RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2814
(176 letters)
>gnl|CDD|239952 cd04516, TBP_eukaryotes, eukaryotic TATA box binding protein (TBP):
Present in archaea and eukaryotes, TBPs are
transcription factors that recognize promoters and
initiate transcription. TBP has been shown to be an
essential component of three different transcription
initiation complexes: SL1, TFIID and TFIIIB, directing
transcription by RNA polymerases I, II and III,
respectively. TBP binds directly to the TATA box
promoter element, where it nucleates polymerase
assembly, thus defining the transcription start site.
TBP's binding in the minor groove induces a dramatic DNA
bending while its own structure barely changes. The
conserved core domain of TBP, which binds to the TATA
box, has a bipartite structure, with intramolecular
symmetry generating a saddle-shaped structure that sits
astride the DNA.
Length = 174
Score = 269 bits (690), Expect = 8e-94
Identities = 103/170 (60%), Positives = 137/170 (80%)
Query: 4 QNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
QN+V T+++GC LDL +I R R +EYNP +F +IM+I P+TT L F SGK++ GAK
Sbjct: 5 QNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAK 64
Query: 64 HEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEP 123
E D KLA+RK+A+I+++LG P K+ FKI NIV +CDV+FP++L+ L H H QFSSYEP
Sbjct: 65 SEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEP 124
Query: 124 ELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKSF 173
ELFPGLIYRMVKP++VLLIFV+G+IV+TGAKSR E+++AF+NIYP+L F
Sbjct: 125 ELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIYQAFENIYPILLQF 174
>gnl|CDD|177693 PLN00062, PLN00062, TATA-box-binding protein; Provisional.
Length = 179
Score = 258 bits (660), Expect = 3e-89
Identities = 100/172 (58%), Positives = 136/172 (79%)
Query: 4 QNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
QN+V T+++ C LDL +I + R +EYNP +F +IM+I P+TT L F SGK++ GAK
Sbjct: 5 QNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAK 64
Query: 64 HEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEP 123
EHD KLA+RK+A+I+++LG P K++ FKI NIV +CDV+FP++L+ L + H FSSYEP
Sbjct: 65 SEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEP 124
Query: 124 ELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKSFKK 175
ELFPGLIYRM +P++VLLIFV+G+IVITGAK R E++ AF+NIYPVL F+K
Sbjct: 125 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYPVLTEFRK 176
>gnl|CDD|238352 cd00652, TBP_TLF, TATA box binding protein (TBP): Present in
archaea and eukaryotes, TBPs are transcription factors
that recognize promoters and initiate transcription. TBP
has been shown to be an essential component of three
different transcription initiation complexes: SL1, TFIID
and TFIIIB, directing transcription by RNA polymerases
I, II and III, respectively. TBP binds directly to the
TATA box promoter element, where it nucleates polymerase
assembly, thus defining the transcription start site.
TBP's binding in the minor groove induces a dramatic DNA
bending while its own structure barely changes. The
conserved core domain of TBP, which binds to the TATA
box, has a bipartite structure, with intramolecular
symmetry generating a saddle-shaped structure that sits
astride the DNA. New members of the TBP family, called
TBP-like proteins (TBLP, TLF, TLP) or TBP-related
factors (TRF1, TRF2,TRP), are similar to the core domain
of TBPs, with identical or chemically similar amino
acids at many equivalent positions, suggesting similar
structure. However, TLFs contain distinct, conserved
amino acids at several positions that distinguish them
from TBP.
Length = 174
Score = 244 bits (626), Expect = 5e-84
Identities = 96/169 (56%), Positives = 133/169 (78%), Gaps = 1/169 (0%)
Query: 4 QNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
QN+V T+++GC LDL +I R +EYNP +F G+IM++ P+TT L F SGK++I GAK
Sbjct: 5 QNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAK 64
Query: 64 HEHDCKLASRKFAKILKQLGHPI-KYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYE 122
E D KLA+RK+A+IL++LG P+ K+ FK+ NIV +CD+ FP++L+ L H + +SYE
Sbjct: 65 SEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYE 124
Query: 123 PELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLK 171
PELFPGLIYRM +P+VVLLIFV+G+IVITGAKSR +++EA + IYP+LK
Sbjct: 125 PELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILK 173
Score = 72.2 bits (178), Expect = 2e-16
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 9/75 (12%)
Query: 92 KIHNIVCTCDVRFPVKLD----ALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGR 147
KI NIV T V +LD AL +++ Y P+ FPG+I R+ +P+ LIF +G+
Sbjct: 3 KIQNIVAT--VNLGCELDLRKIALAARNAE---YNPKRFPGVIMRLREPKTTALIFSSGK 57
Query: 148 IVITGAKSRSELHEA 162
+VITGAKS + A
Sbjct: 58 MVITGAKSEEDAKLA 72
Score = 67.6 bits (166), Expect = 1e-14
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 4 QNMVGTISVGCPLDLNQINSRVR-YSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGA 62
QN+V + +G P+ L ++ + + Y P F GLI ++ P+ L F SGK++I GA
Sbjct: 96 QNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGA 155
Query: 63 KHEHDCKLASRKFAKILKQ 81
K D A K ILK+
Sbjct: 156 KSREDIYEAVEKIYPILKE 174
>gnl|CDD|225012 COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID
and TFIIIB [Transcription].
Length = 185
Score = 204 bits (520), Expect = 8e-68
Identities = 67/175 (38%), Positives = 105/175 (60%), Gaps = 2/175 (1%)
Query: 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLIL 60
+ +N+V ++ +G LDL ++ + +EYNP +F GL+ ++ P+T L F+SGK++
Sbjct: 8 ITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCT 67
Query: 61 GAKHEHDCKLASRKFAKILKQLGHPIKYQ-GFKIHNIVCTCDVRFPVKLDALHHVHSQF- 118
GAK D A +K AK LK G I ++ K+ NIV + D+ + L+A+
Sbjct: 68 GAKSVEDVHRAVKKLAKKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLEN 127
Query: 119 SSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKSF 173
YEPE FPGL+YR+ +PRVVLL+F +G++VITGAKS + +A + I L+
Sbjct: 128 IEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEEL 182
Score = 72.4 bits (178), Expect = 2e-16
Identities = 33/84 (39%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 2 HYQNMVGTISVGCPLDLNQINSRV--RYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLI 59
QN+V + +G L+LN I + EY P +F GL+ ++ PR L F SGKL+I
Sbjct: 100 KVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVI 159
Query: 60 LGAKHEHDCKLASRKFAKILKQLG 83
GAK E D + A K L++LG
Sbjct: 160 TGAKSEEDAEQAVEKIQSRLEELG 183
>gnl|CDD|234746 PRK00394, PRK00394, transcription factor; Reviewed.
Length = 179
Score = 160 bits (406), Expect = 2e-50
Identities = 62/172 (36%), Positives = 103/172 (59%), Gaps = 2/172 (1%)
Query: 4 QNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
+N+V + +G LDL ++ + +EYNP +F GL+ ++ +P+ L F+SGK++ GAK
Sbjct: 4 ENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAK 63
Query: 64 HEHDCKLASRKFAKILKQLGHPIKYQ-GFKIHNIVCTCDVRFPVKLDAL-HHVHSQFSSY 121
D A + K LK+LG + + K+ NIV + D+ + L+A+ + + Y
Sbjct: 64 SVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEY 123
Query: 122 EPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKSF 173
EPE FPGL+YR+ P+VV+L+F +G++VITGAKS + +A + I L+
Sbjct: 124 EPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKILEKLEEL 175
Score = 67.2 bits (165), Expect = 2e-14
Identities = 32/82 (39%), Positives = 48/82 (58%), Gaps = 2/82 (2%)
Query: 4 QNMVGTISVGCPLDLNQI--NSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILG 61
QN+V + +G L+LN I + EY P +F GL+ ++ +P+ L F SGKL+I G
Sbjct: 95 QNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITG 154
Query: 62 AKHEHDCKLASRKFAKILKQLG 83
AK E D + A K + L++LG
Sbjct: 155 AKSEEDAEKAVEKILEKLEELG 176
>gnl|CDD|239954 cd04518, TBP_archaea, archaeal TATA box binding protein (TBP): TBPs
are transcription factors present in archaea and
eukaryotes, that recognize promoters and initiate
transcription. TBP has been shown to be an essential
component of three different transcription initiation
complexes: SL1, TFIID and TFIIIB, directing
transcription by RNA polymerases I, II and III,
respectively. TBP binds directly to the TATA box
promoter element, where it nucleates polymerase
assembly, thus defining the transcription start site.
TBP's binding in the minor groove induces a dramatic DNA
bending while its own structure barely changes. The
conserved core domain of TBP, which binds to the TATA
box, has a bipartite structure, with intramolecular
symmetry generating a saddle-shaped structure that sits
astride the DNA.
Length = 174
Score = 152 bits (385), Expect = 2e-47
Identities = 64/168 (38%), Positives = 103/168 (61%), Gaps = 2/168 (1%)
Query: 5 NMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKH 64
N+V ++ +G LDL ++ + + +EYNP +F GL+ ++ +P+ L F+SGK++ GAK
Sbjct: 6 NIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKS 65
Query: 65 EHDCKLASRKFAKILKQLGHPIKYQ-GFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEP 123
D A ++ K LK G + + K+ NIV + D+ V LDA+ + + YEP
Sbjct: 66 VEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASADLGREVNLDAIA-IGLPNAEYEP 124
Query: 124 ELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLK 171
E FPGL+YR+ +P+VVLL+F +G++VITGAKS + A + + LK
Sbjct: 125 EQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLSRLK 172
Score = 73.1 bits (180), Expect = 1e-16
Identities = 30/79 (37%), Positives = 46/79 (58%)
Query: 4 QNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
QN+V + +G ++L+ I + +EY P +F GL+ ++ P+ L F SGK++I GAK
Sbjct: 96 QNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAK 155
Query: 64 HEHDCKLASRKFAKILKQL 82
E D K A K LK+L
Sbjct: 156 SEEDAKRAVEKLLSRLKEL 174
Score = 65.7 bits (161), Expect = 5e-14
Identities = 35/83 (42%), Positives = 49/83 (59%), Gaps = 5/83 (6%)
Query: 92 KIHNIVCTCDVRFPVKLDALHHVHSQF--SSYEPELFPGLIYRMVKPRVVLLIFVNGRIV 149
KI NIV + V +LD L V ++ + Y P+ FPGL+YR+ P++ LIF +G++V
Sbjct: 3 KIENIVAS--VDLGQELD-LEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMV 59
Query: 150 ITGAKSRSELHEAFDNIYPVLKS 172
TGAKS +LH A I LK
Sbjct: 60 CTGAKSVEDLHRAVKEIIKKLKD 82
>gnl|CDD|239953 cd04517, TLF, TBP-like factors (TLF; also called TLP, TRF, TRP),
which are found in most metazoans. TLFs and TBPs have
well-conserved core domains; however, they only share
about 60% similarity. TLFs, like TBPs, interact with
TFIIA and TFIIB, which are part of the basal
transcription machinery. Yet, in contrast to TBPs, TLFs
seem not to interact with the TATA-box and even have a
negative effect on the transcription of TATA-containing
promoters. Recent results indicate that TLFs are
involved in the transcription via TATA-less promoters.
Length = 174
Score = 148 bits (375), Expect = 5e-46
Identities = 63/168 (37%), Positives = 105/168 (62%), Gaps = 2/168 (1%)
Query: 5 NMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKH 64
N+V S+ C +DL ++ R EYNP ++ + M++ PR T + SGK+ I GA
Sbjct: 7 NVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATS 65
Query: 65 EHDCKLASRKFAKILKQLGHP-IKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEP 123
E + K A+R+ A++L++LG +++ F++ N++ TC + FP++LD L + +SYEP
Sbjct: 66 EEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEP 125
Query: 124 ELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLK 171
EL PG++YR+ PR L IF G + +TGA+S ++ EA + IYP++
Sbjct: 126 ELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVF 173
Score = 40.4 bits (95), Expect = 1e-04
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 5 NMVGTISVGCPLDLNQINSRVR-YSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
N++ T S+ P+ L+++ ++ R + Y P G++ +I PR T F +G + + GA+
Sbjct: 97 NVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGAR 156
Query: 64 HEHDCKLASRKFAKILKQ 81
D + A K I+ +
Sbjct: 157 SMEDVREAVEKIYPIVFE 174
>gnl|CDD|201174 pfam00352, TBP, Transcription factor TFIID (or TATA-binding
protein, TBP).
Length = 86
Score = 129 bits (327), Expect = 9e-40
Identities = 36/84 (42%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 91 FKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVI 150
KI NIV + D+ FP+ L+ + + + YEPE FPGL+YR+ +P+ LIF +G++VI
Sbjct: 4 IKIQNIVASADLGFPIDLEKIALKL-RNAEYEPEQFPGLVYRLREPKATALIFSSGKVVI 62
Query: 151 TGAKSRSELHEAFDNIYPVLKSFK 174
TGAKS + +A I P+LK
Sbjct: 63 TGAKSEEDAKKAVRKIAPILKKLG 86
Score = 106 bits (266), Expect = 2e-30
Identities = 38/80 (47%), Positives = 54/80 (67%)
Query: 4 QNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAK 63
QN+V + +G P+DL +I ++R +EY P +F GL+ ++ P+ T L F SGK++I GAK
Sbjct: 7 QNIVASADLGFPIDLEKIALKLRNAEYEPEQFPGLVYRLREPKATALIFSSGKVVITGAK 66
Query: 64 HEHDCKLASRKFAKILKQLG 83
E D K A RK A ILK+LG
Sbjct: 67 SEEDAKKAVRKIAPILKKLG 86
>gnl|CDD|234886 PRK00996, PRK00996, ribonuclease HIII; Provisional.
Length = 304
Score = 28.3 bits (64), Expect = 1.8
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 16 LDLNQINS-RVRYSEYNPGK-FHGLIMKILNPRTTCLAFQSGKLLILGAKHEH 66
L I + +Y E G + P T A++SGK++ G E
Sbjct: 8 LSDKLIEKLKEQYEEKLTPSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAEA 60
>gnl|CDD|143599 cd07575, Xc-1258_like, Xanthomonas campestris XC1258 and related
proteins, members of the nitrilase superfamily (putative
class 13 nitrilases). Uncharacterized subgroup
belonging to a larger nitrilase superfamily comprised of
nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified in
the literature based on global and structure based
sequence analysis into thirteen different enzyme classes
(referred to as 1-13), class 13 represents proteins that
at the time were difficult to place in a distinct
similarity group; this subgroup either represents a new
class or one that was included previously in class 13.
Members of this superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. XC1258 is a homotetramer.
Length = 252
Score = 28.3 bits (64), Expect = 2.1
Identities = 11/21 (52%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 86 IKYQGFKIHNIVCTCDVRFPV 106
++Y+G+KI VC D+RFPV
Sbjct: 128 VEYKGWKILLQVCY-DLRFPV 147
>gnl|CDD|222691 pfam14337, DUF4393, Domain of unknown function (DUF4393). This
family of proteins is found in bacteria, archaea and
viruses. Proteins in this family are typically between
254 and 285 amino acids in length.
Length = 185
Score = 27.7 bits (62), Expect = 2.6
Identities = 15/42 (35%), Positives = 17/42 (40%), Gaps = 6/42 (14%)
Query: 67 DCKLASRKFAKILKQLGHP----IKYQGFKIHNIVCTCDVRF 104
F ILKQL +KY +NIV T DVR
Sbjct: 51 KNDDVHPSFVDILKQLSPDEARILKY--LYKNNIVPTVDVRL 90
>gnl|CDD|152474 pfam12039, DUF3525, Protein of unknown function (DUF3525). This
family of proteins is functionally uncharacterized. This
protein is found in viruses. Proteins in this family are
about 360 amino acids in length.
Length = 404
Score = 28.1 bits (62), Expect = 2.8
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 108 LDALHHVHSQFSSYEPELFPGL----------IYRMVKPRVVLLI 142
+D H V SQFS Y P + L +YR+ +P + LL+
Sbjct: 306 IDETHRVLSQFSHYAPRILNELTTWLKGLAENLYRVAEPILELLL 350
>gnl|CDD|179184 PRK00961, PRK00961, H(2)-dependent methylenetetrahydromethanopterin
dehydrogenase; Provisional.
Length = 342
Score = 27.4 bits (61), Expect = 3.6
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 61 GAKHEHDCKLASRKFAKILKQLG 83
GA H C + + KFAKI K LG
Sbjct: 169 GAIVTHACTIPTTKFAKIFKDLG 191
>gnl|CDD|180712 PRK06820, PRK06820, type III secretion system ATPase; Validated.
Length = 440
Score = 27.5 bits (61), Expect = 4.7
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 40 MKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPI 86
M +L+P + + G+ + H H ++ + +IL LG PI
Sbjct: 72 MALLSPFASSDGLRCGQW-VTPLGHMHQVQVGADLAGRILDGLGAPI 117
>gnl|CDD|234114 TIGR03121, one_C_dehyd_A, formylmethanofuran dehydrogenase subunit
A. Members of this largely archaeal protein family are
subunit A of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit A. Note
that this model does not distinguish tungsten (FwdA)
from molybdenum-containing (FmdA) forms of this enzyme;
a single gene from this family is expressed
constitutively in Methanobacterium thermoautotrophicum,
which has both tungsten and molybdenum forms and may
work interchangeably.
Length = 556
Score = 27.3 bits (61), Expect = 5.2
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 81 QLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSY 121
LG P Y+ + + V+ P + LH H QF SY
Sbjct: 237 NLGVPGNYE-TTLDTLDAAEGVK-PNRNQVLHLTHVQFHSY 275
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 26.8 bits (60), Expect = 6.6
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 1/24 (4%)
Query: 108 LDALHHVHSQFSSYEPELFPGLIY 131
+DA+ HV S + PG Y
Sbjct: 134 IDAIKHVSPSQSRVRT-ILPGEPY 156
>gnl|CDD|223045 PHA03326, PHA03326, nuclear egress membrane protein; Provisional.
Length = 275
Score = 26.6 bits (59), Expect = 7.2
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 100 CDVRFPVKLDALHHV 114
C V PVKL++L V
Sbjct: 85 CYVHAPVKLESLRRV 99
>gnl|CDD|215134 PLN02242, PLN02242, methionine gamma-lyase.
Length = 418
Score = 26.7 bits (59), Expect = 7.9
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 8/63 (12%)
Query: 36 HGLIMKI---LNPRTTCLAFQ-SGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGF 91
HG +M + +NP+ +AF+ S +L L + + C+ A ++AK +K+LG + Y G
Sbjct: 251 HGALMLLGPTMNPK---VAFELSERLPHLSLRMKEHCRRAM-EYAKRMKELGLKVIYPGL 306
Query: 92 KIH 94
+ H
Sbjct: 307 EDH 309
>gnl|CDD|218891 pfam06090, Ins_P5_2-kin, Inositol-pentakisphosphate 2-kinase. This
is a family of inositol-pentakisphosphate 2-kinases (EC
2.7.1.158) (also known as inositol
1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5
2-kinase) and InsP5 2-kinase). This enzyme
phosphorylates Ins(1,3,4,5,6)P5 to form
Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate).
InsP6 is involved in many processes such as mRNA export,
nonhomologous end-joining, endocytosis and ion channel
regulation.
Length = 301
Score = 26.6 bits (59), Expect = 8.2
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 10/67 (14%)
Query: 115 HSQFSSYEP-ELFPGLIYRM---VKPRVV------LLIFVNGRIVITGAKSRSELHEAFD 164
S+ SSY P +LF G R+ +K V L +F NG +V + K L E
Sbjct: 158 ISRISSYCPLDLFSGDKERVLRAIKALVSEGPQNNLRVFKNGSLVYSDEKFAKLLAEYLL 217
Query: 165 NIYPVLK 171
VL+
Sbjct: 218 KDNSVLQ 224
>gnl|CDD|173675 cd05584, STKc_p70S6K, Catalytic domain of the Protein
Serine/Threonine Kinase, 70 kDa ribosomal protein S6
kinase. Serine/Threonine Kinases (STKs), 70 kDa
ribosomal protein S6 kinase (p70S6K) subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The p70S6K subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. p70S6K (or S6K)
contains only one catalytic kinase domain, unlike p90
ribosomal S6 kinases (RSKs). It acts as a downstream
effector of the STK mTOR (mammalian Target of Rapamycin)
and plays a role in the regulation of the translation
machinery during protein synthesis. p70S6K also plays a
pivotal role in regulating cell size and glucose
homeostasis. Its targets include S6, the translation
initiation factor eIF3, and the insulin receptor
substrate IRS-1, among others. Mammals contain two
isoforms of p70S6K, named S6K1 and S6K2 (or S6K-beta).
Length = 323
Score = 26.3 bits (58), Expect = 8.5
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 11/42 (26%)
Query: 110 ALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVIT 151
AL H+H Q G+IYR +KP +LL G + +T
Sbjct: 112 ALEHLHQQ----------GIIYRDLKPENILLD-AQGHVKLT 142
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
0.326 0.142 0.434
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,899,777
Number of extensions: 803909
Number of successful extensions: 995
Number of sequences better than 10.0: 1
Number of HSP's gapped: 972
Number of HSP's successfully gapped: 44
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.4 bits)