RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5888
(447 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 45.5 bits (108), Expect = 4e-07
Identities = 18/25 (72%), Positives = 21/25 (84%)
Query: 245 NLTRHLRTHTGEQPYKCKYCERSFS 269
NL RH+RTHTGE+PYKC C +SFS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 39.3 bits (92), Expect = 7e-05
Identities = 14/25 (56%), Positives = 19/25 (76%), Gaps = 1/25 (4%)
Query: 273 NLQRHVRNIHNKEKPFKCPLCDRCF 297
NL+RH+R H EKP+KCP+C + F
Sbjct: 1 NLRRHMR-THTGEKPYKCPVCGKSF 24
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 39.6 bits (93), Expect = 6e-05
Identities = 14/21 (66%), Positives = 15/21 (71%)
Query: 233 CKFCGKVFPRSANLTRHLRTH 253
C CGK F R +NL RHLRTH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 35.4 bits (82), Expect = 0.002
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 289 KCPLCDRCFGQQTNLDRHLKKH 310
KCP C + F +++NL RHL+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 32.3 bits (74), Expect = 0.020
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 260 KCKYCERSFSISSNLQRHVR 279
KC C +SFS SNL+RH+R
Sbjct: 1 KCPDCGKSFSRKSNLKRHLR 20
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 38.2 bits (89), Expect = 2e-04
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 231 YACKFCGKVFPRSANLTRHLRTH 253
Y C CGKVF + L H+RTH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 35.1 bits (81), Expect = 0.002
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 288 FKCPLCDRCFGQQTNLDRHLKKH 310
++CP C + F ++ L H++ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 31.7 bits (72), Expect = 0.040
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 259 YKCKYCERSFSISSNLQRHVRNIH 282
Y+C C + F S L+ H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMR-TH 23
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 35.3 bits (81), Expect = 0.002
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 231 YACKFCGKVFPRSANLTRHLRTH 253
+ C CGK F L RHLR H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 34.5 bits (79), Expect = 0.003
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 288 FKCPLCDRCFGQQTNLDRHLKKH 310
FKCPLC + F + L RHL+KH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 34.2 bits (78), Expect = 0.005
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 259 YKCKYCERSFSISSNLQRHVRNIH 282
+KC C +SFS L+RH+R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 36.4 bits (84), Expect = 0.007
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 258 PYKCKYCERSFSISSNLQRHVR-NIHNKEKPFKCPLCDRCF-GQQTNLDRHLKKH 310
PY C C FS S +L++H+R H+K CP+C + F + LD KKH
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK----VCPVCGKEFRNTDSTLDHVCKKH 123
Score = 34.1 bits (78), Expect = 0.036
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 5/86 (5%)
Query: 201 LIRSQLPPLANSPKQFQES---ISNNTGKPKDRYACKFCGKVFPRSANLTRHLRTHTGEQ 257
LIR+ + L +P+ ES T K Y C C F S +L +H+R E
Sbjct: 41 LIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRY--TEH 98
Query: 258 PYKCKYCERSFSISSNLQRHVRNIHN 283
C C + F + + HV HN
Sbjct: 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 33.9 bits (78), Expect = 0.010
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 5/28 (17%)
Query: 260 KCKYCERSFSIS-----SNLQRHVRNIH 282
KCKYC + S S SNL+RH+R H
Sbjct: 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKH 47
Score = 29.7 bits (67), Expect = 0.27
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 233 CKFCGKVFPRSA-----NLTRHLRT 252
CK+CGK RS+ NL RHLR
Sbjct: 21 CKYCGKKLSRSSKGGTSNLRRHLRR 45
>gnl|CDD|202452 pfam02892, zf-BED, BED zinc finger.
Length = 43
Score = 32.2 bits (74), Expect = 0.034
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 260 KCKYCERSFSIS---SNLQRHVRNIH 282
+CKYC + S SNL+RH+
Sbjct: 17 RCKYCGKILSGGGGTSNLKRHLVRKC 42
Score = 31.4 bits (72), Expect = 0.061
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 233 CKFCGKVFPRSA---NLTRHLRT 252
CK+CGK+ NL RHL
Sbjct: 18 CKYCGKILSGGGGTSNLKRHLVR 40
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 30.3 bits (69), Expect = 0.12
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 231 YACKFCGKVFPRSANLTRHLRTH 253
+ C CGK F L H ++H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 33.8 bits (78), Expect = 0.18
Identities = 15/88 (17%), Positives = 26/88 (29%), Gaps = 21/88 (23%)
Query: 233 CKFCGKVFPRSANLTRHLRTHTGEQPYKCKYCERSFSISSNLQRHVRNI--------HNK 284
CK CG+ P + E C CER + + L + +
Sbjct: 395 CKVCGREEPIAE----------DEDEGLCPTCERLYELGKELLKDDSFLVTEKEDGGKKL 444
Query: 285 EKPFKCPLC---DRCFGQQTNLDRHLKK 309
K L + ++ L+ L +
Sbjct: 445 PKFNGYYLLFAYEADEYEELALEDELVR 472
>gnl|CDD|133213 cd05082, PTKc_Csk, Catalytic domain of the Protein Tyrosine Kinase,
C-terminal Src kinase. Protein Tyrosine Kinase (PTK)
family; C-terminal Src kinase (Csk); catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. The Csk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing the Src homology domains, SH3 and
SH2, N-terminal to the catalytic tyr kinase domain. They
negatively regulate the activity of Src kinases that are
anchored to the plasma membrane. To inhibit Src kinases,
Csk is translocated to the membrane via binding to
specific transmembrane proteins, G-proteins, or adaptor
proteins near the membrane. Csk catalyzes the tyr
phosphorylation of the regulatory C-terminal tail of Src
kinases, resulting in their inactivation. Csk is
expressed in a wide variety of tissues. As a negative
regulator of Src, Csk plays a role in cell
proliferation, survival, and differentiation, and
consequently, in cancer development and progression. In
addition, Csk also shows Src-independent functions. It
is a critical component in G-protein signaling, and
plays a role in cytoskeletal reorganization and cell
migration.
Length = 256
Score = 33.0 bits (75), Expect = 0.22
Identities = 31/132 (23%), Positives = 54/132 (40%), Gaps = 18/132 (13%)
Query: 90 NRNLILRSPTPSENLEVNYRSSPASTKDELQVQDDDR-----SSPPNIKSRSLSTYPVLF 144
+R+L R+ SE+ V S TK+ QD + ++P ++ + ST ++
Sbjct: 125 HRDLAARNVLVSED-NVAKVSDFGLTKEASSTQDTGKLPVKWTAPEALREKKFSTKSDVW 183
Query: 145 PHPVMLEAMYR-ARDKVPRLPLP---------YSMNSPPGYPGRPAYPFINSGLLNGHPI 194
++L +Y R PR+PL Y M++P G P P + +
Sbjct: 184 SFGILLWEIYSFGRVPYPRIPLKDVVPRVEKGYKMDAPDGCP--PVVYDVMKQCWHLDAA 241
Query: 195 QSPTIDLIRSQL 206
P+ +R QL
Sbjct: 242 TRPSFLQLREQL 253
>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 = 32.0 bits (73), Expect = 0.27
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 220 ISNNTGKPKDRYACKFCGKVFPRSANLTRHLRTHTGEQPYKCKYCERSF 268
I +G+ + Y C CG+++PR R +R H Y+C C
Sbjct: 109 IEVVSGRKRYIYRCGSCGQLYPR----KRRIRRHK----YRCGRCGGKL 149
>gnl|CDD|220445 pfam09858, DUF2085, Predicted membrane protein (DUF2085). This
domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 93
Score = 30.7 bits (70), Expect = 0.32
Identities = 8/24 (33%), Positives = 10/24 (41%), Gaps = 2/24 (8%)
Query: 275 QRHVRNIHNKEKPFKCPLCDRCFG 298
Q R+ F P+C RC G
Sbjct: 4 QLPERSFFFGGHQF--PVCARCTG 25
>gnl|CDD|233199 TIGR00939, 2a57, Equilibrative Nucleoside Transporter (ENT).
[Transport and binding proteins, Nucleosides, purines
and pyrimidines].
Length = 437
Score = 32.8 bits (75), Expect = 0.33
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 377 YNYYLPHQEDAENNNNINSKKEILSPSEKDNYSSRSSTSSLGSTHAVPHPPRTKDVPE 434
YYL + D + +K E+ S +E++ S P + D P+
Sbjct: 201 ARYYLQKKLDKGAGED-ETKGELRSKAEQNGIPHGGDQPSPTLVLDWEKEPESPDEPQ 257
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 29.6 bits (66), Expect = 0.39
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 231 YACKFCGKVFPRSANLTRHLRTHTGEQPYKCKYCER 266
Y C CG+++ + ++ HLR H K C+R
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHNTN--LKLSNCKR 39
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 32.1 bits (73), Expect = 0.72
Identities = 16/68 (23%), Positives = 22/68 (32%), Gaps = 4/68 (5%)
Query: 185 NSGLLNGHPIQSPTIDLIRSQLPPLANSPKQFQESISNNTGKPKDRYACKFCGKVFPRSA 244
N G + P + + P SP Q +++ N Y C C F
Sbjct: 32 NDGGIKTQPTSDSIAAVANATKPAAVISPPQSKKATPINPSS----YVCNVCMAEFSSMD 87
Query: 245 NLTRHLRT 252
L H RT
Sbjct: 88 QLAEHQRT 95
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 27.9 bits (63), Expect = 0.81
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 287 PFKCPLCDRCFGQQTNLDRHL--KKH 310
F C CD+ F + L+ HL KKH
Sbjct: 1 QFYCVACDKYFKSENALENHLKSKKH 26
Score = 26.4 bits (59), Expect = 2.4
Identities = 5/22 (22%), Positives = 12/22 (54%)
Query: 258 PYKCKYCERSFSISSNLQRHVR 279
+ C C++ F + L+ H++
Sbjct: 1 QFYCVACDKYFKSENALENHLK 22
Score = 26.4 bits (59), Expect = 2.9
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 230 RYACKFCGKVFPRSANLTRHLRT 252
++ C C K F L HL++
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a zinc-finger
domain with the CxxCx(12)Hx(6)H motif, found in multiple
copies in a wide range of proteins from plants to
metazoans. Some member proteins, particularly those from
plants, are annotated as being RNA-binding.
Length = 25
Score = 27.9 bits (63), Expect = 0.86
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 288 FKCPLCDRCFGQQTNLDRHL--KKH 310
F C LC+ F ++ L HL KKH
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|234471 TIGR04104, cxxc_20_cxxc, cxxc_20_cxxc protein. This small,
uncommon, poorly conserved protein is found primarily in
the Firmicutes. It features are pair of CxxC motifs
separated by about 20 amino acids, followed by a highly
hydrophobic region of about 45 amino acids. It has no
conserved gene neighborhood, and its function is
unknown.
Length = 94
Score = 29.3 bits (66), Expect = 0.97
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 260 KCKYCERSFSISSNLQRHVRNIHNKEKPFKCPLC 293
CK C FS L +++ + +P KCP C
Sbjct: 2 ICKNCNEKFSYKELL----KSLFSLYRPIKCPNC 31
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 31.5 bits (72), Expect = 1.0
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 324 GIPSPSMIHNRCRPPSGILNDDSY---FEEIRSFMGKVSADGNRLVQRVSSLSRANYNY 379
GIP P IH R P L D+ Y E+ GK+ D LV+ L Y
Sbjct: 392 GIPLPG-IHIRVDPEG--LEDNDYEVLLNEVPVEQGKIPPDHVLLVEGSDELVSTGIPY 447
>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 29.3 bits (66), Expect = 1.0
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 10/41 (24%)
Query: 228 KDRYACKFCGKVFPRSANLTRHLRTHTGEQPYKCKYCERSF 268
+ ++ C FCG+ T R TG +KC+ C F
Sbjct: 33 RAKHVCPFCGR--------TTVKRIATG--IWKCRKCGAKF 63
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.2 bits (70), Expect = 1.0
Identities = 21/71 (29%), Positives = 31/71 (43%)
Query: 217 QESISNNTGKPKDRYACKFCGKVFPRSANLTRHLRTHTGEQPYKCKYCERSFSISSNLQR 276
+S + +C C F R +LTRH+R+HTGE+P +C Y S S L+
Sbjct: 20 PKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLEL 79
Query: 277 HVRNIHNKEKP 287
+ P
Sbjct: 80 SRHLRTHHNNP 90
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 31.5 bits (72), Expect = 1.1
Identities = 15/65 (23%), Positives = 21/65 (32%), Gaps = 23/65 (35%)
Query: 232 ACKFCGKVF--PR-SANLTRHLRTHTGEQPYKCKYCERSFSISSNLQRHVRNIHNKEKPF 288
C+ CG + P + LT H T +C YC + + P
Sbjct: 437 LCRDCGYIAECPNCDSPLTLHKATG----QLRCHYCG----------------YQEPIPQ 476
Query: 289 KCPLC 293
CP C
Sbjct: 477 SCPEC 481
>gnl|CDD|205139 pfam12907, zf-met2, Zinc-binding. This is small family of metazoan
zinc-binding proteins.
Length = 40
Score = 27.4 bits (61), Expect = 1.4
Identities = 10/36 (27%), Positives = 13/36 (36%), Gaps = 3/36 (8%)
Query: 259 YKCKYCERSF---SISSNLQRHVRNIHNKEKPFKCP 291
CK C ++F + L H N H K C
Sbjct: 2 IICKICMQTFMCTTSEKLLTEHAENKHPKTDVEACF 37
>gnl|CDD|218562 pfam05342, Peptidase_M26_N, M26 IgA1-specific Metallo-endopeptidase
N-terminal region. These peptidases, which cleave
mammalian IgA, are found in Gram-positive bacteria.
Often found associated with pfam00746, they may be
attached to the cell wall.
Length = 252
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 357 KVSADGNRLVQRVSSLSRANYNYYLPHQEDAENNN 391
K++A LVQ + NY +YL ++ E N
Sbjct: 105 KITAKAPDLVQEADNKYSDNYTFYLEKKKPEEGNV 139
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and recognises
the first three GAG bases of the consensus in a manner
similar to that seen in other classical zinc finger-DNA
complexes. The second basic region forms a helix that
interacts in the major groove recognising the last G of
the consensus, while the first basic region wraps around
the DNA in the minor groove and recognises the A in the
fourth position of the consensus sequence.
Length = 54
Score = 28.0 bits (62), Expect = 1.6
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 278 VRNIHNKEKPFKCPLCDRCFGQQTNLDRHLK 308
+++ E+P CP+C Q NL RHL+
Sbjct: 15 IKSKSQSEQPATCPICQAVIRQSRNLRRHLE 45
>gnl|CDD|226201 COG3676, COG3676, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 126
Score = 29.0 bits (65), Expect = 2.6
Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 341 ILNDDSYFEEIRSFMGKVSADGNRLVQRVSSLSRANYNYYLPHQEDAENNNNINSKKEIL 400
+ D + + + G +++ + + + ++ YL E NN+ I ++EIL
Sbjct: 63 VKPDSIVYTDSFKSYDGLDVSGK--LRKYNGIPKKHFELYLKECEWRFNNSEIPQQREIL 120
Query: 401 SPSEK 405
P
Sbjct: 121 KPLSG 125
>gnl|CDD|200340 TIGR03927, T7SS_EssA_Firm, type VII secretion protein EssA.
Members of this family are associated with type VII
secretion of WXG100 family targets in the Firmicutes,
but not in the Actinobacteria. This highly divergent
protein family consists largely of a central region of
highly polar low-complexity sequence containing
occasional LF motifs in weak repeats about 17 residues
in length, flanked by hydrophobic N- and C-terminal
regions [Protein fate, Protein and peptide secretion and
trafficking].
Length = 150
Score = 28.9 bits (65), Expect = 3.3
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 384 QEDAENNNNINSKKEILSPSEKDNYSSRSSTSS 416
E+A NN + + K+ L SE + SS S ++S
Sbjct: 82 SENATENNTVKATKKQLFSSEYEQTSSSSESTS 114
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type zinc
fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 26.4 bits (59), Expect = 3.5
Identities = 7/28 (25%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 258 PYKCKYCERSFSISSNLQRHVRN-IHNK 284
+ CK C +F+ +++ H++ H K
Sbjct: 3 GFYCKLCNVTFTDEISVEAHLKGKKHKK 30
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 26.1 bits (58), Expect = 4.0
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 259 YKCKYCERSF-SISSNLQRHVRNIHN 283
YKC +C + S L+RH++ H
Sbjct: 1 YKCSHC--PYSSTPKKLERHLKLHHG 24
>gnl|CDD|234859 PRK00893, PRK00893, aspartate carbamoyltransferase regulatory
subunit; Reviewed.
Length = 152
Score = 28.6 bits (65), Expect = 4.1
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 259 YKCKYCERSFS 269
+CKYCE+ FS
Sbjct: 135 LRCKYCEKEFS 145
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 29.0 bits (66), Expect = 5.1
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 144 FPHPVMLEAMYRA-RDKVPRLP 164
F HP + E + A RD +L
Sbjct: 437 FYHPTLSEGLRTALRDLFSKLI 458
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 29.0 bits (66), Expect = 5.2
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 343 NDDSYFEEIRSFMGKVSAD-----GNRLVQRVSSLSRANYNYYLPHQEDAENNNNI 393
N D+ F F+ +V+++ GN LV RV S + +P E + + +
Sbjct: 368 NSDTDFTW-EEFVRRVNSELADKYGN-LVNRVLSFIEKYFGGIVPPGELGDEDREL 421
>gnl|CDD|233936 TIGR02578, cas_TM1811_Csm1, CRISPR-associated protein Cas10/Csm1,
subtype III-A/MTUBE. The family is designated Csm2, for
CRISPR/Cas Subtype Mtube Protein 2. A typical example is
TM1811 from Thermotoga maritima. CRISPR are Clustered
Regularly Interspaced Short Palindromic Repeats. This
protein family belongs to a conserved gene cluster
regularly found near CRISPR repeats [Mobile and
extrachromosomal element functions, Other].
Length = 648
Score = 29.3 bits (66), Expect = 5.3
Identities = 10/58 (17%), Positives = 15/58 (25%), Gaps = 12/58 (20%)
Query: 233 CKFCGKVFPRSANLTRHLRTHTGEQPYKCKYCERSFSISSNLQRHVR-NIHNKEKPFK 289
C CG+ E C C +++ L R R + E
Sbjct: 398 CDICGRAASARE----------IEDLALCDLCAEEYNLGEAL-RADRSFVILDEAGIP 444
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing archaeal-type
C2H2 Zn-finger [General function prediction only].
Length = 65
Score = 26.5 bits (58), Expect = 6.2
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 285 EKPFKCPLCDRCFGQQTNLDRHLKK 309
E+ +CP C F ++ + RH+ K
Sbjct: 15 EEFLRCPRCGMVFRRRKDYIRHVNK 39
>gnl|CDD|222050 pfam13332, Fil_haemagg_2, Haemagluttinin repeat.
Length = 170
Score = 27.5 bits (62), Expect = 8.9
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 386 DAENNNNINSKKEILSPSEKDNYSSRSSTSSLG 418
A N+ +N+ +I + ++ S+ S+ S G
Sbjct: 45 KAGNDVILNAANDINLEAAQNTQSTSSTNKSSG 77
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 27.8 bits (62), Expect = 9.0
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 31 SEEMPFDLSQNTTRSHNGPHMSPAGKPPSSPDSERHEEQPLDLRVDHKK 79
++P DL+Q +H+ P + K PS D H E + + HK
Sbjct: 124 QIQVPTDLAQRFADAHSMPLFETSAKDPSEND---HVEAI-FMTLAHKL 168
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 28.1 bits (63), Expect = 9.6
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 229 DRYACK--FCGKVFPRSANLTR-HLRTHTGEQPYKCKY 263
D + FCG FP S + TR +L+ + Q
Sbjct: 15 DMRPTRVLFCGPEFPASYSYTREYLQKYPFIQVDAVAR 52
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
0.312 0.130 0.386
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,226,131
Number of extensions: 2085087
Number of successful extensions: 1521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1499
Number of HSP's successfully gapped: 61
Length of query: 447
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 347
Effective length of database: 6,502,202
Effective search space: 2256264094
Effective search space used: 2256264094
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 61 (27.4 bits)