RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8916
(520 letters)
>gnl|CDD|227431 COG5100, NPL4, Nuclear pore protein [Nuclear structure].
Length = 571
Score = 260 bits (666), Expect = 4e-80
Identities = 129/355 (36%), Positives = 194/355 (54%), Gaps = 26/355 (7%)
Query: 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELN--TYNFALFKQRNKTDEIFSS-RD 231
I R +S G +R+ + SD L K+ FE+N ++ + EIFS +D
Sbjct: 2 IFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKD 60
Query: 232 QTIASVGLSNGDFVYMMNLSSPNDEKPSTSSNHLNIYETKKKASTTPSTPTEFKSKLSNA 291
QT +GL +G +Y+ + +I +K P P + SK
Sbjct: 61 QTPDDLGLRHGQMLYL---------------EYSDIASNNEKKRDVPGKPKQDCSKGIKR 105
Query: 292 FSSSNNIVEDEVDKELWKTDGQVKRKRDDKFCRHGANALCIHCSPLEPYDEEYLREQNVK 351
S +++D +D L K DG ++R C+HG+N +C +CSPL+P+DE+Y ++ +K
Sbjct: 106 EKDSMPVIQDPIDDSLEKEDGLIRRSMT-MLCQHGSNGMCSYCSPLDPWDEKYYKDNKIK 164
Query: 352 HMSFHAYLRKQCAGVDR----GKFVV-LEDLSCRIKEGCRE-HPPWPRGICSKCQPNAIT 405
H+SFH+YL K + ++ ++V LE+ S +KE C + H PWP GIC+KCQP+ I
Sbjct: 165 HLSFHSYLEKMNSNKNKLGSVESYIVPLEEPSFTVKETCEDGHGPWPHGICNKCQPSNII 224
Query: 406 LNRQVYRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIY 465
L QV+R VD+VEF+ + +VE F+ WR +G QR G LYG+Y + ++PLGIKAVV AIY
Sbjct: 225 LAPQVFRMVDHVEFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIY 284
Query: 466 EPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQVGWIFTDLVAEDLQLGTYFQSR 520
EPPQE D + +++ AS GL ++G IFTDL+ E G+ R
Sbjct: 285 EPPQEDEPDGFTIEEWADEGLMDAPASGTGLERIGMIFTDLLDEGSNRGSVTCKR 339
Score = 111 bits (279), Expect = 4e-26
Identities = 53/160 (33%), Positives = 80/160 (50%), Gaps = 37/160 (23%)
Query: 15 GLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYF 74
GL ++G IFTDL+ E G+V R+ DS+FLS+ E +Q +HPN + + G F
Sbjct: 314 GLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEF 373
Query: 75 GSKFVTICVTVNECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQV 134
GSKFVTI ++ G+ D ++ ++ YQV
Sbjct: 374 GSKFVTIVIS------------------------------------GNLDGEIGLQSYQV 397
Query: 135 SNQCMALVRDGCLIPTKDAPELGYIKESSDKQYVPDVFYK 174
SNQCMALV+ ++P++D P + +YVPD+FY+
Sbjct: 398 SNQCMALVKADYILPSED-PRRFLATKEDQTRYVPDIFYR 436
>gnl|CDD|147282 pfam05020, zf-NPL4, NPL4 family, putative zinc binding region. The
HRD4 gene was identical to NPL4, a gene previously
implicated in nuclear transport. Using a diverse set of
substrates and direct ubiquitination assays, analysis
revealed that HRD4/NPL4 is required for a poorly
characterized step in ER-associated degradation after
ubiquitination of target proteins but before their
recognition by the 26S proteasome. This region of the
protein contains possibly two zinc binding motifs
(Bateman A pers. obs.). Npl4p physically associates with
Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex.
The Cdc48-Ufd1-Npl4 complex functions in the recognition
of several polyubiquitin-tagged proteins and facilitates
their presentation to the 26S proteasome for processive
degradation or even more specific processing.
Length = 147
Score = 227 bits (581), Expect = 8e-73
Identities = 80/147 (54%), Positives = 104/147 (70%), Gaps = 6/147 (4%)
Query: 297 NIVEDEVDKELWKTDGQVKRKRDDKFCRHGANALCIHCSPLEPYDEEYLREQNVKHMSFH 356
+ E VD EL K DG++KRKRD K CRHG +C +CSPLEP+DEEYL+E +KHMSFH
Sbjct: 1 KVKELPVDDELEKQDGKIKRKRDSKLCRHGDKGMCEYCSPLEPWDEEYLKEHKIKHMSFH 60
Query: 357 AYLRKQCAGVDR---GKFVV--LEDLSCRIKEGCRE-HPPWPRGICSKCQPNAITLNRQV 410
AYLRK + ++ G + LE+ RIK+ C HPPWP+GICSKCQP+AITL RQ
Sbjct: 61 AYLRKLNSATNKKESGSSYIPPLEEPDYRIKKNCPSGHPPWPKGICSKCQPSAITLQRQE 120
Query: 411 YRHVDNVEFENRTLVERFLEYWRVTGH 437
+R VD+VEF + ++ +FL++WR TG
Sbjct: 121 FRMVDHVEFASSEIINQFLDFWRSTGT 147
>gnl|CDD|218386 pfam05021, NPL4, NPL4 family. The HRD4 gene was identical to NPL4,
a gene previously implicated in nuclear transport. Using
a diverse set of substrates and direct ubiquitination
assays, analysis revealed that HRD4/NPL4 is required for
a poorly characterized step in ER-associated degradation
after ubiquitination of target proteins but before their
recognition by the 26S proteasome. Npl4p physically
associates with Cdc48p via Ufd1p to form a
Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex
functions in the recognition of several
polyubiquitin-tagged proteins and facilitates their
presentation to the 26S proteasome for processive
degradation or even more specific processing.
Length = 306
Score = 187 bits (476), Expect = 3e-55
Identities = 64/161 (39%), Positives = 87/161 (54%), Gaps = 37/161 (22%)
Query: 14 LGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGY 73
LGL +VGWIFTDL GTV R+ DS+FLS+
Sbjct: 56 LGLERVGWIFTDLTDAGAGDGTVLCKRHKDSYFLSS------------------------ 91
Query: 74 FGSKFVTICVTVNECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQ 133
E IMA LQ HPNP +++ +GYFGSKFVT ++GD + ++ +E YQ
Sbjct: 92 ------------LEVIMAARLQLKHPNPTKYSETGYFGSKFVTCVISGDLNGEISIEAYQ 139
Query: 134 VSNQCMALVRDGCLIPTKDAPELGYIKESSDKQYVPDVFYK 174
VS+Q MALVR + P+ D P + Y++E + +YVPDVFY+
Sbjct: 140 VSDQAMALVRADIIEPSTD-PSVIYVREPNKNRYVPDVFYR 179
Score = 126 bits (319), Expect = 9e-33
Identities = 47/82 (57%), Positives = 54/82 (65%)
Query: 439 RLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQ 498
R G LYG+Y+ VPLGIKAVV AIYEPPQE D + LLPD + + V+ IASSLGL +
Sbjct: 1 RFGFLYGRYEEDDKVPLGIKAVVEAIYEPPQEGEEDGVTLLPDEEEKDVDAIASSLGLER 60
Query: 499 VGWIFTDLVAEDLQLGTYFQSR 520
VGWIFTDL GT R
Sbjct: 61 VGWIFTDLTDAGAGDGTVLCKR 82
>gnl|CDD|163692 cd08061, MPN_NPL4, Mov34/MPN/PAD-1 family: nuclear protein
localization-4 (Npl4) domain. Npl4p (nuclear protein
localization-4) is identical to Hmg-CoA reductase
degradation 4 (HRD4) protein and contains a domain that
is part of the pfam clan MPN/Mov34-like. Npl4 plays an
intermediate role between endoplasmic
reticulum-associated degradation (ERAD) substrate
ubiquitylation and proteasomal degradation. Npl4p
associates with Cdc48p (Cdc48 in yeast and p97 or
valosin-containing protein (VCP) in higher eukaryotes),
the highly conserved ATPase of the AAA family, via
ubiquitin fusion degradation-1 protein (Ufd1p) to form a
Cdc48p-Ufd1p-Npl4p complex which then functions in the
recognition of several polyubiquitin-tagged proteins and
facilitates their presentation to the 26S proteasome for
processive degradation. This family of eukaryotic
MPN-like domains lacks the key residues that coordinate
a metal ion and therefore does not show catalytic
isopeptidase activity.
Length = 274
Score = 172 bits (437), Expect = 6e-50
Identities = 71/116 (61%), Positives = 85/116 (73%), Gaps = 3/116 (2%)
Query: 405 TLNRQVYRHVDNVEFENRTLVERFLE-YWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAA 463
TL RQ YRHVD+VEF+N ++VE FL +WR TG QR+G LYG+Y DVPLGIKAVV A
Sbjct: 1 TLKRQKYRHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEA 60
Query: 464 IYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQVGWIFTDLVAEDLQLGTYFQS 519
IYEPPQE + D +LL DP A+ V+ IA++LGL +VGWIFTDL ED YF S
Sbjct: 61 IYEPPQEGTPDGFELLEDPNADTVDAIAAALGLERVGWIFTDLPREDKD--GYFLS 114
Score = 157 bits (399), Expect = 2e-44
Identities = 70/161 (43%), Positives = 83/161 (51%), Gaps = 55/161 (34%)
Query: 14 LGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGY 73
LGL +VGWIFTDL ED D +FLSA E I+A Q HP
Sbjct: 91 LGLERVGWIFTDLPRED-----------KDGYFLSAEEVILAAKFQLKHP---------- 129
Query: 74 FGSKFVTICVTVNECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQ 133
+G FGSKFVT+ VTGDKD Q+H E YQ
Sbjct: 130 ---------------------------------TGKFGSKFVTVVVTGDKDGQIHFEAYQ 156
Query: 134 VSNQCMALVRDGCLIPTKDAPELGYIKESSDKQYVPDVFYK 174
VS+Q MALVRDG L+PTKDA EL Y++E + ++YVPDVFY
Sbjct: 157 VSDQAMALVRDGLLLPTKDADEL-YVREPTLERYVPDVFYS 196
>gnl|CDD|221132 pfam11543, UN_NPL4, Nuclear pore localisation protein NPL4. Npl4
is part of the heterodimer UN along with Ufd1 which is
involved in the recruitment of p97, an AAA ATPase, for
tasks involving the ubiquitin pathway. Npl4 has a
ubiquitin-like domain which has within its structure a
beta-grasp fold with a helical insert.
Length = 80
Score = 76.3 bits (188), Expect = 3e-17
Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTI 234
I+R+QSP G KRI I+ + T L K+ +E F+L+ +RNKT E+ SS +++
Sbjct: 6 IIRVQSPDGT-KRIEISSTSTLSTLLSKVAEELGFPNNGFSLYLERNKTTELVSSGSKSV 64
Query: 235 ASVGLSNGDFVYMMN 249
+ +GL +GD +Y+
Sbjct: 65 SELGLKHGDMLYLFP 79
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 41.0 bits (96), Expect = 2e-04
Identities = 19/92 (20%), Positives = 29/92 (31%), Gaps = 16/92 (17%)
Query: 433 RVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIAS 492
+ G + +GLLYG + V A+ + + L ++
Sbjct: 10 SINGKEVIGLLYGSKTKK----VLDVDEVIAVPFDEGDKDDNVWFL------MYLDFKKL 59
Query: 493 SLGLTQVGWIFTDLV------AEDLQLGTYFQ 518
+ GL VGW T DL FQ
Sbjct: 60 NAGLRIVGWYHTHPKPSCFLSPNDLATHELFQ 91
Score = 28.6 bits (64), Expect = 3.6
Identities = 15/70 (21%), Positives = 18/70 (25%), Gaps = 27/70 (38%)
Query: 13 NLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSG 72
N GL VGW T FLS ++ Q
Sbjct: 60 NAGLRIVGWYHTHPKPS---------------CFLSPNDLATHELFQR------------ 92
Query: 73 YFGSKFVTIC 82
YF K + I
Sbjct: 93 YFPEKVMIIV 102
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell cycle
progression. Other family members are protein modifiers
that perform a wide range of functions. Ubiquitination
usually results in a covalent bond between the
C-terminus of ubiquitin and the epsilon-amino group of a
substrate lysine. The three-step mechanism requires an
activating enzyme (E1) that forms a thiol ester with the
C-terminal carboxy group, a conjugating enzyme (E2) that
transiently carries the activated ubiquitin molecule as
a thiol ester, and a ligase (E3) that transfers the
activated ubiquitin from the E2 to the substrate lysine
residue. In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 31.0 bits (70), Expect = 0.22
Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 5/72 (6%)
Query: 177 RIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIAS 236
+++ G + + T DL EK+ K+ L L + T+
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLL-----VNGKILPDSLTLED 55
Query: 237 VGLSNGDFVYMM 248
GL +GD + ++
Sbjct: 56 YGLQDGDELVLV 67
>gnl|CDD|149741 pfam08775, ParB, ParB family. ParB is a component of the par
system which mediates accurate DNA partition during cell
division. It recognises A-box and B-box DNA motifs. ParB
forms an asymmetric dimer with 2 extended
helix-turn-helix (HTH) motifs that bind to A-boxes. The
HTH motifs emanate from a beta sheet coiled coil DNA
binding module. Both DNA binding elements are free to
rotate around a flexible linker, this enables them to
bind to complex arrays of A- and B-box elements on
adjacent DNA arms of the looped partition site.
Length = 127
Score = 31.5 bits (72), Expect = 0.41
Identities = 14/87 (16%), Positives = 35/87 (40%)
Query: 238 GLSNGDFVYMMNLSSPNDEKPSTSSNHLNIYETKKKASTTPSTPTEFKSKLSNAFSSSNN 297
LS D+ ++ + ++K + ++ + K + +P E K ++ +
Sbjct: 6 ELSFSDYKLLLKVQEQLEKKNISLDELIDNVSEEIKDIDSELSPDEQKKEIMKLITKELK 65
Query: 298 IVEDEVDKELWKTDGQVKRKRDDKFCR 324
+++D+ K+ + DKF R
Sbjct: 66 LLKDKPVKDKAVVTPLAEFDDKDKFAR 92
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 32.5 bits (74), Expect = 0.44
Identities = 27/144 (18%), Positives = 40/144 (27%), Gaps = 29/144 (20%)
Query: 401 PNAITLNRQVYRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPL----- 455
+A + Y +V V +N E EY G +R+ L+YG
Sbjct: 88 LDATAPDLTGYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDD-GAYGRERLEGFK 146
Query: 456 ------GIKAVVAAIYEPPQESSRD----KIKLLPDPKA----------EVVEEIASSLG 495
GI+ V + E +K P P A ++ G
Sbjct: 147 AALKKAGIEVVAIEYGDLDTEKGFQALLQLLKAAPKPDAIFACNDEMAAGALKAAR-EAG 205
Query: 496 LT--QVGWIFTDLVAEDLQLGTYF 517
LT + I D L
Sbjct: 206 LTPGDISIIGFDGSPAALLAAGEA 229
>gnl|CDD|235832 PRK06567, PRK06567, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase; Validated.
Length = 1028
Score = 31.8 bits (72), Expect = 1.0
Identities = 30/99 (30%), Positives = 42/99 (42%), Gaps = 7/99 (7%)
Query: 400 QPNAITLNRQVYRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKA 459
QP + +N Y HV++VEFENR + + L L + P + K
Sbjct: 662 QP--LRINVDKYGHVESVEFENRNRHCEQSKTAWQSHEFGLTRLPRQCYAFPRNDIKTKT 719
Query: 460 VVAAI-YEPPQESSRDKIKLLPD--PK--AEVVEEIASS 493
V+ AI E + DK D PK VV+ +ASS
Sbjct: 720 VIMAIGIENNTQFDEDKYSYFGDCNPKYSGSVVKALASS 758
>gnl|CDD|172722 PRK14234, PRK14234, camphor resistance protein CrcB; Provisional.
Length = 124
Score = 29.4 bits (66), Expect = 1.7
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 440 LGLLYGKYQLHPDVPLGIKA 459
+GLLYG + L P+VP+ ++A
Sbjct: 49 IGLLYGLFLLRPEVPIELRA 68
>gnl|CDD|145722 pfam02721, DUF223, Domain of unknown function DUF223.
Length = 95
Score = 28.8 bits (65), Expect = 2.2
Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 10/72 (13%)
Query: 239 LSNGDFVYMMNLSSPNDEKPSTSSNH----LNIYETKKKASTTPSTPTEFKSKLSNAFSS 294
+S G++ + + ++H L + +T S T T L N +
Sbjct: 28 ISEGEWKTITTFVVRPNSGSYRITSHEYGILFMDQTVVTKSDTRETV------LFNNLTP 81
Query: 295 SNNIVEDEVDKE 306
+ I+ED VDK
Sbjct: 82 FDYIIEDTVDKN 93
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 30.2 bits (68), Expect = 2.4
Identities = 30/112 (26%), Positives = 49/112 (43%), Gaps = 14/112 (12%)
Query: 188 ININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSR----DQTIASVGLSNGD 243
I++ +T K+L EKI E E + + +Q+ I+S + D+T+ + D
Sbjct: 15 IDMEPDETVKELKEKI--EAEQGKDAYPVAQQK----LIYSGKILSDDKTVKEYKIKEKD 68
Query: 244 FVYMMNLSSPNDEKPSTSSNHLNIYETKKKASTTPSTPTEFKSKLSNAFSSS 295
FV +M +S P K T + TPS P S +S A +S+
Sbjct: 69 FVVVM-VSKP---KTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASA 116
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 29.8 bits (67), Expect = 3.8
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 403 AITLNRQVYRHVDNVEFENRTLVERFLEYWRVTGHQRLGL 442
A++ Q+YR F RTLVE LE +R + LGL
Sbjct: 260 ALSGAAQLYRD----GFAARTLVEGLLEAFRAALYAELGL 295
>gnl|CDD|140204 PTZ00176, PTZ00176, erythrocyte membrane protein 1 (PfEMP1);
Provisional.
Length = 1317
Score = 29.2 bits (65), Expect = 7.3
Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 13/93 (13%)
Query: 188 ININRSDT--CKDLFEKINKEFELNTYNFALFKQRNKTDEIFS---SRDQTIASVGLSNG 242
INI + DT + + I+ E+N + + T +I S + +A++GL G
Sbjct: 795 INIIKFDTDQYRTQLQNISNSMEINPKSVK--TAVDTTKDIVSYGLAGTMGVAAIGLQAG 852
Query: 243 DFV------YMMNLSSPNDEKPSTSSNHLNIYE 269
DF+ P ++K TSS +LNIYE
Sbjct: 853 DFLGKKIQDLYNEFMKPVEKKLDTSSKNLNIYE 885
>gnl|CDD|216403 pfam01271, Granin, Granin (chromogranin or secretogranin).
Length = 585
Score = 28.8 bits (64), Expect = 7.9
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 281 PTEFKSKLSNAFSSSNNIVE-DEVDKELWKTDGQVKRKRDD 320
++ +++ F + + V +E+ K DGQ K+KR+
Sbjct: 153 HSKRTNEIVEVFYNPQSQATLKSVFEEVGKLDGQSKQKRER 193
>gnl|CDD|189016 cd09609, M3B_PepF_4, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 586
Score = 28.7 bits (65), Expect = 8.0
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 39 TRNIDSHFLSAHECIMAGHLQ--NLHPNPCRFAPSGYFGSKFVTICVTVNECIMAGHLQN 96
T N+ F AHE AGH N + + PS YF V T+NE ++A +L
Sbjct: 370 TGNMSEVFTLAHELGHAGHFYLANKNQSILNTEPSLYF----VEAPSTMNELLLANYLLK 425
>gnl|CDD|133237 cd05106, PTKc_CSF-1R, Catalytic domain of the Protein Tyrosine
Kinase, Colony-Stimulating Factor-1 Receptor. Protein
Tyrosine Kinase (PTK) family; Colony-Stimulating
Factor-1 Receptor (CSF-1R); catalytic (c) domain. The
PTKc family is part of a larger superfamily that
includes the catalytic domains of other kinases such as
protein serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. CSF-1R,
also called c-Fms, is a member of the Platelet Derived
Growth Factor Receptor (PDGFR) subfamily of proteins,
which are receptor tyr kinases (RTKs) containing an
extracellular ligand-binding region with five
immunoglobulin-like domains, a transmembrane segment,
and an intracellular catalytic domain. The binding of
CSF-1R to its ligand, CSF-1, leads to receptor
dimerization, trans phosphorylation and activation, and
intracellular signaling. CSF-1R signaling is critical in
the regulation of macrophages and osteoclasts. It leads
to increases in gene transcription and protein
translation, and induces cytoskeletal remodeling. CSF-1R
signaling leads to a variety of cellular responses
including survival, proliferation, and differentiation
of target cells. It plays an important role in innate
immunity, tissue development and function, and the
pathogenesis of some diseases including atherosclerosis
and cancer. CSF-1R signaling is also implicated in
mammary gland development during pregnancy and
lactation. Aberrant CSF-1/CSF-1R expression correlates
with tumor cell invasiveness, poor clinical prognosis,
and bone metastasis in breast cancer. Although the
structure of the human CSF-1R catalytic domain is known,
it is excluded from this specific alignment model
because it contains a deletion in its sequence.
Length = 374
Score = 28.7 bits (64), Expect = 8.7
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 246 YMMNLSSPNDEKPSTSSNHLNIYETKKK-------ASTTPSTPTEFKSKLSNAFSSSNNI 298
+N E TSS++ NI KK +S T E + +S++ S S++
Sbjct: 139 TFLNFVMALPEISETSSDYKNITLEKKYIRSDSGFSSQGSDTYVEMRP-VSSSSSQSSDS 197
Query: 299 VEDEVDKELWKTD 311
++E ++ W D
Sbjct: 198 KDEEDTEDSWPLD 210
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
0.319 0.135 0.414
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,111,976
Number of extensions: 2509211
Number of successful extensions: 2136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2121
Number of HSP's successfully gapped: 32
Length of query: 520
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 419
Effective length of database: 6,457,848
Effective search space: 2705838312
Effective search space used: 2705838312
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)