMIPQDEHPDINFV---GLL 216
+ + KV+ F PPP + V++ + P++ PD++F GLL
Sbjct: 165 VTHLMKVSKNSFNPPPKVESSVVR-----IEPKNPPPDVDFEEWDGLL 207
>gnl|CDD|240364 PTZ00332, PTZ00332, paraflagellar rod protein; Provisional.
Length = 589
Score = 27.6 bits (61), Expect = 9.1
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 154 MNTREYRTRKKLEEERHDLIQKMFKVNPEFKPPPD--------YKPPVIKVNDKVM 201
M Y+ R+ +EEE L +K + FK + + PV + N++V+
Sbjct: 478 MKKELYKLRQGVEEELAMLKEKQAQALEMFKESEEALDAAGIEFVHPVDENNEEVL 533
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
0.315 0.136 0.422
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,978,534
Number of extensions: 1524165
Number of successful extensions: 1268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1251
Number of HSP's successfully gapped: 65
Length of query: 304
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 208
Effective length of database: 6,679,618
Effective search space: 1389360544
Effective search space used: 1389360544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 59 (26.5 bits)