RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9565
(288 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 78.3 bits (194), Expect = 6e-19
Identities = 26/49 (53%), Positives = 36/49 (73%)
Query: 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQ 141
RR RT FT EQL ELE+ F++ YP A REEL+++LGL+E +V+ + Q
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQ 49
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 69.6 bits (171), Expect = 9e-16
Identities = 25/48 (52%), Positives = 35/48 (72%)
Query: 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNF 139
+RR RT+FT EQL ELE+ F + YP REEL+++LGLSE +V+ +
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVW 48
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 67.3 bits (165), Expect = 7e-15
Identities = 24/46 (52%), Positives = 32/46 (69%)
Query: 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN 138
RR RT FT EQL ELE+ F++ YP REEL++ LGL+E +V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 41.7 bits (98), Expect = 9e-05
Identities = 18/50 (36%), Positives = 24/50 (48%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S+ + R T EQL LER F+ YP + R +LS L + VQ
Sbjct: 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96
>gnl|CDD|146451 pfam03826, OAR, OAR domain.
Length = 21
Score = 36.6 bits (86), Expect = 4e-04
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 259 SKNSSIADLRLKAKKHAEA 277
++SSIA LRLKAK+H+ A
Sbjct: 3 PRSSSIASLRLKAKEHSAA 21
>gnl|CDD|221084 pfam11336, DUF3138, Protein of unknown function (DUF3138). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 514
Score = 34.5 bits (79), Expect = 0.051
Identities = 29/94 (30%), Positives = 37/94 (39%), Gaps = 7/94 (7%)
Query: 189 LPTLPFSASTAAAFSAFDPTLLSAAHQYAA-----AAATVAALGNAPNGSIFSAASQYPS 243
LP +AS A+ A L + Q AA AA G A S +AA+ PS
Sbjct: 14 LPGAAAAASDASQIKALQAQLTALQQQVNELRAALAAKPAAAGGGAKIQSAAAAAAAAPS 73
Query: 244 FSLATLAALHQDRLLSKNSSIADLRLKAKKHAEA 277
A AAL D + IA+ LK +A
Sbjct: 74 SDAA--AALTNDDVTQMREQIANQSLKVDSLTDA 105
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 33.1 bits (75), Expect = 0.19
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 168 HQPVSTPL-EPCRVAPYVNVPRLPTLPFSASTAAAFSAFDPTLLSAAHQYAAAAATVAAL 226
+QP+ P+ EP + + P + +P + AA L++ + A A AA
Sbjct: 527 YQPIPEPVKEPEPIKSSLKAPSVAAVPPVEAAAAVSP------LASGVKKATLATGAAAT 580
Query: 227 GNAPNGSIFSAASQYP 242
AP S+ ++ P
Sbjct: 581 VAAPVFSLANSGGPRP 596
>gnl|CDD|220883 pfam10824, DUF2580, Protein of unknown function (DUF2580). This
family of proteins with unknown function appears to be
mainly found in actinobacteria.
Length = 100
Score = 30.4 bits (69), Expect = 0.28
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 1/80 (1%)
Query: 209 LLSAAHQYAAAAATVAALGNAPNGSIFSAASQYPSFSLATLAALHQDRLLSKNSSIADLR 268
L A ++ AAA +A+ A G + A+ + AAL ++ ++ L
Sbjct: 12 LRELAAKHDEAAAQIASAVAAAAGVAAAVAATHGPICAPFNAAL-AAAETARRAAGTALA 70
Query: 269 LKAKKHAEAIEMAAREKEKT 288
+ AE + AA E T
Sbjct: 71 TVSTDLAENLRAAAAAYEAT 90
>gnl|CDD|133398 cd04770, HTH_HMRTR, Helix-Turn-Helix DNA binding domain of Heavy
Metal Resistance transcription regulators.
Helix-turn-helix (HTH) heavy metal resistance
transcription regulators (HMRTR): MerR1 (mercury), CueR
(copper), CadR (cadmium), PbrR (lead), ZntR (zinc),
and other related proteins. These transcription
regulators mediate responses to heavy metal stress in
eubacteria. They belong to the MerR superfamily of
transcription regulators that promote transcription of
various stress regulons by reconfiguring the operator
sequence located between the -35 and -10 promoter
elements. A typical MerR regulator is comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their N-terminal domains are homologous and
contain a DNA-binding winged HTH motif, while the
C-terminal domains are often dissimilar and bind
specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 123
Score = 29.8 bits (68), Expect = 0.71
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 93 RRSRT-NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
RR++ F+L ++ EL L D+ P A +R L ++L EA++
Sbjct: 51 RRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIA 96
>gnl|CDD|238233 cd00400, Voltage_gated_ClC, CLC voltage-gated chloride channel. The
ClC chloride channels catalyse the selective flow of Cl-
ions across cell membranes, thereby regulating
electrical excitation in skeletal muscle and the flow of
salt and water across epithelial barriers. This domain
is found in the halogen ions (Cl-, Br- and I-) transport
proteins of the ClC family. The ClC channels are found
in all three kingdoms of life and perform a variety of
functions including cellular excitability regulation,
cell volume regulation, membrane potential
stabilization, acidification of intracellular
organelles, signal transduction, transepithelial
transport in animals, and the extreme acid resistance
response in eubacteria. They lack any structural or
sequence similarity to other known ion channels and
exhibit unique properties of ion permeation and gating.
Unlike cation-selective ion channels, which form
oligomers containing a single pore along the axis of
symmetry, the ClC channels form two-pore homodimers with
one pore per subunit without axial symmetry. Although
lacking the typical voltage-sensor found in cation
channels, all studied ClC channels are gated (opened and
closed) by transmembrane voltage. The gating is
conferred by the permeating ion itself, acting as the
gating charge. In addition, eukaryotic and some
prokaryotic ClC channels have two additional C-terminal
CBS (cystathionine beta synthase) domains of putative
regulatory function.
Length = 383
Score = 30.2 bits (69), Expect = 1.1
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 217 AAAAATVAALGNAP-NGSIFSAASQYPSFSLATLAAL 252
AAA +AA NAP G++F+ +S+A+L +
Sbjct: 136 CGAAAGIAAAFNAPLAGALFAIEVLLGEYSVASLIPV 172
>gnl|CDD|227324 COG4991, COG4991, Uncharacterized protein with a bacterial SH3
domain homologue [Function unknown].
Length = 155
Score = 29.3 bits (66), Expect = 1.2
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 194 FSASTAAAFSAFDPTLLSAAHQYAAAAATVAALGNAPNGSIFSAASQYPSFSLAT 248
S T SAF LL A YAA +A+ A N +G + YP+ +
Sbjct: 9 LSMKTLMRASAFGLALLMPAAAYAAVSASATANVNVRSGPG----TAYPAVGVIP 59
>gnl|CDD|177566 PHA03242, PHA03242, envelope glycoprotein M; Provisional.
Length = 428
Score = 29.4 bits (66), Expect = 2.6
Identities = 14/40 (35%), Positives = 16/40 (40%)
Query: 185 NVPRLPTLPFSASTAAAFSAFDPTLLSAAHQYAAAAATVA 224
N P L + AF A+ TLL A YA A A
Sbjct: 79 NGYSAPPLFLETPSLVAFYAYTATLLLAVAAYAVAGAVTI 118
>gnl|CDD|181978 PRK09597, PRK09597, lipid A 1-phosphatase; Reviewed.
Length = 190
Score = 28.7 bits (64), Expect = 2.6
Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 14/101 (13%)
Query: 180 VAPYVNVPRLPTLPFSASTAAAFSAFDPTLLSAAHQYAAAAATVAALGNAPNGSIFSAAS 239
AP+ VP+ P++P + ++ F PT+LS A A+G +F
Sbjct: 35 FAPFPKVPKQPSVPLAFHFTEHYARFIPTILSV----AIPLIQRDAIG------LF---- 80
Query: 240 QYPSFSLATLAALHQDRLLSKNSSIADLRLKAKKHAEAIEM 280
Q + S+AT H + + +I D RL + + M
Sbjct: 81 QVANASIATTLLTHTTKRALNHVTINDQRLGERPYGGNFNM 121
>gnl|CDD|226187 COG3661, AguA, Alpha-glucuronidase [Carbohydrate transport and
metabolism].
Length = 684
Score = 29.1 bits (65), Expect = 3.3
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 205 FDPTLLSAAHQYAAAAATVAALGNAP 230
+ P SA YAA A +A + P
Sbjct: 14 YKPVAESARVAYAARFAAIAIVAETP 39
>gnl|CDD|235648 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
Length = 455
Score = 29.0 bits (66), Expect = 3.3
Identities = 26/139 (18%), Positives = 52/139 (37%), Gaps = 30/139 (21%)
Query: 27 DDSNRLPSSESSRHLYFTDSNSDLKVNNENECDDSNRLPSSESSRHHISRHLSLSPISSC 86
+ LP S +Y S S + ++ + ++ES + H+ + L+P S
Sbjct: 60 EIPEELPLDTSWDEIYTAGSPSGSGGDYIDDELPVYQGETTESLQDHLLEQIELTPFSE- 118
Query: 87 KSSNKQRRSRT--NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLN 144
R + ++ L++ E E EE+++ LG+ V+ VL
Sbjct: 119 -------TDRAIATYIIDALDD-EGYLTED-------LEEIAESLGVELDEVEA---VLK 160
Query: 145 LLIDVSTVTINNTLNPAGI 163
+ + +PAG+
Sbjct: 161 RI---------QSFDPAGV 170
>gnl|CDD|150197 pfam09442, DUF2018, Domain of unknown function (DUF2018).
Acid-adaptive protein possibly of physiological
significance when H.pylori colonises the human stomach,
which adopts a unique four alpha-helical triangular
conformations. The biologically active form is thought
to be a tetramer. The protein is expressed along with
six other proteins, some of which are related to iron
storage and haem biosynthesis.
Length = 80
Score = 26.1 bits (58), Expect = 6.2
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 105 NELERLFDETHYPDAFMREELSQRLGLSEARVQNF 139
NELE+L + A + E L ++ GL E ++NF
Sbjct: 23 NELEKLLERL----AALEELLEKK-GLDENDIKNF 52
>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor;
Provisional.
Length = 231
Score = 27.9 bits (62), Expect = 6.2
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 101 LEQLNELERLFDETHYPDAFMREELSQRLGLSEARV 136
L QL+E E+L +Y +E++ L L+EAR+
Sbjct: 181 LSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARI 216
>gnl|CDD|180717 PRK06833, PRK06833, L-fuculose phosphate aldolase; Provisional.
Length = 214
Score = 27.4 bits (61), Expect = 6.6
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 28 DSNRLPSSESSRHLYFTDSNSDLK 51
+ R PSSE HL F + D+
Sbjct: 68 EGERKPSSELDMHLIFYRNREDIN 91
>gnl|CDD|235300 PRK04447, PRK04447, hypothetical protein; Provisional.
Length = 351
Score = 27.9 bits (63), Expect = 6.9
Identities = 24/89 (26%), Positives = 34/89 (38%), Gaps = 9/89 (10%)
Query: 190 PTLPFSASTAAAFSAFDPTLLSAAHQYAAAAATVAALGNAPNGSIFSAASQY----PSFS 245
P A A S+ P LL+ Q A AA + A+G +I A +++ S
Sbjct: 219 PMQAVVAGLAIGASSGGPVLLAGGTQMLAVAALIKAIGKEDLENIAIATTRWVAEDKSAD 278
Query: 246 LATLAALHQDRLLSKNSSIADLRLKAKKH 274
LA LL+ +DL KH
Sbjct: 279 FKGLAEQIGVPLLA-----SDLDFSNSKH 302
>gnl|CDD|129781 TIGR00698, TIGR00698, conserved hypothetical integral membrane
protein. Members of this family are found so far only
in one archaeal species, Archaeoglobus fulgidus, and in
two related bacterial species, Haemophilus influenzae
and Escherichia coli. It has 9 GES predicted
transmembrane regions at conserved locations in all
members. These proteins have a molecular weight of
approximately 35 to 38 kDa [Hypothetical proteins,
Conserved].
Length = 335
Score = 27.9 bits (62), Expect = 7.1
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 199 AAAFSAFDPTLLSAAHQYAAAAATVAALGNAPNGSIFSAASQYPSF 244
AAA +A +P + + + + A A V G IF YPS
Sbjct: 133 AAAVAAIEPVIKAEKEKVSVAIAIVVIFGTT---GIFL----YPSI 171
>gnl|CDD|163544 TIGR03832, Tyr_2_3_mutase, tyrosine 2,3-aminomutase. Members of
this protein family are tyrosine 2,3-aminomutase. It is
variable from member to member as to whether the
(R)-beta-Tyr or (S)-beta-Tyr is the preferred product
from L-Tyr. This enzyme tends to occur in secondary
metabolite biosynthesis systems, as in the production of
chondramides in Chondromyces crocatus.
Length = 507
Score = 27.9 bits (62), Expect = 7.9
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 204 AFDPTLLS--AAHQYAAAA--ATVAALGNAPNGSIFSAASQYPSFSLATLAALHQDRLLS 259
A DP L S A QY A A A +G A S+ S S+ +AA + R+LS
Sbjct: 387 AGDPGLHSGFAGAQYPATALVAENRTIGPASTQSVPSNGDNQDVVSMGLIAARNARRVLS 446
Query: 260 KNSSIADLRLKAKKHAEAIEMAAR 283
N+ I + L A A+A+++A R
Sbjct: 447 NNNKILAVELLAA--AQAVDLAGR 468
>gnl|CDD|187850 cd09719, Cas1_I-E, CRISPR/Cas system-associated protein Cas1.
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;
Cas1 is the most universal CRISPR system protein thought
to be involved in spacer integration; Cas1 is
metal-dependent deoxyribonuclease, also binds RNA; Shown
to possess a unique fold consisting of a N-terminal
beta-strand domain and a C-terminal alpha-helical
domain.
Length = 262
Score = 27.6 bits (62), Expect = 8.2
Identities = 20/70 (28%), Positives = 26/70 (37%), Gaps = 21/70 (30%)
Query: 202 FSAFDPT--LLSAAHQ--YAAAAATVAALGNAPNGSIFSAASQYPSFSLATLAALHQDRL 257
+ A DP LSAA+ Y A + A G +P L +H +
Sbjct: 160 WEAGDPVNRALSAANACLYGICHAAILAAGYSP-----------------ALGFIHTGKP 202
Query: 258 LSKNSSIADL 267
LS IADL
Sbjct: 203 LSFVYDIADL 212
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.0 bits (62), Expect = 8.6
Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 18/107 (16%)
Query: 195 SASTAAAFSAFDPTLLSAAHQYAAAAATVAALGNA------PNGSIFSAASQYPSFSLAT 248
+ S A A ++ + T+ +A + A VAAL A P + + A + AT
Sbjct: 1138 AGSAAVATASPESTVDAAVRAHGVLADAVAALSPAVRDPACPLAFLVALADSAAGYVKAT 1197
Query: 249 LAALHQ----DRLLSKNSSIADLRLKAKK--------HAEAIEMAAR 283
AL RL + ++ ADL + ++ A +E AAR
Sbjct: 1198 RLALDARRAIARLGALGAAAADLAVAVRRENPQAEGDRAALLEAAAR 1244
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
0.311 0.123 0.336
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,785,075
Number of extensions: 1284159
Number of successful extensions: 1349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1338
Number of HSP's successfully gapped: 54
Length of query: 288
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 192
Effective length of database: 6,679,618
Effective search space: 1282486656
Effective search space used: 1282486656
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: 58 (26.1 bits)