RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1895
(140 letters)
>gnl|CDD|216454 pfam01363, FYVE, FYVE zinc finger. The FYVE zinc finger is named
after four proteins that it has been found in: Fab1,
YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been
shown to bind two Zn++ ions. The FYVE finger has eight
potential zinc coordinating cysteine positions. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. We have included members which do not
conserve these histidine residues but are clearly
related.
Length = 68
Score = 85.9 bits (213), Expect = 3e-23
Identities = 33/66 (50%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 69 AQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAA---KPVRVCD 125
+W D + C C K F+ RRRHHCRNCG++FC+ CS K+AL KPVRVCD
Sbjct: 1 PRWVPDSDVTNCMGCGKPFSFFRRRHHCRNCGKVFCSSCSSKKIALLPKLGINKPVRVCD 60
Query: 126 ECNVKL 131
+C KL
Sbjct: 61 DCYDKL 66
>gnl|CDD|214499 smart00064, FYVE, Protein present in Fab1, YOTB, Vac1, and EEA1.
The FYVE zinc finger is named after four proteins where
it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1.
The FYVE finger has been shown to bind two Zn2+ ions.
The FYVE finger has eight potential zinc coordinating
cysteine positions. The FYVE finger is structurally
related to the PHD finger and the RING finger. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. The FYVE finger functions in the
membrane recruitment of cytosolic proteins by binding to
phosphatidylinositol 3-phosphate (PI3P), which is
prominent on endosomes. The R+HHC+XCG motif is critical
for PI3P binding.
Length = 68
Score = 84.0 bits (208), Expect = 1e-22
Identities = 34/65 (52%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 69 AQWAKDKEAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAA--KPVRVCDE 126
W D+E C C KEF +T+RRHHCRNCG IFC+ CS K LP +PVRVCD+
Sbjct: 2 PHWIPDEEVSNCMGCGKEFNLTKRRHHCRNCGRIFCSKCSSKKAPLPKLGIERPVRVCDD 61
Query: 127 CNVKL 131
C L
Sbjct: 62 CYENL 66
>gnl|CDD|238022 cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins
to membrane lipids via interaction with
phosphatidylinositol-3-phosphate, PI3P; present in Fab1,
YOTB, Vac1, and EEA1;.
Length = 57
Score = 75.2 bits (185), Expect = 4e-19
Identities = 34/57 (59%), Positives = 40/57 (70%), Gaps = 2/57 (3%)
Query: 76 EAITCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAA--KPVRVCDECNVK 130
+A +C C K FT+TRRRHHCRNCG IFC+ CS N++ LPS KPVRVCD C
Sbjct: 1 DASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYEL 57
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 40.8 bits (95), Expect = 9e-05
Identities = 31/106 (29%), Positives = 49/106 (46%), Gaps = 21/106 (19%)
Query: 43 GAQLSKSKLQVSDLMEEHQI-----AKRATEAQWAKDKEAI-TCRACDKEF-TVTR---- 91
G + ++ V + EE+++ K W KD E+ +C +C + F +++R
Sbjct: 420 GGGSAAARATVGGVAEENELNTFGLTKLLHNPSWQKDDESSDSCPSCGRAFISLSRPLGT 479
Query: 92 RRHHCRNCGEIFCNMC-------SDNKMALPSA---AKPVRVCDEC 127
R HHCR+CG C C S K+A P + A+ VCD C
Sbjct: 480 RAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCDTC 525
>gnl|CDD|222785 PHA00368, PHA00368, internal virion protein D.
Length = 1315
Score = 35.1 bits (81), Expect = 0.007
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 19/73 (26%)
Query: 12 DHVKMNKIAEHVKDNVSDDK-----------------YKESELALE--ELGAQLSKSKLQ 52
D N + + ++D + D + Y+ LA+E EL A L+K++ +
Sbjct: 561 DQRTYNDLYDAMEDAMKDPEFSTGGAKMSREAARQEIYRRVALAIERPELQANLTKAERK 620
Query: 53 VSDLMEEHQIAKR 65
V D+++EH KR
Sbjct: 621 VMDILKEHFDLKR 633
>gnl|CDD|220403 pfam09788, Tmemb_55A, Transmembrane protein 55A. Members of this
family catalyze the hydrolysis of the 4-position
phosphate of phosphatidylinositol 4,5-bisphosphate, in
the reaction: 1-phosphatidyl-myo-inositol
4,5-bisphosphate + H(2)O =
1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Length = 258
Score = 29.8 bits (67), Expect = 0.34
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 78 ITCRACDKEFTVTRRRH-HCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVEKLT 136
+ CR C +V + H H CG CN + K A P K VR C CN L+ K++
Sbjct: 68 VNCRVCQSLISVEGKEHQHVVKCG--VCNEATPIKNA-PPGKKYVR-C-PCNCLLICKVS 122
>gnl|CDD|214993 smart01047, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterised by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C.
Length = 49
Score = 27.3 bits (61), Expect = 0.51
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 80 CRACDKEFT------VTRRRHHCRNCGEIFCNMC 107
C C F VT R+ C C ++FC C
Sbjct: 1 CFGCQSPFPNSKDKSVTSSRYRCTKCKQVFCIDC 34
>gnl|CDD|239081 cd02341, ZZ_ZZZ3, Zinc finger, ZZ type. Zinc finger present in ZZZ3
(ZZ finger containing 3) and related proteins. The ZZ
motif coordinates two zinc ions and most likely
participates in ligand binding or molecular scaffolding.
Length = 48
Score = 26.2 bits (58), Expect = 1.5
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 78 ITCRACDKEFTVTRRRHHCRNCGEIFCNMCSD 109
C +C E + R+HC C + ++C D
Sbjct: 1 FKCDSCGIE-PIPGTRYHCSECDDGDFDLCQD 31
>gnl|CDD|133049 cd06427, CESA_like_2, CESA_like_2 is a member of the cellulose
synthase superfamily. The cellulose synthase (CESA)
superfamily includes a wide variety of
glycosyltransferase family 2 enzymes that share the
common characteristic of catalyzing the elongation of
polysaccharide chains. The members include cellulose
synthase catalytic subunit, chitin synthase, Glucan
Biosynthesis protein and other families of CESA-like
proteins. Cellulose synthase catalyzes the
polymerization reaction of cellulose, an aggregate of
unbranched polymers of beta-1,4-linked glucose residues
in plants, most algae, some bacteria and fungi, and
even some animals. In bacteria, algae and lower
eukaryotes, there is a second unrelated type of
cellulose synthase (Type II), which produces acylated
cellulose, a derivative of cellulose. Chitin synthase
catalyzes the incorporation of GlcNAc from substrate
UDP-GlcNAc into chitin, which is a linear homopolymer
of beta-(1,4)-linked GlcNAc residues and Glucan
Biosynthesis protein catalyzes the elongation of
beta-1,2 polyglucose chains of glucan.
Length = 241
Score = 26.8 bits (60), Expect = 3.9
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 32 YKESELALEELGAQLS-----KSKLQVSDLMEEHQIAKRA 66
YKE+E+ L +L A LS +SKL V L+EE A
Sbjct: 10 YKEAEV-LPQLIASLSALDYPRSKLDVKLLLEEDDEETIA 48
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 26.6 bits (59), Expect = 4.2
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 4/28 (14%)
Query: 80 CRACDKEFTVTRR----RHHCRNCGEIF 103
C +C + + RR ++ C CG
Sbjct: 122 CGSCGQLYPRKRRIRRHKYRCGRCGGKL 149
>gnl|CDD|218488 pfam05191, ADK_lid, Adenylate kinase, active site lid. Comparisons
of adenylate kinases have revealed a particular
divergence in the active site lid. In some organisms,
particularly the Gram-positive bacteria, residues in the
lid domain have been mutated to cysteines and these
cysteine residues are responsible for the binding of a
zinc ion. The bound zinc ion in the lid domain, is
clearly structurally homologous to Zinc-finger domains.
However, it is unclear whether the adenylate kinase lid
is a novel zinc-finger DNA/RNA binding domain, or that
the lid bound zinc serves a purely structural function.
Length = 36
Score = 24.4 bits (54), Expect = 4.9
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 8/37 (21%)
Query: 96 CRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLV 132
C +CG I+ + P K VCD+C +LV
Sbjct: 4 CPSCGRIY------HVKFNPP--KVEGVCDKCGGELV 32
>gnl|CDD|217297 pfam02945, Endonuclease_7, Recombination endonuclease VII.
Length = 81
Score = 25.5 bits (56), Expect = 5.0
Identities = 10/58 (17%), Positives = 14/58 (24%), Gaps = 7/58 (12%)
Query: 57 MEEHQIAKRATEAQWAKDKEAI--TCRACDKEFTVTRRRH--HCRNCG---EIFCNMC 107
T ++ EA C C + T H G + C C
Sbjct: 1 ERRLGSLYGITAEEYWAIYEAQGGRCAICQRANGGTPALAVDHDHKTGHVRGLLCGPC 58
>gnl|CDD|176721 cd08305, Pyrin, Pyrin: a protein-protein interaction domain. The
Pyrin domain (or PYD), also called DAPIN or PAAD, is a
subfamily of the Death Domain (DD) superfamily and it
functions in several signaling pathways. The Pyrin
domain is found at the N-terminus of a variety of
proteins and serves as a linker that recruits other
domains into signaling complexes. Pyrin-containing
proteins include NALPs, ASC (Apoptosis-associated
speck-like protein containing a CARD), and the
interferon-inducible p200 (IFI-200) family of proteins
which includes the human IFI-16, myeloid cell nuclear
differentiation antigen (MNDA) and absent in melanoma
(AIM) 2. NALPs are members of the NBS-LRR family of
proteins possessing a tripartite domain structure
including a C-terminal LRR (leucine-rich repeats), a
central nucleotide-binding site (NBS) domain or NACHT
(for neuronal apoptosis inhibitor protein, CIITA, HET-E
and TP1), and an N-terminal protein-protein interaction
domain, which is a Pyrin domain in the case of NALPs.
ASC and NALPs are involved in the regulation of
inflammation. ASC, NALP1 and NALP3 are involved in the
assembly of the 'inflammasome', a multiprotein platform
which is formed in response to infection or injury and
is responsible for caspase-1 activation and regulation
of IL-1beta maturation. NALP12 functions as a negative
regulator of inflammation. The p200 proteins are
involved in the regulation of cell cycle and
differentiation. In general, DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including Caspase activation and recruitment domain
(CARD) and Death Effector Domain (DED). They serve as
adaptors in signaling pathways and can recruit other
proteins into signaling complexes.
Length = 73
Score = 25.4 bits (56), Expect = 5.3
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 25 DNVSDDKYKESELALE-----ELGAQLSKSKLQVSDLMEEHQIAKRATE 68
+N++D++ K + L E AQL +++Q++DLME+ A A +
Sbjct: 6 ENITDEELKRFKSLLANDLFLETKAQLEYTRIQIADLMEQKFGAVSALD 54
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 26.5 bits (59), Expect = 5.6
Identities = 13/45 (28%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 79 TCRACDKEFTVTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRV 123
TC C E R C NCG N + + S A P
Sbjct: 144 TCPKCGGE---DARGDQCENCGRTLDPTELINPVCVISGATPEVR 185
>gnl|CDD|128412 smart00101, 14_3_3, 14-3-3 homologues. 14-3-3 homologues mediates
signal transduction by binding to
phosphoserine-containing proteins. They are involved in
growth factor signalling and also interact with MEK
kinases.
Length = 244
Score = 26.4 bits (58), Expect = 5.7
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 7 KRSFDDHVKMNKIAEHVKDNVSDDKYKESELALEELGAQLSKSKLQVSDLMEEHQ 61
K++FD+ IAE D + ++ YK+S L ++ L L+ L SDL ++
Sbjct: 195 KQAFDE-----AIAEL--DTLGEESYKDSTLIMQLLRDNLT---LWTSDLQDDGA 239
>gnl|CDD|235198 PRK04011, PRK04011, peptide chain release factor 1; Provisional.
Length = 411
Score = 26.4 bits (59), Expect = 5.7
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 6/35 (17%)
Query: 73 KDKEAITCRACDKEFTVTRRR------HHCRNCGE 101
KD+ C C E T +R C CG
Sbjct: 324 KDRVTYKCPNCGYEEEKTVKRREELPEKTCPKCGS 358
>gnl|CDD|187666 cd09806, type1_17beta-HSD-like_SDR_c, human estrogenic
17beta-hydroxysteroid dehydrogenase type 1 (type 1
17beta-HSD)-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. This classical SDR subgroup
includes human type 1 17beta-HSD, human retinol
dehydrogenase 8, zebrafish photoreceptor associated
retinol dehydrogenase type 2, and a chicken
ovary-specific 17beta-hydroxysteroid dehydrogenase. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 258
Score = 26.3 bits (58), Expect = 5.8
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 6/82 (7%)
Query: 29 DDKYKESELALE----ELGAQLSKSKLQVSDLMEEHQIAKRATEAQWAKDKEAITCRACD 84
+D Y S+ ALE L QL + +S L+E + E +E + A D
Sbjct: 148 NDVYCASKFALEGLCESLAVQLLPFNVHLS-LIECGPVHTAFMEKVLGSPEEVLDRTA-D 205
Query: 85 KEFTVTRRRHHCRNCGEIFCNM 106
T + + ++F
Sbjct: 206 DITTFHFFYQYLAHSKQVFREA 227
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 26.6 bits (58), Expect = 6.0
Identities = 10/47 (21%), Positives = 20/47 (42%)
Query: 92 RRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVEKLTVV 138
R HC+ IF D+ + +A + ++ C K ++K +
Sbjct: 52 RYFHCKKRHGIFIRPDDDSLLNGNAAYEKIKGGLVCESKGMDKDGEI 98
>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 26.5 bits (59), Expect = 6.1
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 6/50 (12%)
Query: 89 VTRRRHHCRNCGEIFCNMCSDNKMALPSAAKPVRVCDECNVKLVEKLTVV 138
+ + C CG S+ ++ P R C+ C L +V
Sbjct: 125 LKKAVFECPKCGREVEVEQSEFRVEPP------RECENCGKFGKGPLKLV 168
>gnl|CDD|129550 TIGR00458, aspS_nondisc, nondiscriminating aspartyl-tRNA
synthetase. In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_arch, represents
aspartyl-tRNA synthetases from the eukaryotic cytosol
and from the Archaea. In some species, this enzyme
aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn)
is subsequently transamidated to Asn-tRNA(asn) [Protein
synthesis, tRNA aminoacylation].
Length = 428
Score = 26.3 bits (58), Expect = 6.8
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 2 TSGGLKRSFDDHVKMNKIAEHVKDNVSDDKYKESELALEELGAQLSKSKLQVSDLM--EE 59
TS ++ +F+DH + I E + V +D + LE L +L K + + L E
Sbjct: 224 TSIDIEMAFEDHHDVMDILEELVVRVFEDVPERCAHQLETLEFKLEKPEGKFVRLTYDEA 283
Query: 60 HQIAKRA-TEAQWAKD 74
++A E W +D
Sbjct: 284 IEMANAKGVEIGWGED 299
>gnl|CDD|218212 pfam04685, DUF608, Protein of unknown function, DUF608. This
family represents a conserved region with a pankaryotic
distribution in a number of uncharacterized proteins.
Length = 357
Score = 26.1 bits (58), Expect = 7.3
Identities = 4/19 (21%), Positives = 10/19 (52%)
Query: 16 MNKIAEHVKDNVSDDKYKE 34
++A+ + D +Y+E
Sbjct: 171 AIEMAKILGDTEDAARYRE 189
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 26.2 bits (58), Expect = 8.2
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 29 DDKYKESELALEELGAQLSKSKLQVSDLMEEHQIAKRATEAQWAKDKEAITCRACDKE 86
+ E E LE+ +L+K + ++ L+ E + +R E + K ++ +T + +
Sbjct: 307 ERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIE-EERKRRDKLTEEYAELK 363
>gnl|CDD|232882 TIGR00222, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase.
Members of this family are 3-methyl-2-oxobutanoate
hydroxymethyltransferase, the first enzyme of the
pantothenate biosynthesis pathway. An alternate name is
ketopantoate hydroxymethyltransferase [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pantothenate
and coenzyme A].
Length = 263
Score = 25.9 bits (57), Expect = 8.7
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 12/49 (24%)
Query: 24 KDNVSDDKYKESELALEELGAQLSKSKLQVSDLMEEH---QIAKRATEA 69
KD + K E LALEE GAQL L+ E ++A + TEA
Sbjct: 154 KDEEAAKKLLEDALALEEAGAQL---------LVLECVPVELAAKITEA 193
>gnl|CDD|116585 pfam07975, C1_4, TFIIH C1-like domain. The carboxyl-terminal
region of TFIIH is essential for transcription activity.
This regions binds three zinc atoms through two
independent domain. The first contains a C4 zinc finger
motif, whereas the second is characterized by a
CX(2)CX(2-4)FCADCD motif. The solution structure of the
second C-terminal domain revealed homology with the
regulatory domain of protein kinase C (pfam00130).
Length = 48
Score = 23.9 bits (52), Expect = 9.0
Identities = 7/33 (21%), Positives = 11/33 (33%), Gaps = 4/33 (12%)
Query: 79 TCRACDKEFTVTRR----RHHCRNCGEIFCNMC 107
C C ++ + C C +FC C
Sbjct: 1 FCYGCQQKLPDGINKTSSVYRCPKCKNVFCLDC 33
>gnl|CDD|205894 pfam13719, zinc_ribbon_5, zinc-ribbon domain. This family consists
of a single zinc ribbon domain, ie half of a pair as in
family DZR, pfam12773.
Length = 37
Score = 23.7 bits (52), Expect = 9.2
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 7/33 (21%)
Query: 78 ITCRACDKEFTV-------TRRRHHCRNCGEIF 103
ITC C ++ + R+ C CG +F
Sbjct: 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35
>gnl|CDD|183213 PRK11582, PRK11582, flagella biosynthesis protein FliZ;
Provisional.
Length = 169
Score = 25.4 bits (56), Expect = 9.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 96 CRNCGEIFCNMCSD 109
CR C ++ CN SD
Sbjct: 72 CRFCSDLHCNTQSD 85
>gnl|CDD|233876 TIGR02464, ribofla_fusion, conserved hypothetical protein,
ribA/ribD-fused. This model describes a sequence
region that occurs in at least three different
polypeptide contexts. It is found fused to GTP
cyclohydrolase II, the RibA of riboflavin biosynthesis
(TIGR00505), as in Vibrio vulnificus. It is found fused
to riboflavin biosynthesis protein RibD (TIGR00326) in
rice and Arabidopsis. It occurs as a standalone protein
in a number of bacterial species in varied contexts,
including single gene operons and bacteriophage
genomes. The member from E. coli currently is named
YbiA. The function(s) of members of this family is
unknown.
Length = 153
Score = 25.4 bits (56), Expect = 9.8
Identities = 8/34 (23%), Positives = 13/34 (38%), Gaps = 3/34 (8%)
Query: 64 KRATEAQWAKDKEAITCRACDKEFTVTRRRHHCR 97
+ E QW + K + RA +F+ R
Sbjct: 69 RGFLEKQWDQVKYEVMRRALLAKFSTH---ADLR 99
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
0.316 0.128 0.375
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,580,409
Number of extensions: 545772
Number of successful extensions: 741
Number of sequences better than 10.0: 1
Number of HSP's gapped: 733
Number of HSP's successfully gapped: 88
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 41 (21.7 bits)
S2: 54 (24.6 bits)