RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4141
(353 letters)
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 70.8 bits (174), Expect = 9e-16
Identities = 27/66 (40%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQ 139
VTIEV +P VGL++G G+TIK+I+ +T I + +E V E+TG P++VE A +
Sbjct: 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAE 62
Query: 140 EIESHI 145
I +
Sbjct: 63 LILEIL 68
Score = 43.8 bits (104), Expect = 4e-06
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
I + G IK + +T I P G E V +TG E+V +A IL
Sbjct: 18 IGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILE 66
>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 = 68.0 bits (167), Expect = 9e-15
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGAPDSVEIAR 138
T V VP +VG ++G G+TIK I+ +T I P +E + +TG P++VE A+
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAK 60
Query: 139 QEIE 142
+ I
Sbjct: 61 ELIL 64
Score = 46.0 bits (110), Expect = 5e-07
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREIL 50
I + G IK +R +T IK P G EE + +TG E V +AK IL
Sbjct: 15 IGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64
>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 = 66.0 bits (162), Expect = 3e-14
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
T + +P VG ++G G+ IK I+ +T I P D++ ++G P+ VE A++ I
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP-DDRDDTVTISGTPEQVEKAKELI 59
Score = 42.2 bits (100), Expect = 1e-05
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 49
I + G IK +R +T I+ P + ++G E V +AK I
Sbjct: 15 IGKGGSNIKEIREETGVKIRIP-DDRDDTVTISGTPEQVEKAKELI 59
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 58.2 bits (141), Expect = 2e-11
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
C +C +R +PCGH C ECA+R + CP+CR P+
Sbjct: 2 DDLCVICLERPRNVVFLPCGHLCLCEECAKR-LRSKKKCPICRQPIES 48
>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 = 56.4 bits (137), Expect = 9e-11
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQE 140
T EV +P K+ ++G KG+ I++I +T I K +TG ++VE A++E
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEE 60
Query: 141 IE 142
I
Sbjct: 61 IL 62
Score = 41.0 bits (97), Expect = 3e-05
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREIL 50
I + G I+ + +T I+ P G + +TG KE+V +AK EIL
Sbjct: 15 IGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 46.0 bits (109), Expect = 4e-07
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 300 SRQCYLCNDREV-THALIPCGHNFFCSECAERTCDFDRTCPMCR 342
+C +C D L PCGH FC EC R CP+CR
Sbjct: 2 ELECPICLDLLRDPVVLTPCGH-VFCRECILRYLKKKSKCPICR 44
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 41.2 bits (97), Expect = 2e-05
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 301 RQCYLCNDREVTHALI---PCGHNFFCSECAERTCDFDRTCPMCRVP 344
+C +C D + PCGH F EC ++ TCP+CR P
Sbjct: 1 DECPICLDEFEPGEEVVVLPCGH-VFHKECLDKWLRSSNTCPLCRAP 46
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a
specialized type of Zn-finger of 40 to 60 residues that
binds two atoms of zinc; defined by the 'cross-brace'
motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified in
a proteins with a wide range of functions such as viral
replication, signal transduction, and development; has
two variants, the C3HC4-type and a C3H2C3-type (RING-H2
finger), which have different cysteine/histidine
pattern; a subset of RINGs are associated with B-Boxes
(C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 40.1 bits (94), Expect = 4e-05
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPV 345
+C +C + L+PCGH F C C ++ TCP+CR P+
Sbjct: 1 ECPICLEEFREPVVLLPCGHVF-CRSCIDKWLKSGKNTCPLCRTPI 45
>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 = 39.8 bits (94), Expect = 4e-05
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 92 VGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTG 129
VG ++G G TIK I+ +T I P E + +TG
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
Score = 26.8 bits (60), Expect = 2.2
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 4 ISRSGCKIKALRAKTNTYI---KTPVRGEEPVFVVTG 37
I + G IK +R +T I K E + +TG
Sbjct: 6 IGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
>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 = 38.2 bits (90), Expect = 3e-04
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 87 VPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK----EPVFEVTGAPDSVEIARQEI 141
VP G ++G G+TIK I+ +T I E V ++G P +V+ A I
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64
Score = 32.1 bits (74), Expect = 0.047
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 4 ISRSGCKIKALRAKTNTYIK----TPVRGEEPVFVVTGRKEDVARAKREIL 50
I + G IK +R +T I+ E V ++G+ V +A IL
Sbjct: 15 IGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II).
KH binds single-stranded RNA or DNA. It is found in a
wide variety of proteins including ribosomal proteins
(e.g. ribosomal protein S3), transcription factors (e.g.
NusA_K), and post-transcriptional modifiers of mRNA
(e.g. hnRNP K). There are two different KH domains that
belong to different protein folds, but they share a
single KH motif. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In addition to
their KH core domain, KH-II proteins have an N-terminal
alpha helical extension while KH-I proteins have a
C-terminal alpha helical extension.
Length = 68
Score = 36.5 bits (85), Expect = 0.001
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
+ I + V GLV+G KG I+ +Q +
Sbjct: 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and is
likely to be a general function of this domain; Various
RING fingers exhibit binding activity towards E2
ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 35.2 bits (81), Expect = 0.002
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 303 CYLCNDREVTHA-LIPCGHNFFCSECAERTCDFD-RTCPMC 341
C +C + + ++PCGH F C C + + TCP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTF-CRSCIRKWLESGNNTCPIC 40
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 37.7 bits (87), Expect = 0.006
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 4/72 (5%)
Query: 273 DASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTC 332
D + SS W P+ S P + S +C++C D L C H F CS C R
Sbjct: 2 DELDITDSSDWLTTPIPSLYP---LDTSLRCHICKDFFDVPVLTSCSHTF-CSLCIRRCL 57
Query: 333 DFDRTCPMCRVP 344
CP+CR
Sbjct: 58 SNQPKCPLCRAE 69
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 36.9 bits (86), Expect = 0.007
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 90 KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES 143
++ G ++G +G T + I+ T YI K + G + VEIAR+ +E
Sbjct: 111 RIKGRIIGREGKTRRAIEELTGVYISV--YGKT--VAIIGGFEQVEIAREAVEM 160
>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 = 35.3 bits (82), Expect = 0.011
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 13/88 (14%)
Query: 82 TIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE--VTGAPDS 133
T +V +P Y VGL++GP+G T+K+++ +T I R K + +
Sbjct: 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISI--RGKGSMKDGKKEEELRG 58
Query: 134 VEIARQEIESHIIRRTGSCVTPAEAVLN 161
+ A H++ + TP E L
Sbjct: 59 PKYAHLNEPLHVLI---TAETPPEEALA 83
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 35.6 bits (83), Expect = 0.019
Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 7/89 (7%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEI-- 136
+ V++P +G+++G KG T K I+ +T + S E + E T D + +
Sbjct: 1 MMMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLK 60
Query: 137 ARQEIESHIIRRTGSCVTPAEAVLNGDDN 165
AR I++ G +P +A+ DD+
Sbjct: 61 AR-----DIVKAIGRGFSPEKALRLLDDD 84
Score = 29.5 bits (67), Expect = 1.7
Identities = 42/156 (26%), Positives = 65/156 (41%), Gaps = 42/156 (26%)
Query: 1 MKKI-SRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSA-ADHFSA 58
K+I R+G K++ + ++T I P GE+P+ V +A R+I+ A FS
Sbjct: 25 KKEIEERTGVKLE-IDSETGEVIIEPTDGEDPL--------AVLKA-RDIVKAIGRGFSP 74
Query: 59 LRASRKSGALS--------PLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110
+A R L LS P + ++ G ++G G T + I+ T
Sbjct: 75 EKALR---LLDDDYVLEVIDLSDYGDSPNALR-------RIKGRIIGEGGKTRRIIEELT 124
Query: 111 NTYIVTPSRDKEPVFEVT----GAPDSVEIARQEIE 142
I V+ T G P+ VEIAR+ IE
Sbjct: 125 GVDIS--------VYGKTVAIIGDPEQVEIAREAIE 152
>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 = 34.8 bits (81), Expect = 0.028
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 84 EVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKE-PVFEVTGAPDSVEIARQEIE 142
V++P +G+++G G T K I+ +T + S E + E P +V AR
Sbjct: 1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAR---- 56
Query: 143 SHIIRRTGSCVTPAEAVLNGDDN 165
+++ G +P +A+ DD+
Sbjct: 57 -EVVKAIGRGFSPEKALKLLDDD 78
Score = 31.0 bits (71), Expect = 0.50
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 93 GLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIE 142
G ++G G T + I+ T I K + G P+ V+IAR+ IE
Sbjct: 101 GRIIGEGGKTRRIIEELTGVSISV--YGKT--VGIIGDPEQVQIAREAIE 146
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 35.8 bits (84), Expect = 0.030
Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 19/90 (21%)
Query: 58 ALRASRKSGALSPLSPPTGVPGHVTIE-VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116
A+ R LSP +P IE +++P + V+GP G TI+ I +T I
Sbjct: 540 AISEPRAE--LSPYAP--------RIETIKIPPDKIRDVIGPGGKTIREITEETGAKI-- 587
Query: 117 PSRDKEPVFEVT-GAPD--SVEIARQEIES 143
D E V A D + E A++ IE
Sbjct: 588 ---DIEDDGTVKIAATDGEAAEAAKERIEG 614
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 35.8 bits (83), Expect = 0.031
Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 16/83 (19%)
Query: 77 VPGHVTIE--------VRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEV 127
+PG V +E V+VP K + V+G G IK I+ + I V P ++E +V
Sbjct: 474 LPGDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKV 533
Query: 128 TGAPDSVEIARQEIESHIIRRTG 150
VEI E HI+ G
Sbjct: 534 P-----VEIE--EKGKHIVLYVG 549
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 35.4 bits (81), Expect = 0.037
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344
C +C+ R CGH FCS C R CP+CR
Sbjct: 28 CRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCRED 68
>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 = 35.2 bits (81), Expect = 0.047
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIE 142
I V++P +G V+GPKG I +IQ +T I D V+ S E AR I
Sbjct: 580 ITVKIPVDKIGEVIGPKGKMINQIQDETGAEISI--EDDGTVYIGAADGPSAEAARAMIN 637
Query: 143 S 143
+
Sbjct: 638 A 638
>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 = 31.7 bits (73), Expect = 0.050
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 92 VGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAP-DSVEIARQEIE 142
+ V+GP G TIK+I +T I + + + + ++ E A++ IE
Sbjct: 13 IRDVIGPGGKTIKKIIEETGVKIDI---EDDGTVYIAASDKEAAEKAKKMIE 61
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 34.6 bits (79), Expect = 0.069
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 14/61 (22%)
Query: 298 SGSRQCYLCND-------------REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344
+ R C +C D ++T +PCGH C + + +TCP+CR P
Sbjct: 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHL-HCLKNWLERQQTCPICRRP 343
Query: 345 V 345
V
Sbjct: 344 V 344
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 29.7 bits (67), Expect = 0.16
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 303 CYLCNDR-EVTHALIPCGHNFFCSECAERTCDF-DRTCPMC 341
C +C + + ++PCGH FCS+C + + TCP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHL-FCSKCILSWLESGNVTCPLC 40
>gnl|CDD|220401 pfam09786, CytochromB561_N, Cytochrome B561, N terminal. Members
of this family are found in the N terminal region of
cytochrome B561, as well as in various other putative
uncharacterized proteins.
Length = 559
Score = 33.6 bits (77), Expect = 0.16
Identities = 24/105 (22%), Positives = 40/105 (38%), Gaps = 9/105 (8%)
Query: 207 NFNMPLSSSQMN-HHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEG 265
+ M S + H FS S S++ S S + S QL + + SS +
Sbjct: 126 STPMNTSEPLVPGHSSFSDSPSRSASPSRKFSPSSTIQQSPQLTPSNKPASPSSSYQ--- 182
Query: 266 LGDSPSFDAS-PVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDR 309
SPS+ +S SS SS + SG ++ +++
Sbjct: 183 ---SPSYSSSLGPVNSSGNRSNLRSSPW-ALRSSGDKKDITTDEK 223
>gnl|CDD|143417 cd07099, ALDH_DDALDH, Methylomonas sp.
4,4'-diapolycopene-dialdehyde dehydrogenase-like. The
4,4'-diapolycopene-dialdehyde dehydrogenase (DDALDH)
involved in C30 carotenoid synthesis in Methylomonas sp.
strain 16a and other similar sequences are present in
this CD. DDALDH converts 4,4'-diapolycopene-dialdehyde
into 4,4'-diapolycopene-diacid.
Length = 453
Score = 33.0 bits (76), Expect = 0.24
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 10/67 (14%)
Query: 36 TGRKEDVARAKREILSAADHFS--ALRASRKSGALSPLSPPTG--VPGHVTIEVRVPYKV 91
TG+ A E+L A + A A R L+P PTG +P PY V
Sbjct: 68 TGKPRADAGL--EVLLALEAIDWAARNAPR---VLAPRKVPTGLLMPNKKATVEYRPYGV 122
Query: 92 VGLVVGP 98
VG V+ P
Sbjct: 123 VG-VISP 128
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to chromosome
metabolism and cell cycle control.
Length = 73
Score = 30.1 bits (68), Expect = 0.28
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 318 CGHNF-FCSECAERTCDFDRTCPMCR 342
CGH F C R TCP+CR
Sbjct: 50 CGHAFHLH--CISRWLKTRNTCPLCR 73
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 32.2 bits (73), Expect = 0.34
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 299 GSRQCYLCNDREVTHALIPCGHNFFCSEC--AERTCDFDRTCPMCR 342
+C+LC + + PCGH FC C T CP+CR
Sbjct: 214 ADYKCFLCLEEPEVPSCTPCGH-LFCLSCLLISWTKKKYEFCPLCR 258
>gnl|CDD|206613 pfam14447, Prok-RING_4, Prokaryotic RING finger family 4. RING
finger family domain found sporadically in bacteria. The
finger is fused to an N-terminal alpha-helical domain,
ROT/Trove-like repeats and a C-terminal TerD domain. The
architecture suggests a possible role in an
RNA-processing complex.
Length = 55
Score = 29.2 bits (66), Expect = 0.41
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 7/45 (15%)
Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDR--TCPMCRVPV 345
C C L+PCGH + T D +R CP C P
Sbjct: 10 CLFCGTVGTKGVLLPCGH-LIP----DGTFDGERYNGCPFCGTPF 49
>gnl|CDD|188567 TIGR04052, AZL_007920_fam, AZL_007920/MXAN_0976 family protein.
Members of this rare protein family regularly occur next
to a member of the MXAN_0977 subfamily (TIGR04039) of
the di-heme cytochrome c peroxidase/MauG family
(pfam03150). MauG itself (TIGR03791) is a protein
modification enzyme responsible for the tryptophan
tryptophylquinone (TTQ) modification involved in
methylamine dehydrogenase activation. All members of
this family have a motif of four spaced invariant Cys
residues, while additional homologs outside the scope of
this family lack the four Cys residues.
Length = 206
Score = 31.3 bits (71), Expect = 0.56
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 16/75 (21%)
Query: 205 EFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACA-------------PHSST-QLDL 250
+ + N + S V GS+GC+ + + SSAC P+S +LDL
Sbjct: 109 DVSPNASVGKST-GWVVHLGSTGCAGSPARGESSACTNPNRLPVTLPGFDPNSQKVELDL 167
Query: 251 GSIWSGMSSLDKDEG 265
+++ G S+L + G
Sbjct: 168 AALFEG-SNLGANPG 181
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 31.3 bits (71), Expect = 0.59
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 318 CGHNFFCSECAERTCDFDRTCPMCRVP 344
C H FC EC + TCP+CR P
Sbjct: 200 CNH-VFCIECIDIWKKEKNTCPVCRTP 225
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 29.0 bits (66), Expect = 0.69
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQ 109
V + +R G+V+G G+ IK++ +
Sbjct: 27 VIVVIRTSQP--GIVIGKGGSNIKKLGKE 53
>gnl|CDD|131219 TIGR02164, torA, trimethylamine-N-oxide reductase TorA. This
very narrowly defined family represents TorA, part of a
family of related molybdoenzymes that include biotin
sulfoxide reductases, dimethyl sulfoxide reductases,
and at least two different subfamilies of
trimethylamine-N-oxide reductases. A single enzyme from
the larger family may have more than one activity. TorA
typically is located in the periplasm, has a Tat
(twin-arginine translocation)-dependent signal
sequence, and is encoded in a torCAD operon.
Length = 822
Score = 31.8 bits (72), Expect = 0.70
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 47 REILSAADHFSALRASRKSGALSPLSP------PT----GVPGHVTIEVRVPYKVVGL 94
E + H+ A RA K+G + + P PT G+ G V RV Y +V L
Sbjct: 38 DEWKTTGSHWGAFRAKVKNGKVVEVKPFELDKYPTEMINGIRGMVYNPSRVRYPMVRL 95
>gnl|CDD|237909 PRK15102, PRK15102, trimethylamine N-oxide reductase I catalytic
subunit; Provisional.
Length = 825
Score = 31.6 bits (72), Expect = 0.71
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 43 ARAKREILSAADHFSALRASRKSGALSPLSP------PT----GVPGHVTIEVRVPYKVV 92
A +E + H+ A RA K+G P PT G+ GHV R+ Y +V
Sbjct: 37 AETTKEWILTGSHWGAFRAKVKNGRFVEAKPFELDKYPTKMINGIKGHVYNPSRIRYPMV 96
Query: 93 GL 94
L
Sbjct: 97 RL 98
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.3 bits (72), Expect = 0.85
Identities = 29/132 (21%), Positives = 44/132 (33%), Gaps = 37/132 (28%)
Query: 28 GEE----PVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTI 83
GE+ PV + A++EI + +PG V +
Sbjct: 436 GEQTVVVPVEEEEEKSPVWRLAEKEIEREIKRY--------------------LPGPVEV 475
Query: 84 E--------VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVE 135
E V VP K + V+G G IK+I+ + I D+EP + E
Sbjct: 476 EVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP----GEEAEEGE 531
Query: 136 IARQEIES-HII 146
E H+I
Sbjct: 532 EVTVEETKKHVI 543
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 30.5 bits (69), Expect = 1.6
Identities = 18/80 (22%), Positives = 26/80 (32%)
Query: 223 SGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSI 282
S SS + S S SS + + + S S S S + V+P
Sbjct: 287 SSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPS 346
Query: 283 WSYPPVSSTSPSGSISGSRQ 302
S P S P + S +
Sbjct: 347 PSRSPSPSRPPPPADPSSPR 366
Score = 29.4 bits (66), Expect = 3.8
Identities = 22/90 (24%), Positives = 32/90 (35%), Gaps = 1/90 (1%)
Query: 223 SGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLG-DSPSFDASPVNPSS 281
S SS+SSS SS+ + SS++ G+ S S + P D S
Sbjct: 310 SSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRP 369
Query: 282 IWSYPPVSSTSPSGSISGSRQCYLCNDREV 311
S P S + +G + R R
Sbjct: 370 RPSRAPSSPAASAGRPTRRRARAAVAGRAR 399
>gnl|CDD|143397 cd07078, ALDH, NAD(P)+ dependent aldehyde dehydrogenase family.
The aldehyde dehydrogenase family (ALDH) of NAD(P)+
dependent enzymes, in general, oxidize a wide range of
endogenous and exogenous aliphatic and aromatic
aldehydes to their corresponding carboxylic acids and
play an important role in detoxification. Besides
aldehyde detoxification, many ALDH isozymes possess
multiple additional catalytic and non-catalytic
functions such as participating in metabolic pathways,
or as binding proteins, or as osmoregulants, to mention
a few. The enzyme has three domains, a NAD(P)+
cofactor-binding domain, a catalytic domain, and a
bridging domain; and the active enzyme is generally
either homodimeric or homotetrameric. The catalytic
mechanism is proposed to involve cofactor binding,
resulting in a conformational change and activation of
an invariant catalytic cysteine nucleophile. The
cysteine and aldehyde substrate form an oxyanion
thiohemiacetal intermediate resulting in hydride
transfer to the cofactor and formation of a
thioacylenzyme intermediate. Hydrolysis of the
thioacylenzyme and release of the carboxylic acid
product occurs, and in most cases, the reduced cofactor
dissociates from the enzyme. The evolutionary
phylogenetic tree of ALDHs appears to have an initial
bifurcation between what has been characterized as the
classical aldehyde dehydrogenases, the ALDH family
(ALDH) and extended family members or aldehyde
dehydrogenase-like (ALDH-like) proteins. The ALDH
proteins are represented by enzymes which share a number
of highly conserved residues necessary for catalysis and
cofactor binding and they include such proteins as
retinal dehydrogenase, 10-formyltetrahydrofolate
dehydrogenase, non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase,
delta(1)-pyrroline-5-carboxylate dehydrogenases,
alpha-ketoglutaric semialdehyde dehydrogenase,
alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
aldehyde dehydrogenase and succinate-semialdehyde
dehydrogenase. Included in this larger group are all
human, Arabidopsis, Tortula, fungal, protozoan, and
Drosophila ALDHs identified in families ALDH1 through
ALDH22 with the exception of families ALDH18, ALDH19,
and ALDH20 which are present in the ALDH-like group.
Length = 432
Score = 30.3 bits (69), Expect = 1.7
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 35 VTGRKEDVARAKREILSAAD--HFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVV 92
TG+ + A E+ AAD + A A R G P+ PG + I R P VV
Sbjct: 47 ETGKPIEEALG--EVARAADTFRYYAGLARRLHGE----VIPSPDPGELAIVRREPLGVV 100
Query: 93 GLVV 96
G +
Sbjct: 101 GAIT 104
>gnl|CDD|218222 pfam04710, Pellino, Pellino. Pellino is involved in Toll-like
signalling pathways, and associates with the kinase
domain of the Pelle Ser/Thr kinase.
Length = 416
Score = 30.2 bits (68), Expect = 1.8
Identities = 16/45 (35%), Positives = 18/45 (40%), Gaps = 12/45 (26%)
Query: 312 THALIPCGHNFFCSECAER----------TCDFDRTCPMCRVPVN 346
THA +PCGH CSE T F CP C P+
Sbjct: 359 THAFVPCGH--VCSEKTALYWAQIPLPHGTHAFHAACPFCATPLA 401
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is
an essential multifunctional transcription elongation
factor that is universally conserved among prokaryotes
and archaea. NusA anti-termination function plays an
important role in the expression of ribosomal rrn
operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 27.5 bits (62), Expect = 1.9
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
V VP +GL +G G ++ I
Sbjct: 26 RARVVVPDDQLGLAIGKGGQNVRLASKLLGEKI 58
>gnl|CDD|226194 COG3668, ParE, Plasmid stabilization system protein [General
function prediction only].
Length = 98
Score = 28.2 bits (63), Expect = 2.0
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 6/74 (8%)
Query: 36 TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLV 95
R+ + A+R + + F +L + G + G I + +
Sbjct: 21 IARRFGPSAARRYVRALETAFESLAEFPEIG-----RSRDEIRGGRRIVPYGSHYIFYYR 75
Query: 96 VGPKGATIKRIQHQ 109
VG + I R+ H
Sbjct: 76 VGGR-VLILRVLHG 88
>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 = 30.2 bits (69), Expect = 2.0
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
P TI++ P K+ V+GP G I+ I +T I
Sbjct: 550 PRIETIKIN-PDKI-RDVIGPGGKVIREITEETGAKI 584
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 29.6 bits (66), Expect = 2.1
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 92 VGLVVGPKGATIKRIQHQTNT--YIVTPSRDKE 122
VGL++GP+G+T+K+++ + I KE
Sbjct: 165 VGLLIGPRGSTLKQLERISRAKIAIRGSGSVKE 197
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.9 bits (67), Expect = 2.4
Identities = 29/128 (22%), Positives = 43/128 (33%), Gaps = 6/128 (4%)
Query: 135 EIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGP 194
+ I +H + S + E V+ N + +S N + + G+ G
Sbjct: 269 QHHSIGINNHHSKHADSKLQTIE-VIENHSNKSRPSSSSTNGSKETTSNSSSAAAGSIGS 327
Query: 195 ASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAP-HSSTQLDLGSI 253
S N SS +H +GS SS S + S A SS D
Sbjct: 328 KSSKSAKHSNRNKSN----SSPKSHSSANGSVPSSSVSDNESKQKRASKSSSGARDSKKD 383
Query: 254 WSGMSSLD 261
SGMS+
Sbjct: 384 ASGMSANG 391
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 29.9 bits (67), Expect = 2.4
Identities = 22/90 (24%), Positives = 31/90 (34%), Gaps = 8/90 (8%)
Query: 210 MPLSSSQMNHHVF---SGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGL 266
+P Q N V S SS+ S + + L SI SG S +
Sbjct: 251 LPGKHKQRNGAVSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGSSDEN----- 305
Query: 267 GDSPSFDASPVNPSSIWSYPPVSSTSPSGS 296
D F +S V + W + P + S S
Sbjct: 306 EDILKFQSSQVQIRARWLHEPDETDRISAS 335
>gnl|CDD|221368 pfam11999, DUF3494, Protein of unknown function (DUF3494). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria, archaea and eukaryotes.
Proteins in this family are typically between 243 to 678
amino acids in length. This protein has a single
completely conserved residue G that may be functionally
important.
Length = 196
Score = 29.2 bits (66), Expect = 2.8
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 149 TGSCVT--PAEAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAG 202
+ +T P V +G +AD A + L T N G + P GAG
Sbjct: 25 AATAITGFPLGVVSSGTIYAADYAAPTATQAVSDLTTAYNDAAGRTTPDYTGLGAG 80
>gnl|CDD|227909 COG5622, COG5622, Protein required for attachment to host cells
[Cell motility and secretion].
Length = 139
Score = 28.6 bits (64), Expect = 3.1
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 2/49 (4%)
Query: 199 YGAGPGEFNFNMPLSSSQ--MNHHVFSGSSGCSSASSSSSSSACAPHSS 245
+ + N+P N H G+ S+SSS+ S+ S
Sbjct: 23 FRNQGDKATPNLPAKLVLDIDNDHHGRGARQSHSSSSSNPDSSREEEDS 71
>gnl|CDD|171842 PRK13023, PRK13023, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 758
Score = 29.6 bits (66), Expect = 3.3
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 6/77 (7%)
Query: 116 TPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLLASLCN 175
TP D E V+ P + + I TG +T A+A ++ DD + +L +
Sbjct: 139 TPPADSEIVYSFDDPPVGYLLKKTPI------LTGHDITDAKASISADDGQPVITLTLDD 192
Query: 176 SGLGSLGTILNYVNGTS 192
+G L + N S
Sbjct: 193 NGRRRLADLTAQGNENS 209
>gnl|CDD|218608 pfam05495, zf-CHY, CHY zinc finger. This family of domains are
likely to bind to zinc ions. They contain many conserved
cysteine and histidine residues. We have named this
domain after the N-terminal motif CXHY. This domain can
be found in isolation in some proteins, but is also
often associated with pfam00097. One of the proteins in
this family is a mitochondrial intermembrane space
protein called Hot13. This protein is involved in the
assembly of small TIM complexes.
Length = 74
Score = 27.3 bits (61), Expect = 3.4
Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 10/50 (20%)
Query: 303 CYLCNDREVTHALIPC-GHNFFCSEC------AERTCDFDR---TCPMCR 342
C LC+D H L C C E C + CP+C+
Sbjct: 22 CRLCHDELEDHPLDRWNVKAVLCGVCRTEQTVQEYNCGVEFADYYCPICK 71
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 29.3 bits (66), Expect = 3.4
Identities = 20/72 (27%), Positives = 30/72 (41%)
Query: 175 NSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSS 234
+SG GS GT G + G + F +++ + S S SSS
Sbjct: 234 SSGYGSGGTRSGQGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYGRSYGSGSPSYSPSSS 293
Query: 235 SSSSACAPHSST 246
S+SS+ + SST
Sbjct: 294 SNSSSSSSSSST 305
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 29.1 bits (66), Expect = 4.3
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 23/92 (25%)
Query: 58 ALRASRKSGALSPLSPPTGVPGHVTIE-VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116
A+ RK LSP +P IE +++ + V+GP G TIK I +T I
Sbjct: 538 AISEPRKE--LSPYAP--------RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKI-- 585
Query: 117 PSRDKEP-----VFEVTGAPDSVEIARQEIES 143
D E + G +S + A++ IE+
Sbjct: 586 ---DIEDDGTVKIAASDG--ESAKKAKERIEA 612
>gnl|CDD|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional.
Length = 667
Score = 28.7 bits (65), Expect = 5.3
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 6/36 (16%)
Query: 91 VVGLVVGPKGATIKRIQHQ-----TNTYIVTPSRDK 121
VV L+ GPKG+ + R++ T T IVT +RDK
Sbjct: 301 VVALIKGPKGSKV-RLEILPAGKGTKTRIVTLTRDK 335
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 28.8 bits (65), Expect = 5.4
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 8/37 (21%)
Query: 10 KIKALRAKTNTYIKTPVRGE--------EPVFVVTGR 38
KI L ++YI TP R E VF +TGR
Sbjct: 198 KIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGR 234
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 28.4 bits (64), Expect = 6.8
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 10 KIKALRAKTNTYIKTPVRGE--------EPVFVVTGRKEDV-ARAKREILSAAD 54
KI+ L ++YI TP R E VF ++GR V R +R IL +
Sbjct: 188 KIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGE 241
>gnl|CDD|226801 COG4357, COG4357, Zinc finger domain containing protein (CHY type)
[Function unknown].
Length = 105
Score = 26.7 bits (59), Expect = 8.0
Identities = 18/57 (31%), Positives = 21/57 (36%), Gaps = 16/57 (28%)
Query: 303 CYLCNDREVTHALIPCGHNFF------CSEC------AE-RTCDFDRTCPMCRVPVN 346
CY C+D H P G F C C AE C +CP C+ P N
Sbjct: 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCG---SCPYCQSPFN 91
>gnl|CDD|239210 cd02844, PAZ_CAF_like, PAZ domain, CAF_like subfamily. CAF (for
carpel factory) is a plant homolog of Dicer. CAF has
been implicated in flower morphogenesis and in early
Arabidopsis development and might function through
posttranscriptional regulation of specific mRNA
molecules. PAZ domains are named after the proteins
Piwi, Argonaut, and Zwille. PAZ is found in two families
of proteins that are essential components of
RNA-mediated gene-silencing pathways, including RNA
interference, the Piwi and Dicer families. PAZ functions
as a nucleic-acid binding domain, with a strong
preference for single-stranded nucleic acids (RNA or
DNA) or RNA duplexes with single-stranded 3' overhangs.
It has been suggested that the PAZ domain provides a
unique mode for the recognition of the two 3'-terminal
nucleotides in single-stranded nucleic acids and buries
the 3' OH group, and that it might recognize
characteristic 3' overhangs in siRNAs within RISC
(RNA-induced silencing) and other complexes.
Length = 135
Score = 27.0 bits (60), Expect = 8.3
Identities = 16/49 (32%), Positives = 19/49 (38%), Gaps = 10/49 (20%)
Query: 227 GCSSASSSSSSSACAPHS------STQLDLGSIWSGMSSLDKDEGLGDS 269
G A S APH+ S LDL + SS EGLG +
Sbjct: 24 GSFCACDLKGSVVTAPHNGRFYVISGILDL----NANSSFPGKEGLGYA 68
>gnl|CDD|143467 cd07149, ALDH_y4uC, Uncharacterized ALDH (y4uC) with similarity to
Tortula ruralis aldehyde dehydrogenase ALDH21A1.
Uncharacterized aldehyde dehydrogenase (ORF name y4uC)
with sequence similarity to the moss Tortula ruralis
aldehyde dehydrogenase ALDH21A1 (RNP123) believed to
play an important role in the detoxification of
aldehydes generated in response to desiccation- and
salinity-stress, and similar sequences are included in
this CD.
Length = 453
Score = 27.9 bits (63), Expect = 8.5
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 14/70 (20%)
Query: 38 RKEDVAR------------AKREILSAAD--HFSALRASRKSGALSPLSPPTGVPGHVTI 83
R+E+ AR A++E+ A + SA A R +G P G G +
Sbjct: 59 RREEFARTIALEAGKPIKDARKEVDRAIETLRLSAEEAKRLAGETIPFDASPGGEGRIGF 118
Query: 84 EVRVPYKVVG 93
+R P VV
Sbjct: 119 TIREPIGVVA 128
>gnl|CDD|165563 PHA03308, PHA03308, transcriptional regulator ICP4; Provisional.
Length = 1463
Score = 28.2 bits (62), Expect = 9.1
Identities = 20/45 (44%), Positives = 25/45 (55%)
Query: 195 ASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSA 239
A GAG ++ SSS M+ S SS CSS+SSSS SS+
Sbjct: 1229 AQPHVGAGAMPPCPDLSESSSTMHSSSSSSSSSCSSSSSSSDSSS 1273
>gnl|CDD|112657 pfam03854, zf-P11, P-11 zinc finger.
Length = 50
Score = 25.2 bits (55), Expect = 9.3
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 315 LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 350
L+ C ++ C C + CP+C+ P+ +R
Sbjct: 15 LVTCSDHYLCLRCLQLLLSVSERCPICKKPLPTKLR 50
>gnl|CDD|235957 PRK07193, fliF, flagellar MS-ring protein; Reviewed.
Length = 552
Score = 28.0 bits (63), Expect = 9.5
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 255 SGMSSLDKDEGLGDS 269
SG+ LDKD LG S
Sbjct: 113 SGLELLDKDSPLGTS 127
>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
This is a family of conserved proteins of from 500 - 600
residues found from worms to humans. Its function is not
known.
Length = 515
Score = 27.8 bits (62), Expect = 9.9
Identities = 20/93 (21%), Positives = 30/93 (32%), Gaps = 7/93 (7%)
Query: 190 GTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLD 249
GT P S G + + S S S SS S +S +SS+
Sbjct: 51 GTRRPLSRKIGKCSSRRVRSPSSKPNDTLSGASSKLSSKHSGSSHSLASVSDRNSSSS-- 108
Query: 250 LGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSI 282
GS + S E G + + P ++
Sbjct: 109 -GSCANSGSW----EAAGMEEPINTTDTTPENL 136
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 27.7 bits (61), Expect = 9.9
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 302 QCYLC------NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
+C +C NDR ++PC H F + + CP+CR +
Sbjct: 325 ECAICMSNFIKNDRLR---VLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371
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
0.314 0.129 0.385
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,253,066
Number of extensions: 1605028
Number of successful extensions: 1432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1395
Number of HSP's successfully gapped: 96
Length of query: 353
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 255
Effective length of database: 6,590,910
Effective search space: 1680682050
Effective search space used: 1680682050
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 (22.0 bits)
S2: 59 (26.5 bits)