RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy996
(221 letters)
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II. This model
represents eukaryotic transcription elongation factor
S-II. This protein allows stalled RNA transcription
complexes to perform a cleavage of the nascent RNA and
restart at the newly generated 3-prime end.
Length = 299
Score = 158 bits (400), Expect = 1e-47
Identities = 77/206 (37%), Positives = 105/206 (50%), Gaps = 15/206 (7%)
Query: 8 PAPPGISNNKDSSSKKKEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQV 67
+ + S S K E + + + + P N D VR KCRE+L +++
Sbjct: 95 ESVNSVKQEAKSQSDKIEQPKYVSSSPRNAKNDFVPTAVTN--DKVRDKCRELLYDALAK 152
Query: 68 GDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGA 127
E A ++EE +N T+ YK R RS +NL+D NP L N + G
Sbjct: 153 DSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGE 212
Query: 128 ISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLL 187
I+ KLATMTAE EMA+ E+K R + KE++ +AQ A +Q TDL
Sbjct: 213 ITPEKLATMTAE-------------EMASAELKQEREEITKENLFEAQGAKIQKAVTDLF 259
Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTT 213
CGKCK++ CTY Q+QTRSADEPMTT
Sbjct: 260 TCGKCKQKKCTYYQLQTRSADEPMTT 285
>gnl|CDD|219433 pfam07500, TFIIS_M, Transcription factor S-II (TFIIS), central
domain. Transcription elongation by RNA polymerase II
is regulated by the general elongation factor TFIIS.
This factor stimulates RNA polymerase II to transcribe
through regions of DNA that promote the formation of
stalled ternary complexes. TFIIS is composed of three
structural domains, termed I, II, and III. The two
C-terminal domains (II and III), this domain and
pfam01096 are required for transcription activity.
Length = 115
Score = 112 bits (283), Expect = 3e-32
Identities = 50/127 (39%), Positives = 72/127 (56%), Gaps = 13/127 (10%)
Query: 50 TDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIA 109
D VR KCRE+L +++ G D +E LA E+EE ++ + NT +YKN+ RS +
Sbjct: 2 NDKVRDKCRELLYDALAKGSEDSMSEEEVERLAAEIEEELFKLYGNTGKKYKNKYRSLMF 61
Query: 110 NLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKE 169
NLKDPKNP L R + G IS +L M+ E E+A+DE+K R + KE
Sbjct: 62 NLKDPKNPDLRRKVLNGEISPERLVNMSPE-------------ELASDELKKEREEIEKE 108
Query: 170 SIDDAQL 176
++ +AQL
Sbjct: 109 ALREAQL 115
>gnl|CDD|128786 smart00510, TFS2M, Domain in the central regions of transcription
elongation factor S-II (and elsewhere).
Length = 102
Score = 98.5 bits (246), Expect = 9e-27
Identities = 47/115 (40%), Positives = 63/115 (54%), Gaps = 13/115 (11%)
Query: 51 DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIAN 110
D VR KC+EML ++Q + ELA ++E +++EF TD +YKN+ RS N
Sbjct: 1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFN 60
Query: 111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNK 165
LKD KNP L R + G I+ KLATMTAE E+A+ E+K R K
Sbjct: 61 LKDKKNPDLRRKVLNGEITPEKLATMTAE-------------ELASAELKEKREK 102
>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS).
Length = 39
Score = 57.6 bits (140), Expect = 9e-12
Identities = 18/32 (56%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219
KC KC R + Q+QTRSADEPMT FY+
Sbjct: 2 KCPKCGHREAVFFQLQTRSADEPMTL---FYV 30
Score = 36.8 bits (86), Expect = 3e-04
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 139 EVQTRSADEPMTTF 152
++QTRSADEPMT F
Sbjct: 15 QLQTRSADEPMTLF 28
>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger. Nucleic-acid-binding motif
in transcriptional elongation factor TFIIS and RNA
polymerases.
Length = 40
Score = 51.6 bits (124), Expect = 1e-09
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 187 LKCGKCKKRNCTYNQVQTRSADEPMTTLH 215
+C KC R T+ Q+QTRSADEPMT +
Sbjct: 1 AECPKCGNREATFYQLQTRSADEPMTVFY 29
Score = 33.1 bits (76), Expect = 0.008
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 139 EVQTRSADEPMTTF 152
++QTRSADEPMT F
Sbjct: 15 QLQTRSADEPMTVF 28
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription
elongation factor TFIIS [Transcription].
Length = 113
Score = 45.1 bits (107), Expect = 2e-06
Identities = 21/52 (40%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 167 IKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218
+ D+ Q A T KC KC + Y Q+QTRSADEP T FY
Sbjct: 55 VLVVEDETQGAKTL--PTAKEKCPKCGNKEAYYWQLQTRSADEPETR---FY 101
Score = 31.7 bits (72), Expect = 0.090
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 141 QTRSADEPMTTF 152
QTRSADEP T F
Sbjct: 89 QTRSADEPETRF 100
>gnl|CDD|222958 PHA02998, PHA02998, RNA polymerase subunit; Provisional.
Length = 195
Score = 31.2 bits (71), Expect = 0.25
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 187 LKCGKCKKRNCTYNQVQTRSADEPMTTLH 215
C CK +N T +QTR+ADEP H
Sbjct: 144 TPCPNCKSKNTTPMMIQTRAADEPPLVRH 172
>gnl|CDD|180958 PRK07396, PRK07396, dihydroxynaphthoic acid synthetase; Validated.
Length = 273
Score = 31.0 bits (71), Expect = 0.35
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 7/33 (21%)
Query: 57 CREMLQNS------IQVG-DLDMDGLASLEELA 82
CREMLQNS ++ + D DG A L+ELA
Sbjct: 206 CREMLQNSPMALRCLKAALNADCDGQAGLQELA 238
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 30.8 bits (70), Expect = 0.41
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 81 LATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISA 130
LAT + + K+ + +R +KDP N + G +SA
Sbjct: 77 LATRVSPELLEALKDRFADVEYNEAARTLAIKDP-NYEPKKGGKVGVLSA 125
>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal. This model
describes archaeal transcription factor S, a protein
related in size and sequence to certain eukaryotic RNA
polymerase small subunits, and in sequence and function
to the much larger eukaryotic transcription factor IIS
(TFIIS). Although originally suggested to be a subunit
of the archaeal RNA polymerase, it elutes separately
from active polymerase in gel filtration experiments and
acts, like TFIIs, as an induction factor for RNA
cleavage by RNA polymerase. There has been an apparent
duplication event in the Halobacteriaceae lineage
(Haloarcula, Haloferax, Haloquadratum, Halobacterium and
Natromonas). There appears to be a separate duplication
in Methanosphaera stadtmanae [Transcription,
Transcription factors].
Length = 104
Score = 28.3 bits (63), Expect = 1.1
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 189 CGKCKKRNCTYNQVQTRSADEPMT 212
C KC + Y +QTR ADEP T
Sbjct: 65 CPKCGHKEAYYWLLQTRRADEPET 88
>gnl|CDD|220638 pfam10230, DUF2305, Uncharacterized conserved protein (DUF2305).
This family of proteins is conserved from plants to
humans. The function is unknown.
Length = 260
Score = 28.8 bits (65), Expect = 2.3
Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 118 MLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLR---NKFIKESIDDA 174
+L R + S + L T R MA DEM+ +R ++FIK + ++
Sbjct: 159 LLIRKVLGSPSSPAVLGTALFLKSPRVLRN---ALFMARDEMREVREDDDEFIKAANENE 215
Query: 175 Q 175
Sbjct: 216 I 216
>gnl|CDD|185368 PRK15471, PRK15471, chain length determinant protein WzzB;
Provisional.
Length = 325
Score = 28.6 bits (64), Expect = 2.3
Identities = 13/52 (25%), Positives = 25/52 (48%)
Query: 132 KLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTK 183
K ++T++ + + T E+ E K LR K I+E++ A A + +
Sbjct: 165 KDLKDNIALRTKTLQDSLETQEVVAQEQKDLRIKQIQEALQYANQANITKPQ 216
>gnl|CDD|223524 COG0447, MenB, Dihydroxynaphthoic acid synthase [Coenzyme
metabolism].
Length = 282
Score = 28.5 bits (64), Expect = 2.3
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 57 CREMLQNSIQVG-------DLDMDGLASLEELATE 84
REML S + D DGLA L+ELA
Sbjct: 215 AREMLAKSPTALRMLKAAFNADCDGLAGLQELAGN 249
>gnl|CDD|188993 cd06258, M3_like, Peptidase M3-like family, a zincin
metallopeptidase, includes M3 and M32 families. The
peptidase M3-like family, also called neurolysin-like
family, is part of the "zincins" metallopeptidases, and
includes M3 and M32 families of metallopeptidases. The
M3 family is subdivided into two subfamilies: the
widespread M3A, which comprises a number of
high-molecular mass endo- and exopeptidases from
bacteria, archaea, protozoa, fungi, plants and animals,
and the small M3B, whose members are enzymes primarily
from bacteria. Well-known mammalian/eukaryotic M3A
endopeptidases are the thimet oligopeptidase (TOP;
endopeptidase 3.4.24.15), neurolysin (alias
endopeptidase 3.4.24.16), and the mitochondrial
intermediate peptidase. The first two are intracellular
oligopeptidases, which act only on relatively short
substrates of less than 20 amino acid residues, while
the latter cleaves N-terminal octapeptides from proteins
during their import into the mitochondria. The M3A
subfamily also contains several bacterial
endopeptidases, collectively called oligopeptidases A,
as well as a large number of bacterial
carboxypeptidases, called dipeptidyl peptidases (Dcp;
Dcp II; peptidyl dipeptidase; EC 3.4.15.5). The
peptidases in the M3 family contain the HEXXH motif that
forms the active site in conjunction with a
C-terminally-located Glutamic acid (Glu) residue. A
single zinc ion is ligated by the side-chains of the two
Histidine (His) residues, and the more C-terminal Glu.
Most of the peptidases are synthesized without signal
peptides or propeptides, and function intracellularly.
There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 400
Score = 28.5 bits (64), Expect = 3.0
Identities = 20/107 (18%), Positives = 47/107 (43%), Gaps = 13/107 (12%)
Query: 59 EMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKN--RVRSRIANL---KD 113
+L + L++D A LEE EL E+ +N+ + +N + R+R+ +A ++
Sbjct: 4 RVLHAQLVENQLELDEAAELEEREAEL-ESGFNKARALENLLRELVRLRNALARALGYEN 62
Query: 114 PKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMK 160
+ L+ +L + +++ + + F +A E++
Sbjct: 63 FYDASLALQ---EGKDPEQLFAILDDLEDAT-RDA---FPLAKKELE 102
>gnl|CDD|185052 PRK15097, PRK15097, cytochrome d terminal oxidase subunit 1;
Provisional.
Length = 522
Score = 28.7 bits (64), Expect = 3.1
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 123 YIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKF 166
Y G + +KLA + AE +T+ A T F + + E T+ NKF
Sbjct: 243 YEMGDVQKTKLAAIEAEWETQPAPAAFTLFGIPDQE--TMENKF 284
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 27.8 bits (62), Expect = 5.4
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 148 PMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCG 190
P+ +A+DE + LR+ + QLA G D C
Sbjct: 219 PLAALALASDENRPLRDWTLG------QLA--AGAACDAFACA 253
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 27.4 bits (61), Expect = 6.0
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 12 GISNNKDSSSKKKEAKEEKKEDKKP 36
+ +K S KKK+ K+EKKE K
Sbjct: 62 KNNESKKKSEKKKKKKKEKKEPKSE 86
>gnl|CDD|218284 pfam04832, SOUL, SOUL heme-binding protein. This family represents
a group of putative heme-binding proteins. Our family
includes archaeal and bacterial homologues.
Length = 174
Score = 26.8 bits (60), Expect = 6.1
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 122 NYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMK 160
YIFG + + MTA V ++ PMT E +
Sbjct: 49 GYIFGKNRSGEKIAMTAPVLQQA--IPMTADEEGSGAWT 85
>gnl|CDD|130908 TIGR01849, PHB_depoly_PhaZ, polyhydroxyalkanoate depolymerase,
intracellular. This model represents an intracellular
depolymerase for polyhydroxyalkanoate (PHA), a carbon
and energy storing polyester that accumulates in
granules in many bacterial species when carbon sources
are abundant but other nutrients are limiting. This
family is named for PHAs generally, rather than
polyhydroxybutyrate (PHB) specificially as in Ralstonia
eutropha H16, to avoid overcalling chemical specificity
in other species. Note that this family lacks the
classic GXSXG lipase motif and instead shows weak
similarity to some [Fatty acid and phospholipid
metabolism, Degradation].
Length = 406
Score = 27.4 bits (61), Expect = 7.4
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 136 MTAEVQTRSADEPMTTFEMANDEMKTLRNKFIK-ESIDDAQLATVQGTKTDLLKCGKCK 193
MTAE ++ D F + + K + +I L TV+G D+ G+ K
Sbjct: 301 MTAEFYLQTIDVVFQQFLLPQGKFIV-EGKRVDPGAITRVALLTVEGENDDISGLGQTK 358
>gnl|CDD|218055 pfam04386, SspB, Stringent starvation protein B. Escherichia coli
stringent starvation protein B (SspB), is thought to
enhance the specificity of degradation of tmRNA-tagged
proteins by the ClpXP protease. The tmRNA tag, also
known as ssrA, is an 11-aa peptide added to the C
terminus of proteins stalled during translation, targets
proteins for degradation by ClpXP and ClpAP. SspB a
cytoplasmic protein that specifically binds to residues
1-4 and 7 of the tag. Binding of SspB enhances
degradation of tagged proteins by ClpX, and masks
sequence elements important for ClpA interactions,
inhibiting degradation by ClpA. However, more recent
work has cast doubt on the importance of SspB in
wild-type cells. SspB is encoded in an operon whose
synthesis is stimulated by carbon, amino acid, and
phosphate starvation. SspB may play a special role
during nutrient stress, for example by ensuring rapid
degradation of the products of stalled translation,
without causing a global increase in degradation of all
ClpXP substrates.
Length = 153
Score = 26.4 bits (59), Expect = 7.5
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 199 YNQVQTRSADEPMTTLHHFYITV 221
Y V T A E + H YIT
Sbjct: 15 YEWVLTDVAKEGLDNDHTPYITF 37
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 26.9 bits (60), Expect = 9.7
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 87 EAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSAD 146
A+ + R + R+ R+ K KNP ++ IF I A ++A V R A
Sbjct: 6 TALQQQLDELMLRDRQRLSRRLHGAKKIKNPD-AQQAIFQEI-AKEIAQAAQRVLLREAA 63
Query: 147 EPMTTF 152
P T+
Sbjct: 64 RPEITY 69
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 0.127 0.351
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,466,882
Number of extensions: 917475
Number of successful extensions: 1120
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1097
Number of HSP's successfully gapped: 64
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
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 (21.9 bits)
S2: 57 (25.7 bits)