RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3263
(329 letters)
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 57.8 bits (140), Expect = 2e-11
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
C +C +R +PCGH C ECA+R + CP+CR P+
Sbjct: 2 DDLCVICLERPRNVVFLPCGHLCLCEECAKR-LRSKKKCPICRQPIES 48
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 56.5 bits (137), Expect = 1e-10
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGNF 136
VTIEV +P VGL++G G+TIK+I+ +T I + +E V E+TG
Sbjct: 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPP 54
Score = 41.5 bits (98), Expect = 2e-05
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 13 GCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 56
G IK + +T I P G E V +TG E+V +A IL
Sbjct: 22 GSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILE 66
>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 = 54.9 bits (133), Expect = 3e-10
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNF 136
T + +P VG ++G G+ IK I+ +T I P D++ ++G
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP-DDRDDTVTISGTP 49
Score = 39.9 bits (94), Expect = 6e-05
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 13 GCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 54
G IK +R +T I+ P + ++G E V +AK I
Sbjct: 19 GSNIKEIREETGVKIRIP-DDRDDTVTISGTPEQVEKAKELI 59
>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 = 54.5 bits (132), Expect = 4e-10
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGN 135
T V VP +VG ++G G+TIK I+ +T I P +E + +TG
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT 52
Score = 44.5 bits (106), Expect = 2e-06
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 13 GCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREIL 55
G IK +R +T IK P G EE + +TG E V +AK IL
Sbjct: 19 GSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 45.2 bits (107), Expect = 6e-07
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 253 SRQCYLCNDREV-THALIPCGHNFFCSECAERTCDFDRTCPMCR 295
+C +C D L PCGH FC EC R CP+CR
Sbjct: 2 ELECPICLDLLRDPVVLTPCGH-VFCRECILRYLKKKSKCPICR 44
>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 = 42.5 bits (101), Expect = 8e-06
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 128
T EV +P K+ ++G KG+ I++I +T I P +
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKS 42
Score = 39.4 bits (93), Expect = 9e-05
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREIL 55
I G I+ + +T I+ P G + +TG KE+V +AK EIL
Sbjct: 15 IGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62
>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 = 40.6 bits (96), Expect = 3e-05
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 97 VGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTG 134
VG ++G G TIK I+ +T I P E + +TG
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 40.5 bits (95), Expect = 3e-05
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 254 RQCYLCNDREVTHALI---PCGHNFFCSECAERTCDFDRTCPMCRVP 297
+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 = 39.4 bits (92), Expect = 7e-05
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPV 298
+C +C + L+PCGH F C C ++ TCP+CR P+
Sbjct: 1 ECPICLEEFREPVVLLPCGHVF-CRSCIDKWLKSGKNTCPLCRTPI 45
>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 = 36.9 bits (86), Expect = 0.001
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
+ I + V GLV+G KG I+ +Q +
Sbjct: 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58
>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 = 38.8 bits (90), Expect = 0.003
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 4/72 (5%)
Query: 226 DASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTC 285
D + SS W P+ S P + S +C++C D L C H F CS C R
Sbjct: 2 DELDITDSSDWLTTPIPSLYP---LDTSLRCHICKDFFDVPVLTSCSHTF-CSLCIRRCL 57
Query: 286 DFDRTCPMCRVP 297
CP+CR
Sbjct: 58 SNQPKCPLCRAE 69
>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 = 35.5 bits (83), Expect = 0.003
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 92 VPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK----EPVFEVTGNF 136
VP G ++G G+TIK I+ +T I E V ++G
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKP 54
Score = 29.4 bits (67), Expect = 0.34
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 13 GCKIKALRAKTNTYIK----TPVRGEEPVFVVTGRKEDVARAKREIL 55
G IK +R +T I+ E V ++G+ V +A IL
Sbjct: 19 GSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65
>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 = 34.4 bits (79), Expect = 0.004
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 256 CYLCNDREVTHA-LIPCGHNFFCSECAERTCDFD-RTCPMC 294
C +C + + ++PCGH F C C + + TCP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTF-CRSCIRKWLESGNNTCPIC 40
>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 = 0.009
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 87 TIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIV 120
T +V +P Y VGL++GP+G T+K+++ +T I
Sbjct: 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKIS 40
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 36.2 bits (83), Expect = 0.017
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297
C +C+ R CGH FCS C R CP+CR
Sbjct: 28 CRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCRED 68
>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 = 0.045
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 97 VGLVVGPKGATIKRIQHQTNTYI 119
+ V+GP G TIK+I +T I
Sbjct: 13 IRDVIGPGGKTIKKIIEETGVKI 35
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 35.0 bits (81), Expect = 0.057
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 82 VPGHVTIE--------VRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEV 132
+PG V +E V+VP K + V+G G IK I+ + I V P ++E +V
Sbjct: 474 LPGDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKV 533
Query: 133 T 133
Sbjct: 534 P 534
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 33.7 bits (78), Expect = 0.067
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT----------YIVTPSRDKEPV 129
+ V++P +G+++G KG T K I+ +T I+ P+ ++P+
Sbjct: 1 MMMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPL 56
>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 = 0.079
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 20/71 (28%)
Query: 251 SGSRQCYLCND-------------REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297
+ R C +C D ++T +PCGH C + + +TCP+CR P
Sbjct: 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHL-HCLKNWLERQQTCPICRRP 343
Query: 298 VNQAMRIIFNQ 308
V IF+Q
Sbjct: 344 V------IFDQ 348
>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 = 34.1 bits (79), Expect = 0.095
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 10/67 (14%)
Query: 41 TGRKEDVARAKREILSAADHFS--ALRASRKSGALSPLSPPTG--VPGHVTIEVRVPYKV 96
TG+ A E+L A + A A R L+P PTG +P PY V
Sbjct: 68 TGKPRADAGL--EVLLALEAIDWAARNAPR---VLAPRKVPTGLLMPNKKATVEYRPYGV 122
Query: 97 VGLVVGP 103
VG V+ P
Sbjct: 123 VG-VISP 128
>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 = 34.0 bits (78), Expect = 0.099
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
I V++P +G V+GPKG I +IQ +T I
Sbjct: 580 ITVKIPVDKIGEVIGPKGKMINQIQDETGAEI 611
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 34.3 bits (80), Expect = 0.10
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 63 ALRASRKSGALSPLSPPTGVPGHVTIE-VRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
A+ R LSP +P IE +++P + V+GP G TI+ I +T I
Sbjct: 540 AISEPRAE--LSPYAP--------RIETIKIPPDKIRDVIGPGGKTIREITEETGAKI 587
>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 = 29.4 bits (66), Expect = 0.22
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 256 CYLCNDR-EVTHALIPCGHNFFCSECAERTCDF-DRTCPMC 294
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 = 32.8 bits (75), Expect = 0.24
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 20/107 (18%)
Query: 172 HHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDAS--P 229
H FS S S++ S S + S QL + + SS + SPS+ +S P
Sbjct: 139 HSSFSDSPSRSASPSRKFSPSSTIQQSPQLTPSNKPASPSSSYQ------SPSYSSSLGP 192
Query: 230 VNPS--------SIWSYPPVSSTSPSGSISGSR--QCYLCNDREVTH 266
VN S S W+ SS + + + +L E H
Sbjct: 193 VNSSGNRSNLRSSPWAL--RSSGDKKDITTDEKYLETFLAEVDEEQH 237
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 32.6 bits (74), Expect = 0.26
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 252 GSRQCYLCNDREVTHALIPCGHNFFCSEC--AERTCDFDRTCPMCR 295
+C+LC + + PCGH FC C T CP+CR
Sbjct: 214 ADYKCFLCLEEPEVPSCTPCGH-LFCLSCLLISWTKKKYEFCPLCR 258
>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 = 32.1 bits (73), Expect = 0.39
Identities = 20/59 (33%), Positives = 24/59 (40%), Gaps = 15/59 (25%)
Query: 265 THALIPCGHNFFCSECAER----------TCDFDRTCPMCRVPVNQA---MRIIFNQFL 310
THA +PCGH CSE T F CP C P+ +R+IF L
Sbjct: 359 THAFVPCGH--VCSEKTALYWAQIPLPHGTHAFHAACPFCATPLAGERGYVRLIFQGPL 415
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.1 bits (74), Expect = 0.40
Identities = 27/126 (21%), Positives = 40/126 (31%), Gaps = 32/126 (25%)
Query: 33 GEE----PVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTI 88
GE+ PV + A++EI + +PG V +
Sbjct: 436 GEQTVVVPVEEEEEKSPVWRLAEKEIEREIKRY--------------------LPGPVEV 475
Query: 89 E--------VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP 140
E V VP K + V+G G IK+I+ + I D+EP E
Sbjct: 476 EVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVTV 535
Query: 141 GFESHH 146
H
Sbjct: 536 EETKKH 541
>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 = 29.3 bits (66), Expect = 0.44
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 271 CGHNF-FCSECAERTCDFDRTCPMCR 295
CGH F C R TCP+CR
Sbjct: 50 CGHAFHLH--CISRWLKTRNTCPLCR 73
>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 = 31.0 bits (71), Expect = 0.46
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 89 EVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
V++P +G+++G G T K I+ +T +
Sbjct: 1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKL 31
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 32.1 bits (73), Expect = 0.47
Identities = 18/80 (22%), Positives = 26/80 (32%)
Query: 176 SGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSI 235
S SS + S S SS + + + S S S S + V+P
Sbjct: 287 SSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPS 346
Query: 236 WSYPPVSSTSPSGSISGSRQ 255
S P S P + S +
Sbjct: 347 PSRSPSPSRPPPPADPSSPR 366
Score = 30.9 bits (70), Expect = 0.99
Identities = 22/90 (24%), Positives = 32/90 (35%), Gaps = 1/90 (1%)
Query: 176 SGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLG-DSPSFDASPVNPSS 234
S SS+SSS SS+ + SS++ G+ S S + P D S
Sbjct: 310 SSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRP 369
Query: 235 IWSYPPVSSTSPSGSISGSRQCYLCNDREV 264
S P S + +G + R R
Sbjct: 370 RPSRAPSSPAASAGRPTRRRARAAVAGRAR 399
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 29.0 bits (66), Expect = 0.61
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQ 114
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 = 31.4 bits (71), Expect = 0.69
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 52 REILSAADHFSALRASRKSGALSPLSP------PT----GVPGHVTIEVRVPYKVVGL 99
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: 48 ARAKREILSAADHFSALRASRKSGALSPLSP------PT----GVPGHVTIEVRVPYKVV 97
A +E + H+ A RA K+G P PT G+ GHV R+ Y +V
Sbjct: 37 AETTKEWILTGSHWGAFRAKVKNGRFVEAKPFELDKYPTKMINGIKGHVYNPSRIRYPMV 96
Query: 98 GL 99
L
Sbjct: 97 RL 98
>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 = 28.5 bits (64), Expect = 0.73
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 7/45 (15%)
Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDFDR--TCPMCRVPV 298
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 = 30.5 bits (69), Expect = 0.94
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 15/62 (24%)
Query: 171 NHHVFSGSSGCSSASSSSSSSACA-------------PHSST-QLDLGSIWSGMSSLDKD 216
V GS+GC+ + + SSAC P+S +LDL +++ G S+L +
Sbjct: 121 GWVVHLGSTGCAGSPARGESSACTNPNRLPVTLPGFDPNSQKVELDLAALFEG-SNLGAN 179
Query: 217 EG 218
G
Sbjct: 180 PG 181
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 30.5 bits (69), Expect = 1.0
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 271 CGHNFFCSECAERTCDFDRTCPMCRVP 297
C H FC EC + TCP+CR P
Sbjct: 200 CNH-VFCIECIDIWKKEKNTCPVCRTP 225
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 30.6 bits (70), Expect = 1.1
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 12/52 (23%)
Query: 124 RDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSFFDCRIFQRMNHHVF 175
R+ +P TG P GP H G K+VF + Q +V+
Sbjct: 62 RNGKPFAVYTGFMPSGP---MHIGHKMVFDEL---------KWHQEFGANVY 101
>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 = 30.6 bits (70), Expect = 1.2
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 40 VTGRKEDVARAKREILSAAD--HFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVV 97
TG+ + A E+ AAD + A A R G P+ PG + I R P VV
Sbjct: 47 ETGKPIEEALG--EVARAADTFRYYAGLARRLHGE----VIPSPDPGELAIVRREPLGVV 100
Query: 98 GLVV 101
G +
Sbjct: 101 GAIT 104
>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 = 30.5 bits (70), Expect = 1.3
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 83 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
P TI++ P K+ V+GP G I+ I +T I
Sbjct: 550 PRIETIKIN-PDKI-RDVIGPGGKVIREITEETGAKI 584
>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 = 1.5
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
V VP +GL +G G ++ I
Sbjct: 26 RARVVVPDDQLGLAIGKGGQNVRLASKLLGEKI 58
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 29.9 bits (67), Expect = 1.5
Identities = 11/45 (24%), Positives = 24/45 (53%)
Query: 97 VGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPG 141
VGL++GP+G+T+K+++ + I +++ + PE
Sbjct: 165 VGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLK 209
>gnl|CDD|226194 COG3668, ParE, Plasmid stabilization system protein [General
function prediction only].
Length = 98
Score = 28.6 bits (64), Expect = 1.6
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 6/74 (8%)
Query: 41 TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLV 100
R+ + A+R + + F +L + G + G I + +
Sbjct: 21 IARRFGPSAARRYVRALETAFESLAEFPEIG-----RSRDEIRGGRRIVPYGSHYIFYYR 75
Query: 101 VGPKGATIKRIQHQ 114
VG + I R+ H
Sbjct: 76 VGGR-VLILRVLHG 88
>gnl|CDD|223580 COG0506, PutA, Proline dehydrogenase [Amino acid transport and
metabolism].
Length = 391
Score = 29.6 bits (67), Expect = 2.0
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 292 PMCRVPVNQAMRIIFNQFLFGKLWEPVAMNQNT 324
P+ R ++ A RI+ F+ G + + N
Sbjct: 120 PVIRKALDNARRILGEAFVHGITIVEIDLEDNK 152
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 29.5 bits (66), Expect = 2.9
Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 8/84 (9%)
Query: 169 RMNHHVF---SGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSF 225
+ N V S SS+ S + + L SI SG S + D F
Sbjct: 257 QRNGAVSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGSSDEN-----EDILKF 311
Query: 226 DASPVNPSSIWSYPPVSSTSPSGS 249
+S V + W + P + S S
Sbjct: 312 QSSQVQIRARWLHEPDETDRISAS 335
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 29.1 bits (66), Expect = 3.8
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 63 ALRASRKSGALSPLSPPTGVPGHVTIE-VRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
A+ RK LSP +P IE +++ + V+GP G TIK I +T I
Sbjct: 538 AISEPRKE--LSPYAP--------RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKI 585
>gnl|CDD|236141 PRK08032, fliD, flagellar capping protein; Reviewed.
Length = 462
Score = 28.9 bits (65), Expect = 4.2
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 55 LSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEV 90
L+ AD FS+ + S + A S + G TI V
Sbjct: 64 LNKADLFSSTKVSSSTTAFSATTDSGASAGKYTISV 99
>gnl|CDD|216760 pfam01881, Cas_Cas6, CRISPR associated protein Cas6. This group of
families is one of several protein families that are
always found associated with prokaryotic CRISPRs,
themselves a family of clustered regularly interspaced
short palindromic repeats, DNA repeats found in nearly
half of all bacterial and archaeal genomes. These DNA
repeat regions have a remarkably regular structure:
unique sequences of constant size, called spacers, sit
between each pair of repeats. It has been shown that the
CRISPRs are virus-derived sequences acquired by the host
to enable them to resist viral infection. The Cas
proteins from the host use the CRISPRs to mediate an
antiviral response. After transcription of the CRISPR, a
complex of Cas proteins termed Cascade cleaves a CRISPR
RNA precursor in each repeat and retains the cleavage
products containing the virus-derived sequence. Assisted
by the helicase Cas3, these mature CRISPR RNAs then
serve as small guide RNAs that enable Cascade to
interfere with virus proliferation. Cas5 contains an
endonuclease motif, whose inactivation leads to loss of
resistance, even in the presence of phage-derived
spacers.
Length = 152
Score = 28.0 bits (63), Expect = 4.3
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 2 FIFVVPSINPFGCKIKALRAKTNTYIK 28
F F K K ++ K NTYI+
Sbjct: 89 FKFEPLVFKKKVVKHKRIKIKKNTYIR 115
>gnl|CDD|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional.
Length = 667
Score = 28.7 bits (65), Expect = 4.4
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 6/36 (16%)
Query: 96 VVGLVVGPKGATIKRIQHQ-----TNTYIVTPSRDK 126
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 = 4.5
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 8/37 (21%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVFVVTGR 43
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 = 28.8 bits (65), Expect = 4.8
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVFVVTGRKEDV-ARAKREILSAAD 59
KI+ L ++YI TP R E VF ++GR V R +R IL +
Sbjct: 188 KIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGE 241
>gnl|CDD|237017 PRK11904, PRK11904, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1038
Score = 28.6 bits (65), Expect = 5.1
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 292 PMCRVPVNQAMRIIFNQFLFG 312
P+ R + QAM+I+ QF+ G
Sbjct: 163 PVIRKAMRQAMKIMGKQFVLG 183
>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 = 28.7 bits (65), Expect = 5.2
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 14/70 (20%)
Query: 43 RKEDVAR------------AKREILSAAD--HFSALRASRKSGALSPLSPPTGVPGHVTI 88
R+E+ AR A++E+ A + SA A R +G P G G +
Sbjct: 59 RREEFARTIALEAGKPIKDARKEVDRAIETLRLSAEEAKRLAGETIPFDASPGGEGRIGF 118
Query: 89 EVRVPYKVVG 98
+R P VV
Sbjct: 119 TIREPIGVVA 128
>gnl|CDD|235957 PRK07193, fliF, flagellar MS-ring protein; Reviewed.
Length = 552
Score = 28.4 bits (64), Expect = 6.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 208 SGMSSLDKDEGLGDS 222
SG+ LDKD LG S
Sbjct: 113 SGLELLDKDSPLGTS 127
>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 = 26.1 bits (58), Expect = 6.1
Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 10/50 (20%)
Query: 256 CYLCNDREVTHALIPC-GHNFFCSEC------AERTCDFDR---TCPMCR 295
C LC+D H L C C E C + CP+C+
Sbjct: 22 CRLCHDELEDHPLDRWNVKAVLCGVCRTEQTVQEYNCGVEFADYYCPICK 71
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 27.6 bits (62), Expect = 6.2
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 95 KVVGLVVGPKGATIKRIQHQTNTYIV 120
++ G ++G +G T + I+ T YI
Sbjct: 111 RIKGRIIGREGKTRRAIEELTGVYIS 136
>gnl|CDD|200334 TIGR03892, thiopep_precurs, thiazolylpeptide-type bacteriocin
precursor. Members of this protein family are the
precursors of a family of small bacteriocins (i.e.
microcins) with thiopeptide type modifications, a highly
modified subclass of heterocycle-containing peptide
antibiotics. Members tend to be found clustered in
genomes with proteins recognized by TIGR03891 and
proteins/domains annotated as lantibiotic dehydratase
(pfam04737, pfam04738), and with a
cyclodehydratase/docking protein fusion protein
characteristic of heterocycle formation. The seed
alignment includes both an N-terminal leader peptide
region and a C-terminal low-complexity region consisting
mostly of Cys and Ser residues. Members with known
function block translation by inhibiting translation
factor activity [Cellular processes, Toxin production
and resistance].
Length = 43
Score = 25.4 bits (56), Expect = 7.2
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 175 FSGSSGCSSASSSSSSSAC 193
SGS+ CSS+SS +++S
Sbjct: 22 ASGSTSCSSSSSCTTTSCT 40
>gnl|CDD|227952 COG5665, NOT5, CCR4-NOT transcriptional regulation complex, NOT5
subunit [Transcription].
Length = 548
Score = 28.1 bits (62), Expect = 7.7
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 2/68 (2%)
Query: 184 ASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSS 243
SSS++ + Q L SI S + +P D S + ++ P V S
Sbjct: 200 IQPSSSNNEAPKEGNNQTSLSSIRSSKKQERSPKK--KAPQRDVSISDRATTPIAPGVES 257
Query: 244 TSPSGSIS 251
S S S +
Sbjct: 258 ASQSISST 265
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 27.8 bits (63), Expect = 8.6
Identities = 17/46 (36%), Positives = 19/46 (41%), Gaps = 15/46 (32%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 45
KI L ++YI TP R E VF VVTGR E
Sbjct: 190 KILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVE 235
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 28.0 bits (63), Expect = 8.7
Identities = 13/37 (35%), Positives = 15/37 (40%), Gaps = 8/37 (21%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVFVVTGR 43
I L + YI TP R E VF +TGR
Sbjct: 188 AIMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGR 224
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 27.7 bits (61), Expect = 9.3
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 232 PSSIWSYPPVSSTSPSGSISGSRQ-CYLCNDREVTHALIPCGHNFFCSECAERTCDFDRT 290
+ S P +TS + C +C A PCGH C CA R
Sbjct: 39 KKNNLSAEPNLTTSSADDTDEENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQ 97
Query: 291 --CPMCR 295
CP+CR
Sbjct: 98 KGCPLCR 104
>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 = 9.5
Identities = 16/49 (32%), Positives = 19/49 (38%), Gaps = 10/49 (20%)
Query: 180 GCSSASSSSSSSACAPHS------STQLDLGSIWSGMSSLDKDEGLGDS 222
G A S APH+ S LDL + SS EGLG +
Sbjct: 24 GSFCACDLKGSVVTAPHNGRFYVISGILDL----NANSSFPGKEGLGYA 68
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 27.5 bits (62), Expect = 9.8
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 15/46 (32%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 45
KI L ++YI P R E VF VVTGR E
Sbjct: 190 KILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVE 235
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
0.319 0.133 0.413
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: 16,289,761
Number of extensions: 1495793
Number of successful extensions: 1665
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1640
Number of HSP's successfully gapped: 83
Length of query: 329
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 232
Effective length of database: 6,635,264
Effective search space: 1539381248
Effective search space used: 1539381248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)