RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1414
(551 letters)
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 66.6 bits (163), Expect = 9e-13
Identities = 49/204 (24%), Positives = 89/204 (43%), Gaps = 39/204 (19%)
Query: 303 YEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSCNLV 362
+E++ +L+ E+ ++RDL ++ +VFL+ + K + P +E++ +F N+ +IYEF +
Sbjct: 1 RQEVIKELLQTERNYVRDLKLLVEVFLKPLDKELLPLSPEEVELLFGNIEEIYEFHRIFL 60
Query: 363 GILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKNPEVS 422
LE+ +E + S IG +LA F +YS Y + +LL++LK + +
Sbjct: 61 KSLEERVEE-WDKSGPRIGDVFLKLAPF--FKIYSEYCSNHPDA---LELLKKLK--KFN 112
Query: 423 IPLQSDCCAKDITYYKCPEKLLEELKNPEVSIPLQSGGQGFKEAVKYYLPKLFLHPLWHC 482
Q + LE+ + E + L L L P+
Sbjct: 113 KFFQ---------------EFLEKAE---------------SECGRLKLESLLLKPVQRL 142
Query: 483 FLYFDYI-RILRGLSPDKEDRESL 505
Y + +L+ EDRE L
Sbjct: 143 TKYPLLLKELLKHTPDGHEDREDL 166
Score = 49.6 bits (119), Expect = 5e-07
Identities = 19/59 (32%), Positives = 39/59 (66%)
Query: 226 YEEIVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSLNF 284
+E++ +L+ E+ ++RDL ++ +VFL+ + K + P +E++ +F N+ +IYEF F
Sbjct: 1 RQEVIKELLQTERNYVRDLKLLVEVFLKPLDKELLPLSPEEVELLFGNIEEIYEFHRIF 59
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 65.0 bits (159), Expect = 2e-12
Identities = 50/201 (24%), Positives = 85/201 (42%), Gaps = 38/201 (18%)
Query: 306 IVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSCNLVGIL 365
++ +L+ E+ ++RDL ++ +VFL+ + K + EL+ +F N+ +IYEF + + L
Sbjct: 1 VLKELLQTERNYVRDLKLLVEVFLKPLKKELKLLSPNELETLFGNIEEIYEFHRDFLDEL 60
Query: 366 EDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKNPEVSIPL 425
E+ +E + S IG +L E F +YS Y + + E L + KNP
Sbjct: 61 EERIEE-WDDSVERIGDVFLKLEEF--FKIYSEYCSN--HPDALELLKKLKKNP------ 109
Query: 426 QSDCCAKDITYYKCPEKLLEELKNPEVSIPLQSGGQGFKEAVKYYLPKLFLHPLWHCFLY 485
+ + LK E S + + L L L P+ Y
Sbjct: 110 ----------------RFQKFLKEIESSPQCR----------RLTLESLLLKPVQRLTKY 143
Query: 486 FDYI-RILRGLSPDKEDRESL 505
+ +L+ D EDRE L
Sbjct: 144 PLLLKELLKHTPEDHEDREDL 164
Score = 44.6 bits (106), Expect = 3e-05
Identities = 18/56 (32%), Positives = 36/56 (64%)
Query: 229 IVHDLVTDEKQHLRDLHMINKVFLEEIVKLIPPGKCKELDQMFANLMDIYEFSLNF 284
++ +L+ E+ ++RDL ++ +VFL+ + K + EL+ +F N+ +IYEF +F
Sbjct: 1 VLKELLQTERNYVRDLKLLVEVFLKPLKKELKLLSPNELETLFGNIEEIYEFHRDF 56
>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
substrate binding proteins. Prokaryotic homologues are
represented by a separate alignment: PBPb.
Length = 133
Score = 57.3 bits (139), Expect = 5e-10
Identities = 17/32 (53%), Positives = 23/32 (71%)
Query: 16 IGSPWRDRISLAILELQEKGTIQMLYDKWWKN 47
GSP RD +S AIL+L E G ++ L +KWWK+
Sbjct: 102 KGSPLRDDLSRAILKLSESGELEKLRNKWWKD 133
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 59.6 bits (145), Expect = 7e-10
Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 16 IGSPWRDRISLAILELQEKGTIQMLYDKWWKNTGD 50
GSP RD++S AILEL+E G +Q L +KWWK G+
Sbjct: 205 KGSPLRDKLSRAILELRESGELQKLENKWWKKKGE 239
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 54.9 bits (133), Expect = 8e-09
Identities = 29/115 (25%), Positives = 58/115 (50%), Gaps = 12/115 (10%)
Query: 306 IVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSCNLVG 363
++ +L+ E+ ++RDL ++ +VFL+ + + ++ +E+ +F+N+ +I E +
Sbjct: 1 VIQELLQTERSYVRDLKILVEVFLKPLRESPILSE---EEIKTIFSNIEEILELHQEFLE 57
Query: 364 ILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYSRYAKDITYYKCPEKLLEELKN 418
LE+ LE IG + A F VYS Y + Y +LL++L+
Sbjct: 58 ELEERLE--EWPDIQRIGDIFLKFAPF--FKVYSTY---CSNYPRALELLKKLRK 105
Score = 43.0 bits (102), Expect = 1e-04
Identities = 14/58 (24%), Positives = 35/58 (60%), Gaps = 5/58 (8%)
Query: 229 IVHDLVTDEKQHLRDLHMINKVFLEEIVK--LIPPGKCKELDQMFANLMDIYEFSLNF 284
++ +L+ E+ ++RDL ++ +VFL+ + + ++ +E+ +F+N+ +I E F
Sbjct: 1 VIQELLQTERSYVRDLKILVEVFLKPLRESPILSE---EEIKTIFSNIEEILELHQEF 55
>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
nucleosome is an octamer containing two H2A, H2B, H3,
and H4 subunits. The H2A subunit performs essential
roles in maintaining structural integrity of the
nucleosome, chromatin condensation, and binding of
specific chromatin-associated proteins.
Length = 115
Score = 50.4 bits (121), Expect = 7e-08
Identities = 28/89 (31%), Positives = 48/89 (53%), Gaps = 5/89 (5%)
Query: 113 KEAIEKSKKKIS-----CLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILK 167
K +K KK S L PV +IH L K +V +Y+ AVLEY++A++L+
Sbjct: 1 KGGGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLE 60
Query: 168 LAGNYVKNIRHVEVAQQDIKVAMYADKVL 196
LAGN ++ + + + +++A+ D+ L
Sbjct: 61 LAGNAARDNKKKRITPRHLQLAVRNDEEL 89
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 50.9 bits (121), Expect = 9e-08
Identities = 32/108 (29%), Positives = 59/108 (54%), Gaps = 7/108 (6%)
Query: 112 AKEAIEKSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGN 171
K+A+ +S K + L PV +I L K ++ +Y+ AVLEY++A++L+LAGN
Sbjct: 11 GKKAVSRSAK--AGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGN 68
Query: 172 YVKNIRHVEVAQQDIKVAMYADKVLMDMFYQDEHTSDSGSI---VHSV 216
++ + + + I++A+ D+ L + E T SG + +H+V
Sbjct: 69 AARDNKKNRIVPRHIQLAIRNDEELGKLL--GEVTIASGGVLPNIHAV 114
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 49.1 bits (118), Expect = 1e-07
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 118 KSKKKISCLVLPVEKIHYLLSKDVLQYK-VEMNVSIYITAVLEYISADILKLAGNYVKNI 176
S+ I L LP ++ L + + + + LE + +IL+ AG ++
Sbjct: 1 SSRLLI--LKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHA 58
Query: 177 RHVEVAQQDIKVAMYAD 193
+ + +DI++A+ D
Sbjct: 59 KRKTITPRDIQLAVRLD 75
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 50.2 bits (120), Expect = 1e-07
Identities = 25/88 (28%), Positives = 49/88 (55%), Gaps = 3/88 (3%)
Query: 112 AKEAIEKSKKKISC---LVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKL 168
K A + + S L+ PV ++ LL K + ++ +Y+ AVLEY++A+IL+L
Sbjct: 8 GKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILEL 67
Query: 169 AGNYVKNIRHVEVAQQDIKVAMYADKVL 196
AGN ++ + + + +++A+ D+ L
Sbjct: 68 AGNAARDNKKKRIIPRHLQLAIRNDEEL 95
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 48.8 bits (116), Expect = 4e-07
Identities = 25/85 (29%), Positives = 51/85 (60%), Gaps = 3/85 (3%)
Query: 113 KEAIEKSKKKISCLVLPVEKIHYLLSKDVLQY-KVEMNVSIYITAVLEYISADILKLAGN 171
K+ +S + + L PV +IH L + V + +V ++Y A+LEY++A++L+LAGN
Sbjct: 26 KKPTSRSSR--AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGN 83
Query: 172 YVKNIRHVEVAQQDIKVAMYADKVL 196
K+++ + + +++A+ D+ L
Sbjct: 84 ASKDLKVKRITPRHLQLAIRGDEEL 108
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 47.3 bits (113), Expect = 7e-07
Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 126 LVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKNIRHVEVAQQD 185
L PV +IH LL K +V +Y+ AVLEY++A++L+LAGN ++ + + +
Sbjct: 8 LQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRH 67
Query: 186 IKVAMYADKVLMDMF 200
+++A+ D+ L +
Sbjct: 68 LQLAIRNDEELNKLL 82
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 47.0 bits (112), Expect = 2e-06
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 12/77 (15%)
Query: 118 KSKKKIS-----CLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNY 172
KK +S L PV ++H L K +V +Y+ AVLEY++A++L+LAGN
Sbjct: 13 GKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNA 72
Query: 173 VKNI-------RHVEVA 182
K+ RH+++A
Sbjct: 73 AKDNKKKRITPRHIQLA 89
>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
Length = 139
Score = 46.5 bits (110), Expect = 3e-06
Identities = 25/86 (29%), Positives = 50/86 (58%), Gaps = 2/86 (2%)
Query: 111 EAKEAIEKSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAG 170
+A +++ +S K + L PV +I L +V +Y++AVLEY++A++L+LAG
Sbjct: 15 KATKSVSRSSK--AGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAG 72
Query: 171 NYVKNIRHVEVAQQDIKVAMYADKVL 196
N ++ + + + I++A+ D+ L
Sbjct: 73 NAARDNKKNRIVPRHIQLAVRNDEEL 98
>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
Length = 132
Score = 46.0 bits (109), Expect = 5e-06
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 112 AKEAIEKSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYITAVLEYISADILKLAGN 171
K+A +S K + L PV +I L +V +Y+ AVLEY++A++L+LAGN
Sbjct: 13 GKKATSRSAK--AGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGN 70
Query: 172 YVKNIRHVEVAQQDIKVAMYADKVL 196
++ + + + I++A+ D+ L
Sbjct: 71 AARDNKKSRIVPRHIQLAVRNDEEL 95
>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
Length = 134
Score = 39.6 bits (92), Expect = 7e-04
Identities = 34/117 (29%), Positives = 57/117 (48%), Gaps = 21/117 (17%)
Query: 109 MHEAKEAIEKSKKKISC------LVLPVEKIHYLLSKDVLQYKVEMNVS--IYITAVLEY 160
M K+A +K+ K S L+ PV ++ LL + QY + S +Y+ AVLEY
Sbjct: 1 MATPKQAKKKASKSGSGRSAKAGLIFPVGRVGSLLRRG--QYARRIGASGAVYMAAVLEY 58
Query: 161 ISADILKLAGNYVKNIRHVEVAQQDIKVAMYADKVLMDMFYQDEHTSDSGSIVHSVS 217
++A++L+L+ VK AQQ K + + D+ D GS++ +V+
Sbjct: 59 LTAELLELS---VK-----AAAQQAKKPKRLTPRTVTLAVRHDD---DLGSLLKNVT 104
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 33.0 bits (76), Expect = 0.26
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 17 GSPWRDRISLAILELQEKGTIQMLYDKW 44
++ A+ EL+ GT+ LY+KW
Sbjct: 190 DPELLAALNKALAELKADGTLAKLYEKW 217
>gnl|CDD|239873 cd04408, RhoGAP_GMIP, RhoGAP_GMIP: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain of GMIP (Gem
interacting protein). GMIP plays important roles in
neurite growth and axonal guidance, and interacts with
Gem, a member of the RGK subfamily of the Ras small
GTPase superfamily, through the N-terminal half of the
protein. GMIP contains a C-terminal RhoGAP domain. GMIP
inhibits RhoA function, but is inactive towards Rac1 and
Cdc41. Small GTPases cluster into distinct families, and
all act as molecular switches, active in their GTP-bound
form but inactive when GDP-bound. The Rho family of
GTPases activates effectors involved in a wide variety
of developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 200
Score = 30.2 bits (68), Expect = 1.9
Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 12/99 (12%)
Query: 82 SKPSPHTTSDVEERVRRQFPTPIDKWAMHE-----AKEAIEKSKKKISCLVLPVEKIHYL 136
S SPH + V + ++ P P+ + +++ AKE S+K + I L
Sbjct: 64 SGHSPHDITSVLKHFLKELPEPVLPFQLYDDFIALAKELQRDSEKAAESPSIVENIIRSL 123
Query: 137 LSKDVLQYKVEMNVSIYITAVLEYISADILKLAGNYVKN 175
K++L + VS Y T L ++ A + ++A + N
Sbjct: 124 --KELL---GRLPVSNYNT--LRHLMAHLYRVAERFEDN 155
>gnl|CDD|238285 cd00515, HAM1, NTPase/HAM1. This family consists of the HAM1
protein and pyrophosphate-releasing xanthosine/ inosine
triphosphatase. HAM1 protects the cell against
mutagenesis by the base analog 6-N-hydroxylaminopurine
(HAP) in E. Coli and S. cerevisiae. A Ham1-related
protein from Methanococcus jannaschii is a novel NTPase
that has been shown to hydrolyze nonstandard nucleotides
such as XTP to XMP and ITP to IMP, but not the standard
nucleotides, in the presence of Mg or Mn ions. The
enzyme exists as a homodimer. The HAM1 protein may be
acting as an NTPase by hydrolyzing the HAP triphosphate.
Length = 183
Score = 29.8 bits (68), Expect = 2.5
Identities = 28/111 (25%), Positives = 38/111 (34%), Gaps = 42/111 (37%)
Query: 338 PGKCKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEASNVV-IGSCLEELA-----EAA 391
GK KE ++ A GI + + ++ GS EE A AA
Sbjct: 8 KGKLKEFKEILAPF-----------GI---EVVSLKDIIDIEETGSTFEENALLKARAAA 53
Query: 392 E--------------FD-------VYS-RYAKDITYYKCPEKLLEELKNPE 420
E D VYS R+A + + EKLLE L+ E
Sbjct: 54 EALGLPVLADDSGLCVDALNGFPGVYSARFAGEHDDAENNEKLLELLEGDE 104
>gnl|CDD|221400 pfam12059, DUF3540, Protein of unknown function (DUF3540). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 212 to 238 amino acids in length.
This protein has a conserved SCL sequence motif.
Length = 195
Score = 29.6 bits (67), Expect = 3.2
Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 17/97 (17%)
Query: 95 RVRRQFPTPIDKWAMHEAKEAIEKSKKKISCLVLPVEKIHYLLSKDVLQYKVEMNVSIYI 154
V + + ++++ SCL+ P VL V +YI
Sbjct: 5 TVTGAAGD----GFSVVDPDGVLRARRAASCLLQPEVGDL------VLICAVADGPHLYI 54
Query: 155 TAVLEYISAD--ILKLAGNYVKNIRHVEVAQQDIKVA 189
A+LE +AD L L G + A + +++A
Sbjct: 55 LAILERAAADTATLSLPGR-----GLLRSAAKGLELA 86
>gnl|CDD|226509 COG4022, COG4022, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 286
Score = 29.7 bits (67), Expect = 3.7
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 4/85 (4%)
Query: 338 PGKCKELDQMFANLMDIYEFSCNLVGILEDNLEMCNEASNVVIGSCLEELAEAAEFDVYS 397
K L ++ A+ +D+ + ++ GI E+ + E S++V + + E A+
Sbjct: 178 AETAKRLRKLEADELDLLVIAVHVTGIDEEEAQGLVENSDIVTSCASKYIRELAKRRPIL 237
Query: 398 RYAKDITYYKCPEK----LLEELKN 418
+ I + +K L+E K+
Sbjct: 238 QVGSAIPLFALTQKGKELLIERAKD 262
>gnl|CDD|220970 pfam11077, DUF2616, Protein of unknown function (DUF2616). This
cysteine-rich family is expressed by the
double-stranded Nucleopolyhedrovirus, a member of the
Baculoviridae family of dsDNA viruses. The function is
not known.
Length = 172
Score = 28.9 bits (65), Expect = 4.4
Identities = 7/49 (14%), Positives = 17/49 (34%), Gaps = 3/49 (6%)
Query: 38 QMLYDKWWKNTGD---VLQQVHPTLTAREDACLYVESLVLKILAMLCSK 83
++Y KW L+ + + D C + ++ + C +
Sbjct: 24 NLVYKKWLSEIEKIRLALEDIRSSDYGGSDKCDFCFTVNTDTDRLFCKQ 72
>gnl|CDD|223904 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 29.2 bits (65), Expect = 5.8
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 20 WRDRISLAILELQEKGTIQMLYDKWWK 46
+ ++ A+ EL+ GT+Q + DKW+
Sbjct: 238 LLEAVNKALKELKADGTLQKISDKWFG 264
>gnl|CDD|133004 cd02510, pp-GalNAc-T, pp-GalNAc-T initiates the formation of
mucin-type O-linked glycans. UDP-GalNAc: polypeptide
alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T)
initiate the formation of mucin-type, O-linked glycans
by catalyzing the transfer of
alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to
hydroxyl groups of Ser or Thr residues of core proteins
to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These
enzymes are type II membrane proteins with a GT-A type
catalytic domain and a lectin domain located on the
lumen side of the Golgi apparatus. In human, there are
15 isozymes of pp-GalNAc-Ts, representing the largest of
all glycosyltransferase families. Each isozyme has
unique but partially redundant substrate specificity for
glycosylation sites on acceptor proteins.
Length = 299
Score = 29.1 bits (66), Expect = 6.7
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 213 VHSVSETTSSELTYEEIVHDLVTD--EKQHLRDLHMINKVFLEEIVKLI 259
VHSV T EL +EI+ LV D +K L+ L VK++
Sbjct: 18 VHSVINRTPPEL-LKEII--LVDDFSDKPELKLLLEEYYKKYLPKVKVL 63
>gnl|CDD|226624 COG4143, TbpA, ABC-type thiamine transport system, periplasmic
component [Coenzyme metabolism].
Length = 336
Score = 28.9 bits (65), Expect = 7.8
Identities = 34/126 (26%), Positives = 48/126 (38%), Gaps = 22/126 (17%)
Query: 355 YEFSCNLVGILEDNLEMCNEA--------SNVVIGSCLEELAEAAEFDVYSRYAKDITYY 406
Y N V L D +E+ N ++VV+G LA A E +++ Y D +
Sbjct: 54 YGCKVNFVA-LGDGVELLNRLILEGKNPKADVVVGLDNNLLARARETGLFAPYGVDAS-- 110
Query: 407 KCPEKLLEELKNPEVSIPLQSDCCA--KDITYYKCPEKLLEELKNPE------VSIPLQS 458
+ E K ++P A D T K P K L++L PE P S
Sbjct: 111 --DVPVPEGWKIDTFALPYDYGYFAFVYDKTKLKNPPKSLKDLVEPEYAGKIIYQDPRTS 168
Query: 459 G-GQGF 463
G GF
Sbjct: 169 SPGLGF 174
>gnl|CDD|176131 cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 28.3 bits (64), Expect = 8.2
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 511 LLKALQVDLSDSLQNYP--RNGRDTGIRALIDATLRR 545
L + V ++ L YP GR +G+RALID L
Sbjct: 84 LARRRSVTWAE-LAGYPLIALGRGSGVRALIDRALAA 119
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
0.320 0.136 0.398
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,590,711
Number of extensions: 2870392
Number of successful extensions: 2505
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2497
Number of HSP's successfully gapped: 56
Length of query: 551
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 449
Effective length of database: 6,413,494
Effective search space: 2879658806
Effective search space used: 2879658806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.3 bits)