RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6789
(331 letters)
>gnl|CDD|238016 cd00059, FH, Forkhead (FH), also known as a "winged helix". FH is
named for the Drosophila fork head protein, a
transcription factor which promotes terminal rather than
segmental development. This family of transcription
factor domains, which bind to B-DNA as monomers, are
also found in the Hepatocyte nuclear factor (HNF)
proteins, which provide tissue-specific gene regulation.
The structure contains 2 flexible loops or "wings" in
the C-terminal region, hence the term winged helix.
Length = 78
Score = 94.5 bits (236), Expect = 1e-24
Identities = 33/77 (42%), Positives = 47/77 (61%), Gaps = 4/77 (5%)
Query: 51 KPPFTYTELIEQALKEKH--QLTVSGIYQWISERFPYYNQNDDRWKNSVRHNLSINPHFR 108
KPP++Y+ LI A++ +LT+S IY+WIS+ FPY+ W+NS+RHNLS+N F
Sbjct: 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFV 60
Query: 109 KGVKAS--QGAGHLWNL 123
K + G G W L
Sbjct: 61 KVPREPDEPGKGSYWTL 77
>gnl|CDD|214627 smart00339, FH, FORKHEAD. FORKHEAD, also known as a "winged
helix".
Length = 89
Score = 91.9 bits (229), Expect = 2e-23
Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 51 KPPFTYTELIEQALKEKH--QLTVSGIYQWISERFPYYNQNDDRWKNSVRHNLSINPHFR 108
KPP++Y LI A+ +LT+S IY+WI + FPYY +N W+NS+RHNLS+N F
Sbjct: 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFV 60
Query: 109 K--GVKASQGAGHLW 121
K G G W
Sbjct: 61 KVPREGDRPGKGSYW 75
>gnl|CDD|189470 pfam00250, Fork_head, Fork head domain.
Length = 96
Score = 90.8 bits (226), Expect = 6e-23
Identities = 38/80 (47%), Positives = 49/80 (61%), Gaps = 6/80 (7%)
Query: 51 KPPFTYTELIEQALK---EKHQLTVSGIYQWISERFPYYNQNDDRWKNSVRHNLSINPHF 107
KPP++Y LI A++ EK LT+S IYQWI + FPYY QN W+NS+RHNLS+N F
Sbjct: 1 KPPYSYIALITMAIQQSPEK-MLTLSEIYQWIMDLFPYYRQNKQGWQNSIRHNLSLNKCF 59
Query: 108 RKGVKA--SQGAGHLWNLSD 125
K ++ G G W L
Sbjct: 60 IKVPRSPDKPGKGSYWTLDP 79
>gnl|CDD|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family
[Transcription].
Length = 610
Score = 60.6 bits (147), Expect = 3e-10
Identities = 31/109 (28%), Positives = 44/109 (40%), Gaps = 2/109 (1%)
Query: 47 KTHRKPPFTYTELIEQALKEKHQ--LTVSGIYQWISERFPYYNQNDDRWKNSVRHNLSIN 104
KP F+Y I QA+ +T+S IY WIS PYY W+NS+RHNLS+N
Sbjct: 333 NRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLN 392
Query: 105 PHFRKGVKASQGAGHLWNLSDMEPVEDASKSNWKKNRLKTYLESLQPSE 153
F K +++ G +S K + +
Sbjct: 393 KSFEKVPRSASQPGKGCFWKIDYSYIYEKESKRNPRSPKKSPSAHSVHQ 441
Score = 52.5 bits (126), Expect = 2e-07
Identities = 30/78 (38%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 48 THRKPPFTYTELIEQALKEKH--QLTVSGIYQWISERFPYYNQNDDRWKNSVRHNLSINP 105
T+ PP++Y A+ LT+S IY WI F YY + RW+NS+RHNLS+N
Sbjct: 83 TYYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLND 142
Query: 106 HFRKGVKAS--QGAGHLW 121
F K + + GH W
Sbjct: 143 AFIKIEGRNGAKVKGHFW 160
>gnl|CDD|203018 pfam04449, Fimbrial_CS1, CS1 type fimbrial major subunit.
Fimbriae, also known as pili, form filaments radiating
from the surface of the bacterium to a length of 0.5-1.5
micrometres. They enable the cell to colonise host
epithelia. This family constitutes the major subunits of
CS1 like pili, including CS2 and CFA1 from Escherichia
coli, and also the Cable type II pilin major subunit
from Burkholderia cepacia. The major subunit of CS1 pili
is called CooA. Periplasmic CooA is mostly complexed
with the assembly protein CooB. In addition, a small
pool of CooA multimers, and CooA-CooD complexes exists,
but the functional significance is unknown. A member of
this family has also been identified in Salmonella typhi
and Salmonella enterica.
Length = 143
Score = 31.9 bits (73), Expect = 0.18
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 183 NTMSLAHDPLQPFEVYSQESKTFPYEECKDVLYIQSNDNVL 223
+ + L + P + E Y+ +K ++ KDV + D VL
Sbjct: 27 SAVKLTYLPGKGLESYTVNTKIHTNDKTKDVQVKLAADPVL 67
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 32.2 bits (74), Expect = 0.40
Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 202 SKTFPYEECKDVLYIQSNDNVLY-TP----HEDHKLYHNDNVLYTPGEDHKLYQYEPSKN 256
K + + KD + +S+ LY T H D ++Y G D + +
Sbjct: 296 LKFKKFGDDKDRVLQKSDGTYLYFTRDIAYHLYKFERGFDKLIYVLGADQHGHFKQLKAV 355
Query: 257 LIMAAYDGGQEKVE 270
L + Y +E +
Sbjct: 356 LELLGYGPDKEVLL 369
>gnl|CDD|176898 cd08889, SRPBCC_PITPNM1-2_like, Lipid-binding SRPBCC domain of
mammalian PITPNM1-2 and related proteins (Class IIA
PITPs). This subgroup includes an N-terminal SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class II phosphatidylinositol transfer protein
(PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal
domain-interacting receptor2) and
PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related
proteins. These are membrane associated multidomain
proteins belonging to the PITP family of lipid transfer
proteins, and to the SRPBCC domain superfamily of
proteins that bind hydrophobic ligands. SRPBCC domains
have a deep hydrophobic ligand-binding pocket. In vitro,
PITPs bind phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Ablation of the mouse gene encoding PITPNM1
results in early embryonic death. PITPNM1 is localized
chiefly to the Golgi apparatus, and under certain
conditions translocates to the lipid droplets. Targeting
to the latter is dependent on a specific threonine
residue within the SRPBCC domain. PITPNM1 plays a part
in Golgi-mediated transport. It regulates diacylglycerol
(DAG) production at the trans-Golgi network (TGN) via
the CDP-choline pathway. Drosophila RdgB, the founding
member of the PITP family, is implicated in the visual
and olfactory transduction. RdgB is required for
maintenance of ultra structure in photoreceptors and for
sensory transduction. The mouse PITPNM1 gene rescues the
phenotype of Drosophila rdgB mutant flies. In addition
to the SRPBCC domain, PITPNM1 and -2 contain a
Rho-inhibitory domain (Rid), six hydrophobic stretches,
a DDHD calcium binding region, and a C-terminal tyrosine
kinase Pyk2-binding / HAD-like phosphohydrolase domain.
PITPNM1 has a role in regulating cell morphogenesis
through its Rho inhibitory domain (Rid). This
SRPBCC_PITPNM1-2_like domain model includes the first 52
residues of the 224 residues Rid (Rho-inhibitory
domain).
Length = 260
Score = 31.3 bits (71), Expect = 0.52
Identities = 30/93 (32%), Positives = 37/93 (39%), Gaps = 20/93 (21%)
Query: 224 YTPHEDHKLYHNDNVLYTPGEDHKL--YQYEPSKNLIMAAYDGGQEKVEIFASDTISKNL 281
Y ED KLY ++ P D + Y+ P K IM AY KVE
Sbjct: 153 YKAEEDPKLYVSEKTGRGPLSDDWIEEYKDPPGKGPIMCAYK--LCKVE----------- 199
Query: 282 IMAAYDGGQEKVEIFASDTISRKSI---HRRKW 311
Y G Q K+E F D RK + HR+ W
Sbjct: 200 --FRYWGMQTKIERFIHDVALRKVMLRAHRQAW 230
>gnl|CDD|237764 PRK14607, PRK14607, bifunctional glutamine
amidotransferase/anthranilate phosphoribosyltransferase;
Provisional.
Length = 534
Score = 28.1 bits (63), Expect = 6.9
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 275 DTISKNLIMAAYDGGQEKVEIFASDTISRKSIHRRKWKSSRRIRFPG 321
D+ + N+ + G E++E+ +D I+ + I S + PG
Sbjct: 9 DSFTYNIYQYIGELGPEEIEVVRNDEITIEEI--EALNPSHIVISPG 53
>gnl|CDD|238657 cd01347, ligand_gated_channel, TonB dependent/Ligand-Gated channels
are created by a monomeric 22 strand (22,24)
anti-parallel beta-barrel. Ligands apparently bind to
the large extracellular loops. The N-terminal 150-200
residues form a plug from the periplasmic end of barrel.
Energy (proton-motive force) and TonB-dependent
conformational alteration of channel (parts of plug, and
loops 7 and 8) allow passage of ligand. FepA residues
12-18 form the TonB box, which mediates the interaction
with the TonB-containing inner membrane complex. TonB
preferentially interacts with ligand-bound receptors.
Transport thru the channel may resemble passage thru an
air lock. In this model, ligand binding leads to
closure of the extracellular end of pore, then a
TonB-mediated signal facillitates opening of the
interior side of pore, deforming the N-terminal plug and
allowing passage of the ligand to the periplasm. Such a
mechanism would prevent the free diffusion of small
molecules thru the pore.
Length = 635
Score = 28.2 bits (63), Expect = 7.5
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 5/67 (7%)
Query: 69 QLTVSGIYQWISERFPYYNQNDDRWKNS--VRHNLSINPHFRKGVKASQGAGHLWNLSDM 126
LT G ++ +++ ++ K +LS + F K + G NL D
Sbjct: 548 GLTAGGGVRYRGKQYADTANGNNTVKVPGYTLVDLSASYQFTKNLTLRLGVN---NLFDK 604
Query: 127 EPVEDAS 133
+ S
Sbjct: 605 DYYTSLS 611
>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional.
Length = 332
Score = 27.8 bits (62), Expect = 8.2
Identities = 12/42 (28%), Positives = 16/42 (38%), Gaps = 5/42 (11%)
Query: 161 QNSTETPAPSMETMPQPQPQPLNTMSLAHDPLQPFEVYSQES 202
Q +T P +ET P P QP + EV Q+
Sbjct: 57 QPNTLNPQSYVETTPPPFQQPQT-----EESESENEVQIQQE 93
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
0.313 0.129 0.395
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,332,615
Number of extensions: 1472806
Number of successful extensions: 1016
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1013
Number of HSP's successfully gapped: 18
Length of query: 331
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 234
Effective length of database: 6,635,264
Effective search space: 1552651776
Effective search space used: 1552651776
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: 59 (26.4 bits)