RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15370
(393 letters)
>gnl|CDD|220714 pfam10357, Kin17_mid, Domain of Kin17 curved DNA-binding protein.
Kin17_mid is the conserved central 169 residue region of
a family of Kin17 proteins. Towards the N-terminal end
there is a zinc-finger domain, and in human and mouse
members there is a RecA-like domain further downstream.
The Kin17 protein in humans forms intra-nuclear foci
during cell proliferation and is re-distributed in the
nucleoplasm during the cell cycle.
Length = 127
Score = 190 bits (484), Expect = 5e-60
Identities = 73/126 (57%), Positives = 100/126 (79%)
Query: 52 RQLLLFADNADQYLDEFSREFEEGYLELLRRQFSTRRVFANKVYQDYIADREHVHMNATQ 111
RQ+LLF N +++D+FS+EFE+ +L+LLR + +R+ ANKVY +YIAD++HVHMNAT+
Sbjct: 1 RQMLLFGQNPKKFIDQFSKEFEKDFLQLLRTRHGEKRIHANKVYNEYIADKDHVHMNATR 60
Query: 112 WETLTEFVKHLGKSGKCVVDETEKGWFVTYIDRDPETIAFQQKMAKKEKMEQDDNERNME 171
W +LTEFVK+LG+ GKC V+ETEKGWF+TYIDR PE + Q+++ KKEK E+ D ER +
Sbjct: 61 WTSLTEFVKYLGREGKCKVEETEKGWFITYIDRSPEALKRQEELRKKEKQEKTDEEREQK 120
Query: 172 FLERQI 177
LE QI
Sbjct: 121 LLEEQI 126
>gnl|CDD|240519 cd13155, KOW_KIN17, KOW_Kin17 is a RNA-binding motif. KOW domain
of the KIN17protein contributes to the RNA-binding
properties of the whole protein. KOW domain is known as
an RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. KIN17 is conserved from yeast
to human that ubiquitously expressed at low levels in
mammals tissue and have functions in DNA replication,
DNA repair and cell cycle control.
Length = 54
Score = 60.2 bits (147), Expect = 4e-12
Identities = 18/53 (33%), Positives = 29/53 (54%)
Query: 341 GRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHICKI 393
G +VL++ G Y+G +A L+ I+ D +A V L +VV + Y I K+
Sbjct: 2 GGRVLVVNGAYRGCEATLESIDEDKFSATVRLDSGPLKGRVVEGVPYEDISKL 54
>gnl|CDD|240517 cd13153, KOW_GPKOW_B, KOW motif of the "G-patch domain and KOW
motifs-containing protein" (GPKOW) repeat B. GPKOW
contains one G-patch domain and two KOW motifs. GPKOW is
a nuclear protein that regulated by catalytic (C)
subunit of Protein Kinase A (PKA) and bind RNA in vivo.
PKA may be involved in regulating multiple steps in
post-transcriptional processing of pre-mRNAs. KOW domain
is known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. GPKOW is also known
as the T54 protein or MOS2 homolog.
Length = 51
Score = 37.5 bits (88), Expect = 5e-04
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 344 VLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHIC 391
V+++ GK++G+ L + + A V+L+D D VV + Y IC
Sbjct: 4 VMVVRGKHRGQVGKLLERDKKKETAVVQLLD---DFSVVT-LSYDDIC 47
>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 = 34.4 bits (80), Expect = 0.004
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 26 WYCQMCQKQCRDENGFKCHTSSEAH 50
+YC++C E+ K H + H
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>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 = 31.8 bits (73), Expect = 0.029
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 25 RWYCQMCQKQCRDENGFKCHTSSEAHQ 51
++YC C K + EN + H S+ H+
Sbjct: 1 QFYCVACDKYFKSENALENHLKSKKHK 27
>gnl|CDD|227493 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 35.8 bits (82), Expect = 0.041
Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 5/45 (11%)
Query: 338 PNLGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVV 382
P +G+ V I CG+YKG V+KD +D A VEL H +NK V
Sbjct: 352 PAIGKTVRIRCGEYKGHLGVVKD--VDRNIARVEL---HSNNKFV 391
>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 = 31.1 bits (71), Expect = 0.065
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 25 RWYCQMCQKQCRDENGFKCHTSSEAHQRQLLLF 57
+YC++C DE + H + H++ +
Sbjct: 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
>gnl|CDD|240509 cd06085, KOW_Spt5_5, KOW domain of Spt5, repeat 5. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 52
Score = 30.9 bits (71), Expect = 0.090
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 340 LGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHI 390
+G+ V I G YKG ++KD A VEL H NK + +D S +
Sbjct: 6 IGKTVRIRKGPYKGYIGIVKDAT--GTTARVEL---HSKNKTI-TVDRSRL 50
>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames (Kyrpides,
Ouzounis and Woese). KOW domain is known as an
RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The KOW motif contains an
invariants glycine residue and comprises alternating
blocks of hydrophilic and hydrophobic residues.
Length = 49
Score = 30.7 bits (70), Expect = 0.13
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 341 GRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRNIDYSHIC 391
G V +L G YKG + V+ DI+ V+ + + +
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKG--ATGSKGAELKVRFDDVD 49
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 32.9 bits (75), Expect = 0.29
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 4/96 (4%)
Query: 174 ERQIALGKEKAAQNAQQQDPVSNELIRNEDEKLSLKLE--TFKKPS--SSSISLKKVNLD 229
++ I L E A+ Q D EL R + + LKLE K S +S L +N +
Sbjct: 388 DKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLNEE 447
Query: 230 KDVSESGPSSSSKKFSGEKRKLTALEQIKLEEEEAK 265
E S +++ EK L+ + IK E E+AK
Sbjct: 448 LSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAK 483
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 28.2 bits (64), Expect = 0.51
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 341 GRQVLILCGKYKGEKAVLKDINIDDCNANVE 371
G V ++ G +KG+K + +++ +VE
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains separated
by a hinge in the middle. The eukaryotic SMC proteins
form two kind of heterodimers: the SMC1/SMC3 and the
SMC2/SMC4 types. These heterodimers constitute an
essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 31.9 bits (72), Expect = 0.68
Identities = 26/192 (13%), Positives = 74/192 (38%), Gaps = 6/192 (3%)
Query: 147 ETIAFQQKMAKKEKMEQDDNERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRNEDEKL 206
+ + +E++E+ + E E L +++ L +E+ + + + S E E++K
Sbjct: 843 LKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKE 902
Query: 207 SLKLETFK-KPSSSSISLKKVNLDKDVSESGPSSSSKKFSGEKRKLTALEQIKLEEEEAK 265
+ +++ ++ + S ++ E+ E+ EEEE +
Sbjct: 903 LEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEER 962
Query: 266 KKRIDQERQNSGEESWLHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSKHK 325
KR+ ++ G N++ + E++ K + E++ ++ ++ + +
Sbjct: 963 NKRLLLAKEELGN-----VNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREIIEETC 1017
Query: 326 IKLDQEHLETVI 337
+ + V
Sbjct: 1018 QRFKEFLELFVS 1029
Score = 30.7 bits (69), Expect = 1.7
Identities = 27/139 (19%), Positives = 63/139 (45%), Gaps = 4/139 (2%)
Query: 142 IDRDPETIAFQQKMAKKEKMEQDDNERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRN 201
+ + + +K KKEK E ++ E+ ++ LE + +E+ Q + Q +L +
Sbjct: 317 LKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQ----EKLEQL 372
Query: 202 EDEKLSLKLETFKKPSSSSISLKKVNLDKDVSESGPSSSSKKFSGEKRKLTALEQIKLEE 261
E+E L+ K ++ SS++ ++ K+ E + E+ L ++ +L+
Sbjct: 373 EEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKI 432
Query: 262 EEAKKKRIDQERQNSGEES 280
E ++ ++ ++ EE
Sbjct: 433 VEELEESLETKQGKLTEEK 451
>gnl|CDD|225322 COG2602, COG2602, Beta-lactamase class D [Defense mechanisms].
Length = 254
Score = 30.4 bits (69), Expect = 1.4
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 123 GKSGKCVVDETEKGWFVTYIDRDPETIAF 151
GK+G +V+ GWFV +++ + F
Sbjct: 195 GKTGTGIVNTKNLGWFVGWVETNENKYVF 223
>gnl|CDD|225811 COG3272, COG3272, Uncharacterized conserved protein [Function
unknown].
Length = 163
Score = 29.7 bits (67), Expect = 1.4
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 47 SEAHQRQLLLFADNADQY-LDEFSREFEEGYLELLRRQFSTRR 88
S+ R+L F Q+ LD+F E+ E ++LL +
Sbjct: 43 SQPEYRKLGPFVAEIHQWQLDDFINEYRERLMQLLSHPAKPKN 85
>gnl|CDD|218311 pfam04888, SseC, Secretion system effector C (SseC) like family.
SseC is a secreted protein that forms a complex together
with SecB and SecD on the surface of Salmonella. All
these proteins are secreted by the type III secretion
system. Many mucosal pathogens use type III secretion
systems for the injection of effector proteins into
target cells. SecB, SseC and SecD are inserted into the
target cell membrane. where they form a small pore or
translocon. In addition to SseC, this family includes
the bacterial secreted proteins PopB, PepB, YopB and
EspD which are thought to be directly involved in pore
formation, and type III secretion system translocon.
Length = 303
Score = 30.5 bits (69), Expect = 1.5
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 153 QKMAKKEKMEQDDNERNMEFLERQIALGKEKAAQNAQQQD 192
QK A K + + ME L+ I KE+ + +Q
Sbjct: 240 QKEAGKLEADLALLRAEMEQLQAVIKQLKEEFKKLQEQFQ 279
>gnl|CDD|240510 cd06086, KOW_Spt5_6, KOW domain of Spt5, repeat 6. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 58
Score = 27.9 bits (63), Expect = 1.6
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 331 EHLETVIPNLGRQVLILCGKYKGEKAVLKDINID 364
EHLE V P G +V ++ G+ +G L I+ID
Sbjct: 1 EHLEPVPPEKGDRVKVIKGEDRGSTGEL--ISID 32
>gnl|CDD|171815 PRK12911, PRK12911, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 1403
Score = 29.8 bits (67), Expect = 3.6
Identities = 34/168 (20%), Positives = 66/168 (39%), Gaps = 30/168 (17%)
Query: 166 NERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRNEDEKL---SLKLETFKKPSSSSIS 222
+ + FL R + ++ A ++ + +E ++ ++L +L + +SIS
Sbjct: 211 SRKTQAFLSRFFSSERDFTAFLSRLESLSQDEEVKEARQELLDAVYELLHSRACRWNSIS 270
Query: 223 LKKVNLDKDVSESGPSSSSKKFSGEKRK---------------LTALEQIKLEEEEAK-K 266
K V D SE P SS + + ++RK L+ +++ + A K
Sbjct: 271 PKIVGNVLDCSELSPFFSSMELTAKERKLLFHLDADVLAKRQQLSGEQRLDFDSLLAVEK 330
Query: 267 KRIDQERQNSGEES-------WLHKNIIVKIVTKNLGEKFYKKKGTVE 307
+ + S EE+ K+ KIV + G + +G VE
Sbjct: 331 QHLATRLNRSVEETEFGFAFRLRDKDASGKIVLQ--GHRVC--QGIVE 374
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 28.9 bits (65), Expect = 3.8
Identities = 29/142 (20%), Positives = 53/142 (37%), Gaps = 14/142 (9%)
Query: 171 EFLERQIALGKEK------AAQNAQQQDPVSNELIRNEDEKLSLKLETFKKPSSSSISLK 224
E E + A +K + SNE ++DE+ +K + ++ + +S +
Sbjct: 62 ELEEAERAHKSKKENKLAIEDADKSTNLDASNEGDEDDDEEDEIKRKRIEEDARNSDADD 121
Query: 225 KVNLDKDVSESGPSSSSKKFSGEKRKLTALEQIK---LEEEEAKKKRIDQERQNSGEESW 281
+ S S L LE+IK EE+E +++ E + + EE
Sbjct: 122 SDSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEKAAEEEKAREEEI 181
Query: 282 LHKNIIVKIVTKNLGEKFYKKK 303
L N ++ N F K+
Sbjct: 182 LTGNPLL-----NTSGDFKVKR 198
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.3 bits (66), Expect = 4.6
Identities = 26/170 (15%), Positives = 67/170 (39%), Gaps = 5/170 (2%)
Query: 173 LERQIALGKEKAAQNAQQQDPVSNELIRNEDEKLSLKLETFKKPSSSSISLKKVNLDKDV 232
LE +I+L +E+ + + + + L +++ +LK E ++ + + + ++
Sbjct: 300 LEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEA 359
Query: 233 SESGPSSSSKKFSGEKRKLTAL--EQIKLEEEEAK---KKRIDQERQNSGEESWLHKNII 287
E S + AL E +LE E A+ + + S EE +
Sbjct: 360 KEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSER 419
Query: 288 VKIVTKNLGEKFYKKKGTVEKVIDKYAAIVSLLDSKHKIKLDQEHLETVI 337
++ + + L E + + ++ + + L + +++ + LE +
Sbjct: 420 LEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELEREL 469
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 28.7 bits (65), Expect = 5.5
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 249 RKLTALEQIKLEEEEAKK-KRIDQERQNSGEESWLH 283
R+LT LE KLE+E + K I+ + E WL+
Sbjct: 409 RRLTKLEVEKLEKELKELEKEIEDLEKILASEEWLN 444
>gnl|CDD|225074 COG2163, RPL14A, Ribosomal protein L14E/L6E/L27E [Translation,
ribosomal structure and biogenesis].
Length = 125
Score = 27.4 bits (61), Expect = 6.0
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 340 LGRQVLILCGKYKGEKAVLKDINIDDCNANVELIDPHYDNKVVRN--IDYSHI 390
+GR V++ G++ G+K V+ I IDD N LI K V I+ H+
Sbjct: 7 VGRVVVVTAGRFAGKKVVIVKI-IDD---NFVLITGPKKVKGVPRRRINIKHL 55
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.5 bits (64), Expect = 6.2
Identities = 28/133 (21%), Positives = 54/133 (40%), Gaps = 13/133 (9%)
Query: 152 QQKMAKKEKMEQDDNERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRNEDEKLSLKLE 211
++ E+ ++ + E+ E E + L KEK + +Q+ + +
Sbjct: 102 KKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQK----------AQQAAKQRTP 151
Query: 212 TFKKPSSSSISLKKVNLDKDVSESGPSSSSKKF-SGEKRKLTALEQIKLEEEEA--KKKR 268
KK ++ S S K + K+ E +KL +Q + EE KK++
Sbjct: 152 KHKKEAAESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQ 211
Query: 269 IDQERQNSGEESW 281
++ER+ EE+W
Sbjct: 212 EEEERKQKAEEAW 224
>gnl|CDD|240512 cd06088, KOW_RPL14, KOW motif of Ribosomal Protein L14. RPL14 is a
component of the large ribosomal subunit in both archaea
and eukaryotes with KOW motif at its N terminal. KOW
domain is known as an RNA-binding motif that is shared
so far among some families of ribosomal proteins, the
essential bacterial transcriptional elongation factor
NusG, the eukaryotic chromatin elongation factor Spt5,
the higher eukaryotic KIN17 proteins and Mtr4.
Auto-antibodies to RPL14 in humans have been associated
with systemic lupus erythematosus . Although RPL14 is
well conserved, it is not found in all archaea, and
therefore it is presumably not essential.
Length = 76
Score = 26.3 bits (59), Expect = 7.3
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 4/35 (11%)
Query: 340 LGRQVLILCGKYKGEKAVLKDINIDDCNANVELID 374
+GR VL G+ KG+ V+ DI ID+ NV L+D
Sbjct: 3 IGRVVLSKAGRDKGKLYVIVDI-IDE---NVVLVD 33
>gnl|CDD|233409 TIGR01429, AMP_deaminase, AMP deaminase. This model describes AMP
deaminase, a large, well-conserved eukaryotic protein
involved in energy metabolism. Most members of the
family have an additional, poorly alignable region of
150 amino acids or more N-terminal to the region
included in the model.
Length = 611
Score = 28.7 bits (64), Expect = 7.4
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 14/86 (16%)
Query: 306 VEKVIDKYAAIVSLLDSKH-----KIKLDQEHLETVIPNLGRQVLILCGKYKGEKAVLKD 360
V KV D + + ++ KH K KL E ETVI G+++ + + V
Sbjct: 169 VRKV-DTHIHAAASMNQKHLLRFIKHKLKTEPDETVIERDGKKLTL--------REVFDS 219
Query: 361 INIDDCNANVELIDPHYDNKVVRNID 386
+++D + +V+ +D H D D
Sbjct: 220 LHLDPYDLSVDTLDVHADRNTFHRFD 245
>gnl|CDD|225821 COG3283, TyrR, Transcriptional regulator of aromatic amino acids
metabolism [Transcription / Amino acid transport and
metabolism].
Length = 511
Score = 28.2 bits (63), Expect = 7.9
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 11/56 (19%)
Query: 59 DNADQYLDEFSREFEEGYLELLRRQF-STRRV----------FANKVYQDYIADRE 103
D + LDE FE L L R + STR++ ANK+ Q I ++
Sbjct: 456 DALEGSLDEIVSRFERSVLTRLYRSYPSTRKLAKRLGVSHTAIANKLRQYGIGQKK 511
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 25.0 bits (56), Expect = 7.9
Identities = 5/24 (20%), Positives = 14/24 (58%)
Query: 341 GRQVLILCGKYKGEKAVLKDINID 364
G V ++ G +KG+ + +++ +
Sbjct: 5 GDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|220410 pfam09798, LCD1, DNA damage checkpoint protein. This is a family
of proteins which regulate checkpoint kinases. In
Schizosaccharomyces pombe this protein is called Rad26
and in Saccharomyces cerevisiae it is called LCD1.
Length = 648
Score = 28.2 bits (63), Expect = 8.3
Identities = 39/187 (20%), Positives = 66/187 (35%), Gaps = 15/187 (8%)
Query: 155 MAKKEKMEQDDNERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRNEDEKLSLKLET-- 212
+ K M Q + + ++ KEK Q Q+ + EL EDE+ L LE
Sbjct: 2 LRDKLDMLQQQKQEERNKQKSRVNELKEKHDQELQK---LKQELQSLEDERKFLVLEQRG 58
Query: 213 FKKPSSSSISLKKVNLDKDVSESGPSSSSKKFSGEKRKLTALEQIKLEEEEAKKKRIDQE 272
+ NL K S++ + + + K+K + +K + I +
Sbjct: 59 LSANDLRTELSPPSNLLKT-SDASHIADESQPNSIKQKKREISPVKELVPLNPNRIIKDD 117
Query: 273 RQNSGEESWLHKNIIVKIVTKNLGEKFYKKKGTVEKVIDKY--------AAIVSLL-DSK 323
+ + HK K+ T + K +K +IVSLL K
Sbjct: 118 KSLFLDHILNHKIEGSKLSTLEMLNHIKLDKIDEILGKNKKISSGDPLGKSIVSLLLRLK 177
Query: 324 HKIKLDQ 330
+KLD+
Sbjct: 178 SNLKLDE 184
>gnl|CDD|221595 pfam12479, DUF3698, Protein of unknown function (DUF3698). This
domain family is found in eukaryotes, and is typically
between 89 and 105 amino acids in length.
Length = 107
Score = 26.8 bits (59), Expect = 8.3
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 4/75 (5%)
Query: 161 MEQDDNERNMEFLERQIALGKEKAAQNAQQQDPVSNELIRN--EDEKLSLKLETFK--KP 216
+ D E LE + + +Q DP N R + + SL+L
Sbjct: 18 KNEADAIDTKEKLEICFGIAYKTGNYYLEQGDPFFNVAPRPFEQSSRKSLRLSESGNQDR 77
Query: 217 SSSSISLKKVNLDKD 231
+ + L L K
Sbjct: 78 HWNPLILFAEVLSKY 92
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 0.131 0.371
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,577,799
Number of extensions: 1905921
Number of successful extensions: 2040
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1995
Number of HSP's successfully gapped: 125
Length of query: 393
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 294
Effective length of database: 6,546,556
Effective search space: 1924687464
Effective search space used: 1924687464
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: 60 (27.0 bits)