RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15967
(280 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 60.8 bits (148), Expect = 6e-12
Identities = 32/147 (21%), Positives = 46/147 (31%), Gaps = 55/147 (37%)
Query: 15 VFSPGDYICRKGDVGKEMYIVKRGKLNVVADDE---ETVLATLSAGSVFGEVRHVLGVDL 71
F G+ I R+GD +YIV G + V DE E ++ L G +F
Sbjct: 21 RFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLF----------- 69
Query: 72 GRITSFCSKGYEIPNTKWLNLIVKAQPMKLRKTVLNKVSVLEIAGNRTGNRRTANVRSLG 131
G + R+A VR+L
Sbjct: 70 GELALLG-----------------------------------------NGPRSATVRALT 88
Query: 132 YSDLFCLAKRDLWETLADYPEARHSLM 158
S+L L + D L +YPE L+
Sbjct: 89 DSELLVLPRSDFRRLLQEYPELARRLL 115
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a
prokaryotic homologue of eukaryotic cNMP-binding
domains, present in ion channels, and cNMP-dependent
kinases.
Length = 120
Score = 60.1 bits (146), Expect = 1e-11
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 15 VFSPGDYICRKGDVGKEMYIVKRGKLNVVA---DDEETVLATLSAGSVFGE 62
+ G+ I R+GDVG YI+ G++ V D EE ++ TL G FGE
Sbjct: 21 RYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGE 71
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 53.5 bits (129), Expect = 1e-09
Identities = 22/50 (44%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 16 FSPGDYICRKGDVGKEMYIVKRGKLNVVADDE---ETVLATLSAGSVFGE 62
F G+ I R+GD +YIV GK+ V DE E +LA L G FGE
Sbjct: 4 FKKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGE 53
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator
and regulatory subunit of cAMP-dependent protein
kinases [Signal transduction mechanisms].
Length = 214
Score = 37.1 bits (86), Expect = 0.005
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 16 FSPGDYICRKGDVGKEMYIVKRGKLNVV---ADDEETVLATLSAGSVFGE 62
G+ + +G+ +YI+ G + + D E +L L G FGE
Sbjct: 28 LPKGEVLFTEGEEADSLYIILSGIVKLYANTEDGREIILGFLGPGDFFGE 77
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator
Crp; Provisional.
Length = 211
Score = 31.9 bits (73), Expect = 0.24
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 22 ICRKGDVGKEMYIVKRGKLNVVADDE---ETVLATLSAGSVFGEV 63
+ G+ + +Y + +G + V+ DE E +L+ L+ G GE+
Sbjct: 31 LIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGEL 75
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 32.4 bits (74), Expect = 0.28
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 16 FSPGDYICRKGDVGKEMYIVKRGKLNVVADDEE--TVLATLSAGSVFG 61
+ G+Y+ R+G+ G +Y + +G+ V EE L FG
Sbjct: 36 YGKGEYVVREGEPGDGLYFIWKGEAEVSGPAEEESRPEFLLKRYDYFG 83
>gnl|CDD|224264 COG1345, FliD, Flagellar capping protein [Cell motility and
secretion].
Length = 483
Score = 31.2 bits (71), Expect = 0.64
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 1/57 (1%)
Query: 186 LKDTVRRLDTTLEHLQTRFARLMAEYLSQQAKMKQRLALLE-QGASVNQATSSKRNS 241
L ++ LD ++ L R Y +Q + + + Q + + Q S NS
Sbjct: 427 LNKQIKSLDKDIKSLDKRLEAAEERYKTQFNTLDDMMTQMNSQSSYLTQQLVSVSNS 483
Score = 28.9 bits (65), Expect = 3.7
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 184 EALKDTVRRLDTTLEHLQTRFARL---MAEYLSQQAKMKQRLA 223
+ +K +RL+ E +T+F L M + SQ + + Q+L
Sbjct: 436 KDIKSLDKRLEAAEERYKTQFNTLDDMMTQMNSQSSYLTQQLV 478
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 31.3 bits (71), Expect = 0.71
Identities = 24/159 (15%), Positives = 44/159 (27%), Gaps = 23/159 (14%)
Query: 82 YEIPNTKWLNLIVKAQPMKLRKTVLNKVSVLEIAGNRTGNRRTAN-----VRSLGYSDLF 136
E + I K +++ + +L + I +R A ++ +
Sbjct: 351 KEEFKGFAVFEIYKFLDLQINQFILYQWLDAFIEDWFGDSRLLAKKLLERLKLPENRRIK 410
Query: 137 CLAKRDL--------WETLADYPEARHSLMERGCQLLRKDGLLDEEAFRNSQVEHEALKD 188
LA L W+ D PE+R L E+ L +
Sbjct: 411 ELALTPLLLALECLIWQAQGDLPESRAELYEQAVDALLGREDETRGIKWSKTYAKLTTDQ 470
Query: 189 T---VRRLDT-TLEHLQTRFA------RLMAEYLSQQAK 217
+ +L L + +YL QA+
Sbjct: 471 QDKWLLQLLAALLFEKLDEEFTEFLLKDDIVDYLLNQAE 509
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 30.7 bits (70), Expect = 0.82
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 190 VRR--LDTTLEHLQTRFARLMAEYLSQQAKMKQRLALLEQGASVNQA 234
RR LD L ++ + ++ Y + +KQR ALL+Q
Sbjct: 131 DRRRFLDWLLFQIEPVYLEALSNY---EKLLKQRNALLKQLQGDYAW 174
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the family
being composed of Afadin- and alpha -Actinin-Binding
Proteins Localised at Cell-Cell Adherens Junctions.
Length = 149
Score = 29.6 bits (67), Expect = 0.88
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 10/54 (18%)
Query: 184 EALKDTVRRLDTTLEHLQTRFARL----------MAEYLSQQAKMKQRLALLEQ 227
E+L++T+R+L+ +E LQ RL +A +++ +++++L LEQ
Sbjct: 53 ESLEETLRKLEAEIERLQNTIERLKTQLEDLERELALLQAKERQLEKKLKTLEQ 106
>gnl|CDD|203244 pfam05400, FliT, Flagellar protein FliT. This family contains
several bacterial flagellar FliT proteins. The flagellar
proteins FlgN and FliT have been proposed to act as
substrate specific export chaperones, facilitating
incorporation of the enterobacterial hook-associated
axial proteins (HAPs) FlgK/FlgL and FliD into the
growing flagellum. In Salmonella typhimurium flgN and
fliT mutants, the export of target HAPs is reduced,
concomitant with loss of unincorporated flagellin into
the surrounding medium.
Length = 82
Score = 28.1 bits (63), Expect = 1.3
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 18/90 (20%)
Query: 138 LAKRDLWETLADYPEARHSLMERGCQLLRKDGLLDEEAFRNSQVEHEALKDTVRRL---- 193
A+ W+ LA+ + R L+ER LR+ L S E E ++ +RR+
Sbjct: 4 AAEAGDWDELAELEDEREQLLER----LREAPL--------SPPESEEKRELLRRILAND 51
Query: 194 DTTLEHLQTRFARLMAEYLSQQAKMKQRLA 223
LQ R L QA+ +++
Sbjct: 52 AEIRALLQPRLDELSQLL--GQARRQKKAN 79
>gnl|CDD|213979 TIGR04366, cupin_WbuC, cupin fold metalloprotein, WbuC family.
Members of this family show sequence similarity to cupin
fold proteins (see pfam07883), including conserved His
residues likely to serve as metal-binding ligands. Many
members occur in bacterial O-antigen biosynthesis
regions. Some members have acquired the gene symbol wbuC
(e.g. Jarvis, et al, 2011), but publications using this
term do not ascribe a function.
Length = 132
Score = 29.1 bits (66), Expect = 1.4
Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 20/67 (29%)
Query: 31 EMYIVKRGKLNVVADDEETVLATLSAGSVFGEV--RHVLGVDLGRITSFCSKGYEIPNTK 88
E +IV G+L+V+ D++ GEV R VL G G EIP
Sbjct: 57 ETFIVLEGELDVLLFDDD------------GEVTERVVLSAGGGTF------GVEIPPGT 98
Query: 89 WLNLIVK 95
W L+
Sbjct: 99 WHTLVAL 105
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 30.0 bits (68), Expect = 1.7
Identities = 14/63 (22%), Positives = 26/63 (41%)
Query: 173 EEAFRNSQVEHEALKDTVRRLDTTLEHLQTRFARLMAEYLSQQAKMKQRLALLEQGASVN 232
EE + E + L + L+ +E + R +L EY + +++ A LE+
Sbjct: 321 EERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEF 380
Query: 233 QAT 235
T
Sbjct: 381 AET 383
>gnl|CDD|237135 PRK12555, PRK12555, chemotaxis-specific methylesterase;
Provisional.
Length = 337
Score = 29.5 bits (67), Expect = 1.7
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 199 HLQTRFARLMAEYLSQQAKMKQRLA 223
H+ FA MAE+L Q + R A
Sbjct: 188 HVDAAFAAGMAEWLDGQTALPVREA 212
>gnl|CDD|220614 pfam10174, Cast, RIM-binding protein of the cytomatrix active zone.
This is a family of proteins that form part of the CAZ
(cytomatrix at the active zone) complex which is
involved in determining the site of synaptic vesicle
fusion. The C-terminus is a PDZ-binding motif that binds
directly to RIM (a small G protein Rab-3A effector). The
family also contains four coiled-coil domains.
Length = 774
Score = 30.0 bits (67), Expect = 1.7
Identities = 18/66 (27%), Positives = 27/66 (40%)
Query: 171 LDEEAFRNSQVEHEALKDTVRRLDTTLEHLQTRFARLMAEYLSQQAKMKQRLALLEQGAS 230
E F Q E E + L TLE LQ R RL ++ ++K+ L +L+
Sbjct: 111 KSEGQFSRIQAERERQAMELFLLRDTLEKLQLRMERLQQTLDARDEEIKKLLEMLQSKGL 170
Query: 231 VNQATS 236
+A
Sbjct: 171 SAKAEE 176
Score = 28.4 bits (63), Expect = 5.6
Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 145 ETLADYPEARHSLMERGCQLLRKDGLLDEEAFRNSQVEHEALKDTVRRL-------DTTL 197
E L + ++ER + +D ++E F + E E LK+ V+ L + L
Sbjct: 436 EKLEKALAEKERIIERLKEQRDRDERYEQEEFETYKKEFEDLKEEVQNLQLKLSERELQL 495
Query: 198 EHLQTRFARLMAEYLSQQAKMKQRLALLEQ 227
E L+ ++L + L Q++ +++ LE+
Sbjct: 496 ELLKEEVSKLASNQLKQRSDLERAHIELEK 525
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 29.8 bits (67), Expect = 1.7
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 8/52 (15%)
Query: 20 DYICRKGDV------GKEMYIVKRGKLNVVADD--EETVLATLSAGSVFGEV 63
+YI + DV ++YIV G++ ++ + +E V+ TL G +FGEV
Sbjct: 400 EYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEV 451
>gnl|CDD|238717 cd01437, parp_like, Poly(ADP-ribose) polymerase (parp) catalytic
domain catalyses the covalent attachment of ADP-ribose
units from NAD+ to itself and to a limited number of
other DNA binding proteins, which decreases their
affinity for DNA. Poly(ADP-ribose) polymerase is a
regulatory component induced by DNA damage. The
carboxyl-terminal region is the most highly conserved
region of the protein. Experiments have shown that a
carboxyl 40 kDa fragment is still catalytically active.
Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP,
tankyrase) catalyze the addition of up to 100 ADP_ribose
units from NAD+. PARPs 1 and 2 are localized in the
nucleaus, bind DNA, and are activated by DNA damage.
VPARP is part of the vault ribonucleoprotein complex.
Tankyrases regulates telomere length through
interactions with telomere repeat binding factor 1.
Length = 347
Score = 29.5 bits (67), Expect = 1.8
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 11/88 (12%)
Query: 183 HEALKDTVRRLDTTLEHLQTRFARL------MAEY--LSQQAKMKQRLALLEQGASVNQA 234
EALK + LE L F L M++ + + +K + LLE + A
Sbjct: 56 EEALKRG-SSQGSQLEELSNEFYTLIPHDFGMSKPPVIDNEELLKAKRELLEALRDIEIA 114
Query: 235 TSSKRNSQAEPTHPEDV--RNSKCLLSP 260
+ ++ + + P D KC + P
Sbjct: 115 SKLLKDDEDDSDDPLDANYEKLKCKIEP 142
>gnl|CDD|223943 COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General
function prediction only].
Length = 229
Score = 29.5 bits (66), Expect = 1.8
Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 3/69 (4%)
Query: 142 DLWETLADYPEARHSLMERGCQLLRKDGLLDEEAFRNSQVEHEAL---KDTVRRLDTTLE 198
DL TL D+ A + + L+E A + EA + TLE
Sbjct: 10 DLDGTLLDFDSAEFRAVLAEFAEIGVPETLEELALLKLIEKLEARFLRGEYTGEYGLTLE 69
Query: 199 HLQTRFARL 207
L RL
Sbjct: 70 RLLELLERL 78
>gnl|CDD|227780 COG5493, COG5493, Uncharacterized conserved protein containing a
coiled-coil domain [Function unknown].
Length = 231
Score = 28.7 bits (64), Expect = 2.7
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 3/75 (4%)
Query: 136 FCLAKRDLWETLADYPEARHSLMERGCQLLRKDGLLDEEA---FRNSQVEHEALKDTVRR 192
LA + E L E R + +RK E+ R + E A K+ ++R
Sbjct: 40 QQLATKQDVEELRKETEQRQKELADEKLEVRKQKATKEDLKLLQRFQEEEFRATKEDIKR 99
Query: 193 LDTTLEHLQTRFARL 207
L+T + L R+ L
Sbjct: 100 LETIITGLGARWGIL 114
>gnl|CDD|192987 pfam12325, TMF_TATA_bd, TATA element modulatory factor 1 TATA
binding. This is the C-terminal conserved coiled coil
region of a family of TATA element modulatory factor 1
proteins conserved in eukaryotes. The proteins bind to
the TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding of
TATA binding protein. TMF1_TATA_bd is the most conserved
part of the TMFs. TMFs are evolutionarily conserved
golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells. The Rab6-binding
domain appears to be the same region as this C-terminal
family.
Length = 121
Score = 27.9 bits (63), Expect = 3.2
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 184 EALKDTVRRLDTTLEHLQTRFARLMAE 210
E L T+RRL+ L L+ ARL AE
Sbjct: 20 ERLSSTLRRLEGELASLKDELARLEAE 46
>gnl|CDD|191367 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of
eukaryotic proteins includes 5' nucleotidase enzymes,
such as purine 5'-nucleotidase EC:3.1.3.5.
Length = 448
Score = 28.8 bits (65), Expect = 3.5
Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 7/77 (9%)
Query: 132 YSDLFCLAKRDLWETLADYPEARHSLM------ERGCQLLRKDGLLDE-EAFRNSQVEHE 184
Y D+ KR W T PE + R +L R D LL+ + E
Sbjct: 305 YGDILKSKKRHGWRTALVVPELEREIEIWNTEQYRFEELQRLDILLERLYDHLDVHAELS 364
Query: 185 ALKDTVRRLDTTLEHLQ 201
L+ + LD + L+
Sbjct: 365 TLRPDLSELDAEIRELR 381
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 28.6 bits (65), Expect = 3.5
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 5/40 (12%)
Query: 190 VRR--LDTTLEHLQTRFARLMAEYLSQQAKMKQRLALLEQ 227
RR LD L ++ +A +++Y ++A +KQR ALL+Q
Sbjct: 131 ERRRFLDRLLFQIEPVYASALSQY--ERA-LKQRNALLKQ 167
>gnl|CDD|170468 PRK10474, PRK10474, putative PTS system fructose-like transporter
subunit EIIB; Provisional.
Length = 88
Score = 26.8 bits (59), Expect = 4.5
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 162 CQLLRKD-GLLDEEAFRNSQVEHEALKDTVRRLDTTLEHLQTRFAR 206
+L KD G+ EE F + + D V+R D + ++ A+
Sbjct: 41 MVILTKDIGIKFEERFAGKTIVRVNISDAVKRADAIMSKIEAHLAQ 86
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 28.2 bits (62), Expect = 6.1
Identities = 41/141 (29%), Positives = 59/141 (41%), Gaps = 33/141 (23%)
Query: 127 VRSLGYSDLFCLAKRD-------LWETLADYPEARHSLMERGCQLLRKDGLLDE-----E 174
VRSL YS + A +D L P +ME + L++ G +D E
Sbjct: 2202 VRSLPYSRVTARAMQDGRFDPEQTKLLLQRMPSMAAGVMEDALEALQQAGWIDRSQPPAE 2261
Query: 175 AFRNSQVEHEALKDTV-----RRLDTTL-EHLQTRFAR----------LMAEYLSQQAKM 218
R+ Q + ALK R+++ + + LQ AR + Y S Q K+
Sbjct: 2262 RLRDVQPQDIALKAQTLLGRARQMEPQVTDMLQNIAARHGGQLAGTQHQLKSYSSLQEKL 2321
Query: 219 KQRLALLEQ-----GASVNQA 234
KQR+AL +Q ASVN A
Sbjct: 2322 KQRVALKKQSLEEAAASVNDA 2342
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 27.9 bits (62), Expect = 6.5
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 177 RNSQVEHEALKDTVRRLDTTLEHLQ 201
R SQVE E LK +RRL+ E L
Sbjct: 117 RQSQVEFEGLKHEIRRLEEETELLN 141
>gnl|CDD|215612 PLN03169, PLN03169, chalcone synthase family protein; Provisional.
Length = 391
Score = 27.7 bits (62), Expect = 6.5
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 10/70 (14%)
Query: 163 QLLRKDGLLDEEAFRNSQVEHEALKDTVRRLDTTLEHLQTRFARLMAEYLSQ-------- 214
QL+ ++ L+D FR+++ + ALK+ + RL T ++TR+ + E L +
Sbjct: 34 QLVPQEYLVDG-YFRDTKCDDPALKEKLERLCKTTT-VKTRYVVMSKEILDKYPELATEG 91
Query: 215 QAKMKQRLAL 224
+KQRL +
Sbjct: 92 TPTIKQRLDI 101
>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
recombination, and repair].
Length = 440
Score = 27.6 bits (62), Expect = 7.5
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 7/95 (7%)
Query: 140 KRDLWETLADYPEARHSLM---ERGCQLLRKDGLLDEEAFRNSQVEHEALKDTVRRLDTT 196
K+ E LA + R E+ +L L ++ + L+ +RL+
Sbjct: 288 KKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRLRRALENQLALKKQRLERLTQRLNPQ 347
Query: 197 L----EHLQTRFARLMAEYLSQQAKMKQRLALLEQ 227
+ + LQ RL Q + ++RL L +
Sbjct: 348 IQRQQQRLQQLERRLDKALRRQLKRKRERLEALVE 382
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 27.7 bits (63), Expect = 7.8
Identities = 15/65 (23%), Positives = 23/65 (35%), Gaps = 3/65 (4%)
Query: 173 EEAFRNSQVEHEALKDTVRRLDTTLEHLQTRFARLMAEYLSQQ---AKMKQRLALLEQGA 229
E A + LK+ L L R L+ E + ++K +LA G
Sbjct: 690 EAALEYLNEQEALLKELAALLKAKPSELPERVEALLEELKELEKELEQLKAKLAAAAAGD 749
Query: 230 SVNQA 234
+ QA
Sbjct: 750 LLAQA 754
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 27.7 bits (62), Expect = 8.1
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 14/86 (16%)
Query: 153 ARHSLMERGCQLLRKDGLLDEEAFRNSQVEH----------EALKDTVRRLDTTLEHLQT 202
+ +++ G L K +LDE +R + EA+K+ + ++D E +
Sbjct: 124 ENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRAGMGAEAIKELLEKIDLDKEIEEL 183
Query: 203 RFARLMAEYLSQQAKMK--QRLALLE 226
+ + E S Q + K +RL ++E
Sbjct: 184 KIQ--LRESKSDQKRKKLLKRLEIVE 207
>gnl|CDD|203495 pfam06657, Cep57_MT_bd, Centrosome microtubule-binding domain of
Cep57. This C-terminal region of Cep57 binds, nucleates
and bundles microtubules. The N-terminal part, family
Cep57_CLD, pfam14073, is the centrosome localisation
domain Cep57.
Length = 79
Score = 25.7 bits (57), Expect = 8.2
Identities = 11/39 (28%), Positives = 17/39 (43%)
Query: 184 EALKDTVRRLDTTLEHLQTRFARLMAEYLSQQAKMKQRL 222
EAL + ++ L+ LEHL+ L Y + R
Sbjct: 13 EALAEVLKELEDELEHLKMEHQELADMYKQLDPSLGVRK 51
>gnl|CDD|223671 COG0598, CorA, Mg2+ and Co2+ transporters [Inorganic ion transport
and metabolism].
Length = 322
Score = 27.3 bits (61), Expect = 8.3
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 186 LKDTVRRLDTTLEHLQTRFARLMAEYLSQ 214
+ D + +L LE L+ R + L+ YLS
Sbjct: 225 VLDHLTQLIEMLEALRERLSSLLDAYLSL 253
>gnl|CDD|236601 PRK09637, PRK09637, RNA polymerase sigma factor SigZ; Provisional.
Length = 181
Score = 26.9 bits (60), Expect = 8.4
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 153 ARHSLMERGCQLLRKDGLLDEEAFRNSQVEHEALKDTVRRLDTTLEHL--QTRFARLMAE 210
A +++++ + R + L D+ F + + E A K+ L ++ L + A + E
Sbjct: 60 ANNTIIDFYRKKNRSEELPDDLLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTE 119
Query: 211 Y--LSQQA 216
LSQ+
Sbjct: 120 LEGLSQKE 127
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 27.7 bits (62), Expect = 9.2
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 9/95 (9%)
Query: 166 RKDGLLDEEAFRNSQVEH-EALKDTVRRLDTTLEHLQTRFARLMAEYLSQQAKMKQRLAL 224
R+ + + AF H ++L++ L L L++ L E K R
Sbjct: 793 RRPEVREYRAFMQETWLHRDSLREERPNLAIQLRELESSAEELQQELTRLIKDTKLRRKK 852
Query: 225 LEQGASVNQATSSKRNSQAEPTHPEDVRNSKCLLS 259
LEQ K+ Q + E +R + +
Sbjct: 853 LEQERK----ALEKQLDQLD----ELLRGLRDEMR 879
>gnl|CDD|187855 cd09724, CsaX_III-U, CRISPR/Cas system-associated protein CsaX.
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;
No prediction.
Length = 296
Score = 27.2 bits (60), Expect = 9.5
Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 16/93 (17%)
Query: 163 QLLRKDGLLDEEAFRNSQVEHEALKDTVRRLDTTLEHLQTRFARLMAEYLSQQAKMKQRL 222
+LL K L+DE+ + +AL D D+ R + L+ E L + + +
Sbjct: 220 KLLEKKELIDEDLIAVEALARDALND-----DSGKRDFAIRISNLLYEVLGGSKRSEDLM 274
Query: 223 ALLEQGASVNQATSSKRNSQAEPTHPEDVRNSK 255
+ +N T +K ED R ++
Sbjct: 275 YFANRELLMN-LTKAK----------EDCRLNE 296
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 27.3 bits (61), Expect = 9.6
Identities = 29/119 (24%), Positives = 45/119 (37%), Gaps = 11/119 (9%)
Query: 139 AKRDLWETLADYPEARHSLMERGCQLLRKDGLLDEEAFRNSQV----EHEA-LKDTVRRL 193
A R E +++ EAR L E+G L+ + LL+ E R EA L+ R++
Sbjct: 169 ALRQQLEVISEELEARRKLKEKG--LVSRLELLELERERAEAQGELGRLEAELEVLKRQI 226
Query: 194 DTTLEHLQTRFARLMAEYLSQQAKMKQRLALLEQGASVNQATSSKRNSQAEPTHPEDVR 252
D Q E L + + + RLA L + + R + P D
Sbjct: 227 DELQLERQQIEQTFREEVLEELTEAQARLAELRE----RLNKARDRLQRLIIRSPVDGT 281
>gnl|CDD|185333 PRK15435, PRK15435, bifunctional DNA-binding transcriptional dual
regulator/O6-methylguanine-DNA methyltransferase;
Provisional.
Length = 353
Score = 27.5 bits (61), Expect = 9.9
Identities = 27/113 (23%), Positives = 43/113 (38%), Gaps = 16/113 (14%)
Query: 137 CLAKRDLWETLADYPEARHSLME--RGCQLLRKDGLLDEEAFRNSQVEHEAL---KDTVR 191
C A+ L E + Y A +L R C+ + D + + R ++ H ++T
Sbjct: 42 CRARHALRENVRFYANASEALAAGFRPCKRCQPDK-ANPQQHRLDKITHACRLLEQETPV 100
Query: 192 RLDTTLE-------HLQTRFARL--MAEYLSQQAKMKQRL-ALLEQGASVNQA 234
L+ + HL F M QQA +RL L +G SV +
Sbjct: 101 TLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVTTS 153
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
0.318 0.133 0.381
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,076,463
Number of extensions: 1324216
Number of successful extensions: 1357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1349
Number of HSP's successfully gapped: 73
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)