RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11740
(563 letters)
>gnl|CDD|201894 pfam01630, Glyco_hydro_56, Hyaluronidase.
Length = 339
Score = 289 bits (741), Expect = 2e-93
Identities = 116/376 (30%), Positives = 175/376 (46%), Gaps = 48/376 (12%)
Query: 63 AVPKEQFHVYWNVPTFQCHQYGLNFSEVRRWGIIENENGNFRGNEIALLYDP--GVFPAL 120
+P F V WNVPT C +V + II N F G I + Y G++P +
Sbjct: 6 VIPNRPFLVVWNVPTEMCLGRFGVPLDVSLFSIIANPRQTFVGQNITIFYVDRLGLYPYI 65
Query: 121 LRAGGGDFVKRNGGVPQEGDLTQHMQTLEAHVVGKLIPDPAFSGELYFISFIDHQLTAKF 180
G NGG+PQ G LT H+ + + IPDP F+G
Sbjct: 66 DPTGE---KPVNGGIPQLGSLTAHLAKAKKDIE-HYIPDPDFNG---------------- 105
Query: 181 KSVRARVSLSTRLGIIDFEHWRPVFEENFGSLDEYRKLSRRIERGRHPLWTYSAVNQEAS 240
L +ID+E WRP + N+G D Y+K S + + +HP W + V Q+A
Sbjct: 106 ------------LAVIDWEEWRPTWARNWGPKDIYKKRSIELVQQQHPDWDPTEVEQKAK 153
Query: 241 VRFEQAAKDFMFSSLVLLRKLRPKAKWGYYGFPLCFNYTPR--NQKPQCTPSVRDNNDRN 298
+FE+AA+ FM +L L + LRP A WGYY FP C+N+ N QC ND+
Sbjct: 154 RQFEKAARAFMEETLKLGKALRPNALWGYYLFPDCYNHDYNQPNYTGQCPAVEMKRNDQL 213
Query: 299 HWLFSASTSLYPSLYVKQANM-TEFDRMRFMQGRLDETNRIKAGKPVYPFIWLQSDSSEL 357
WL+ ST+L+PS+Y+ + + +++ R+ E R+ S L
Sbjct: 214 SWLWKESTALFPSIYLPPRLKSSRKVGL-YVRHRVKEAIRVSKVG---------DASHPL 263
Query: 358 YVCTFIWFKYFDNKD-FLKDSDMINALIIPKKMGTNGVIIWGSSHDVNTERKCRSLLNYL 416
V +I + ++D D FL + D+++ + +G G++IWGSS N++ C+ L Y+
Sbjct: 264 PVFVYIRYVFYDRTDTFLSEDDLVSTIGESAALGAAGIVIWGSSSLTNSKESCQHLREYM 323
Query: 417 HNTLGPAVKTVRRTPK 432
TLGP + V K
Sbjct: 324 DTTLGPYIVNVTLAAK 339
>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand
binding domain. This family is the extracellular ligand
binding domain of these ion channels. This domain forms
a pentameric arrangement in the known structure.
Length = 215
Score = 40.3 bits (95), Expect = 0.001
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 483 LYLSNSLDDLPAGTPYNTIFGNTLTDIRSDGNVSYMNFVTLKAMCTSQLSHFPRDEHECQ 542
+ L N D + ++ NT + DG V + K+ C L++FP D+ C
Sbjct: 87 IVLYNKADGI-----HDITTPNTNVRVYPDGTVLWSPPAIYKSSCPMDLTYFPFDQQNCS 141
Query: 543 VTMETF 548
+ ++
Sbjct: 142 LKFGSW 147
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 33.1 bits (76), Expect = 0.34
Identities = 15/52 (28%), Positives = 23/52 (44%)
Query: 499 NTIFGNTLTDIRSDGNVSYMNFVTLKAMCTSQLSHFPRDEHECQVTMETFHH 550
N L I +G+V Y +TL C L +FP D C + E++ +
Sbjct: 128 GITMTNVLVRIHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGY 179
>gnl|CDD|185717 cd09232, Snurportin-1_C, C-terminal m3G cap-binding domain of
nuclear import adaptor snurportin-1. Snurportin-1 (SPN1
or SNUPN) is a nuclear import adaptor for m3G-capped
spliceosomal U small nucleoproteins (snRNPs), which are
assembled in the cytoplasm. After capping and assembly,
the U snRNPs are transported into the nucleus by SPN1
and importin beta; SPN1 is then returned to the
cytoplasm by exportin 1 (CRM1), which also transports
the non-capped U snRNPs. The U snRNPs are essential
elements of the spliceosome, which catalyzes the
excision of introns and the ligation of exons to form a
mature mRNA. SPN1 contains two domains, an N-terminal
importin beta-binding (IBB) domain and a C-terminal m3G
cap-binding domain.
Length = 186
Score = 31.1 bits (71), Expect = 0.88
Identities = 10/60 (16%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 320 TEFDRMRFMQGRLDETNR--IKAGKPVYPFIWLQSDSSELYVCTFIWFKYFDNKDFLKDS 377
TEF R +++ +L+E + K + F+ L + ++ + D
Sbjct: 104 TEF-RFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPCTKESLQSAYSGPLNDDPYELDG 162
>gnl|CDD|217381 pfam03134, TB2_DP1_HVA22, TB2/DP1, HVA22 family. This family
includes members from a wide variety of eukaryotes. It
includes the TB2/DP1 (deleted in polyposis) protein,
which in humans is deleted in severe forms of familial
adenomatous polyposis, an autosomal dominant oncological
inherited disease. The family also includes the plant
protein of known similarity to TB2/DP1, the HVA22
abscisic acid-induced protein, which is thought to be a
regulatory protein.
Length = 94
Score = 29.1 bits (66), Expect = 1.7
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 438 SIDNIISIYTADDVPFIIIYYRNIILLSLFILVESFVYVLLSENPLY 484
S + S DD ++ Y+ ++ S L ESF ++LS P Y
Sbjct: 21 SYKALESKDKEDDTQWLT-YW---VVYSFLTLFESFSDIILSWIPFY 63
>gnl|CDD|119344 cd06552, ASCH_yqfb_like, ASC-1 homology domain, subfamily similar
to Escherichia coli Yqfb. The ASCH domain, a small
beta-barrel domain found in all three kingdoms of life,
resembles the RNA-binding PUA domain and may also
interact with RNA. ASCH has been proposed to function as
an RNA-binding domain during coactivation,
RNA-processing and the regulation of prokaryotic
translation.
Length = 100
Score = 28.0 bits (63), Expect = 4.3
Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 164 GELYFISFIDHQL-TAKFKSVRARVSLSTRLG-IIDFEHWRPVFEENFGSLDEYRKLSRR 221
G++ + + A+ SV + LG + D + + E F SL+E ++ +
Sbjct: 32 GDVVEVHTGERIFGEAEITSVEEK-----TLGELTDEDARQ----EGFPSLEELKEALKE 82
Query: 222 I 222
I
Sbjct: 83 I 83
>gnl|CDD|233362 TIGR01340, aconitase_mito, aconitate hydratase, mitochondrial.
This model represents mitochondrial forms of the TCA
cycle enzyme aconitate hydratase, also known as
aconitase and citrate hydro-lyase [Energy metabolism,
TCA cycle].
Length = 745
Score = 29.8 bits (67), Expect = 4.4
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 490 DDLPAGTPYNTIFG--NTLTDIRSDGNVSYMNFVT----LKAMCTSQLSHF 534
DD+ G P NTI N R+DGN + MNF+ + AM + F
Sbjct: 425 DDVKKGEP-NTILTSYNRNFRGRNDGNPATMNFLASPEIVTAMSYAGSLTF 474
>gnl|CDD|129954 TIGR00876, tal_mycobact, transaldolase, mycobacterial type. This
model describes one of three related but easily
separable famiiles of known and putative transaldolases.
This family and the family typified by E. coli TalA and
TalB both contain experimentally verified examples
[Energy metabolism, Pentose phosphate pathway].
Length = 350
Score = 29.7 bits (66), Expect = 4.7
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 167 YFISFIDHQLTAKFKSVRARVSLSTR--LGIIDFEHWRPVFEENFGSLDEYRKLSRRIER 224
+F+S D ++ + +R +L + GI + + E F D YR++ + +
Sbjct: 192 FFVSRFDKEIDKLLDKIGSRQALELQAQAGIANARLAYATYREVFEDSDCYRQIKQDAAK 251
Query: 225 GRHPLWTYSAV 235
+ PL+ + V
Sbjct: 252 LQRPLFASTGV 262
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 303
Score = 29.2 bits (66), Expect = 4.8
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 223 ERGRHPLWTYSAVNQEASVRFEQAAKD-----FMFSSLV 256
++G PL Y VN E + R +AA F+F S V
Sbjct: 73 DQGADPLSDYRKVNTELTRRLARAAARQGVKRFVFLSSV 111
>gnl|CDD|235877 PRK06850, PRK06850, hypothetical protein; Provisional.
Length = 507
Score = 29.6 bits (67), Expect = 5.2
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 427 VRRTPKMYLDDSIDNIISIYTADDVPFIIIY 457
V +++ I+ I +Y AD+ P++I Y
Sbjct: 11 VEYEDGEPIEELIEEIQELYCADNRPWVIGY 41
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 29.6 bits (67), Expect = 5.2
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 112 YDPGVFPALLRAGGG 126
+PGV P ++RAGGG
Sbjct: 199 VEPGVLPLVIRAGGG 213
>gnl|CDD|214410 MTH00043, ND4L, NADH dehydrogenase subunit 4L; Validated.
Length = 98
Score = 27.6 bits (62), Expect = 6.8
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 461 IILLSLFILVESFVYVLLSENPLYLSNSL 489
++L+SLF+ + ++ L N LS SL
Sbjct: 35 LLLISLFLNI--SIWSLNYGNFSNLSFSL 61
>gnl|CDD|234528 TIGR04264, hyperosmo_Ebh, hyperosmolarity resistance protein Ebh,
N-terminal domain. Staphylococcal protein Ebh
(extracellular matrix-binding protein homolog) is a giant
protein, sometimes over 10,000 amino acids long as
reported. This model describes a non-repetitive
amino-terminal domain of about 2400 amino acids.
Length = 2354
Score = 29.0 bits (65), Expect = 8.9
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 18 IKVEVDQMSFPGMEALKTAYGGVTVSSTLNPNNNGQGFGYYEPENAVPKEQFHVYWN 74
+KV V + F ++ Y TV +T N + + E N +P + FH WN
Sbjct: 1931 VKVYVYKFDFA-----QSEYT-TTVGTTFAGGTNVNNYVHLENANGLPTDGFHYVWN 1981
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
0.322 0.139 0.428
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: 29,332,441
Number of extensions: 2906955
Number of successful extensions: 2333
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2328
Number of HSP's successfully gapped: 22
Length of query: 563
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 461
Effective length of database: 6,413,494
Effective search space: 2956620734
Effective search space used: 2956620734
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 (21.9 bits)
S2: 62 (27.6 bits)