RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16496
(245 letters)
>gnl|CDD|201590 pfam01085, HH_signal, Hedgehog amino-terminal signalling domain.
For the carboxyl Hint module, see pfam01079. Hedgehog is
a family of secreted signal molecules required for
embryonic cell differentiation.
Length = 160
Score = 177 bits (449), Expect = 2e-56
Identities = 70/85 (82%), Positives = 79/85 (92%)
Query: 16 QRLKEKLNTLAISVMNEWPGVRLRVIEGWDEEGHHASDSLHYEGRAVDITTSDRDSSKYG 75
QR K+KLN LAISVMN+WPGV+LRV EGWDE+GHH+ +SLHYEGRAVDITTSDRD SKYG
Sbjct: 76 QRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYG 135
Query: 76 LLARMAVEAGFDWVYYESRNHIHCS 100
+LAR+AVEAGFDWVYYES+ HIHCS
Sbjct: 136 MLARLAVEAGFDWVYYESKAHIHCS 160
>gnl|CDD|216288 pfam01079, Hint, Hint module. This is an alignment of the Hint
module in the Hedgehog proteins. It does not include any
Inteins which also possess the Hint module.
Length = 214
Score = 123 bits (312), Expect = 6e-35
Identities = 47/116 (40%), Positives = 65/116 (56%), Gaps = 3/116 (2%)
Query: 110 GKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHN 169
K GCF GD+TVTL++ T ++DL IGD+VL ++ G++ YS V+LFL RDP
Sbjct: 7 AKSGGCFPGDATVTLEDGGTKPMSDLRIGDRVLAADS-DGKLVYSPVILFLDRDPEQRRE 65
Query: 170 FVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKNGK 225
F I TE+G + +TP+HLI S E +A VR D ++V NG
Sbjct: 66 FYVIETENGRKLTLTPAHLIFVADCNTTSS--ALFEAVFASDVRPGDYVLVQDNGG 119
>gnl|CDD|197642 smart00306, HintN, Hint (Hedgehog/Intein) domain N-terminal region.
Hedgehog/Intein domain, N-terminal region. Domain has
been split to accommodate large insertions of
endonucleases.
Length = 100
Score = 86.9 bits (216), Expect = 3e-22
Identities = 37/109 (33%), Positives = 58/109 (53%), Gaps = 9/109 (8%)
Query: 114 GCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQI 173
GCF GD+ V ++ I +L GDKVL L+ G ++YS V +FL R+P F +I
Sbjct: 1 GCFPGDTLVLTEDGGIKKIEELEEGDKVLALD--EGTLKYSPVKVFLVREPKGEKKFYRI 58
Query: 174 TTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHK 222
TE+G I +TP HL+L R + + +A ++ D ++V +
Sbjct: 59 KTENGREITLTPDHLLLV--RDG-----GKLVWVFASELKPGDYVLVPR 100
>gnl|CDD|238035 cd00081, Hint, Hedgehog/Intein domain, found in Hedgehog proteins
as well as proteins which contain inteins and undergo
protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In
protein splicing an intervening polypeptide sequence -
the intein - is excised from a protein, and the flanking
polypeptide sequences - the exteins - are joined by a
peptide bond. In addition to the autocatalytic splicing
domain, many inteins contain an inserted endonuclease
domain, which plays a role in spreading inteins.
Hedgehog proteins are a major class of intercellular
signaling molecules, which control inductive
interactions during animal development. The mature
signaling forms of hedgehog proteins are the N-terminal
fragments, which are covalently linked to cholesterol at
their C-termini. This modification is the result of an
autoprocessing step catalyzed by the C-terminal
fragments, which are aligned here.
Length = 136
Score = 78.5 bits (194), Expect = 2e-18
Identities = 37/108 (34%), Positives = 58/108 (53%), Gaps = 12/108 (11%)
Query: 115 CFTGDSTVTLDNHKTINITDL--NIGDKVLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQ 172
CFTGD+ V L++ I +L GDKVL L+ TG++ +S+VL L RD F +
Sbjct: 1 CFTGDTLVLLEDGGRKKIEELVEKKGDKVLALD-ETGKLVFSKVLKVLRRDYE--KKFYK 57
Query: 173 ITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIV 220
I TESG I +TP HL+ ++++ +A ++ D ++V
Sbjct: 58 IKTESGREITLTPDHLLFVLED-------GELKWVFASDLKPGDYVLV 98
>gnl|CDD|116875 pfam08291, Peptidase_M15_3, Peptidase M15.
Length = 110
Score = 40.0 bits (94), Expect = 1e-04
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 51 ASDSLHYEGRAVDITTSDRDSSKYGLLARMAVEAG-FDWVYYESRNHIHCS 100
A DS H G A DIT S ++ + LA++A G F + +H
Sbjct: 63 ARDSQHLTGLAADITVSGKNPEE---LAQIARAHGPFGIGIGGHNSFVHVD 110
>gnl|CDD|233416 TIGR01445, intein_Nterm, intein N-terminal splicing region. This
model is based on interated search results, starting
with a curated collection of intein N-terminal splicing
regions from InBase, the New England Biolabs Intein
Database, as presented on its web site. It is designed
to recognize inteins but not the related region of the
sonic hedgehog protein.
Length = 81
Score = 39.2 bits (92), Expect = 1e-04
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 14/85 (16%)
Query: 115 CFTGDSTVTLDNHKTINITDL---------NIGDKVLTLNTITGEMEYSEVLLFLHRDPN 165
C TGD+ V ++ + I +L I KVL+L+ V+ +
Sbjct: 1 CLTGDTKVLTED-GEVKIGELVEKKKDEKEPIKVKVLSLDGGKIVKARPVVVWKRRGEGK 59
Query: 166 LVHNFVQITTESGSLIKMTPSHLIL 190
L+ +I TE+G IK TP H L
Sbjct: 60 LI----RIKTENGREIKATPDHPFL 80
>gnl|CDD|236203 PRK08255, PRK08255, salicylyl-CoA 5-hydroxylase; Reviewed.
Length = 765
Score = 30.7 bits (70), Expect = 0.79
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 6/22 (27%)
Query: 78 ARMAVEAGFDWVYYESRNHIHC 99
AR A EAGFDW+ +HC
Sbjct: 557 ARRAAEAGFDWL------ELHC 572
>gnl|CDD|224291 COG1372, COG1372, Intein/homing endonuclease [DNA replication,
recombination, and repair].
Length = 420
Score = 30.4 bits (68), Expect = 0.80
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 8/61 (13%)
Query: 173 ITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKNGKARNGIQR 232
I T+SG IK TP H L ++ + A ++ D I V + +
Sbjct: 68 IKTKSGREIKATPDHPFLT--------RNGELGWVKAGELKEGDRIAVPRRLPGPEDEKI 119
Query: 233 G 233
Sbjct: 120 P 120
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and
an RS domain at their C-terminus.
Length = 72
Score = 27.5 bits (61), Expect = 1.4
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 57 YEGRAVDITTSDRDSSKYGLLARMAVEAGFDWVYYE 92
Y+ R +I +R KYG + R+ +++GF +VY E
Sbjct: 10 YDARQSEI---ERLFGKYGRVDRVDMKSGFAFVYME 42
>gnl|CDD|237309 PRK13211, PRK13211, N-acetylglucosamine-binding protein A;
Reviewed.
Length = 478
Score = 29.6 bits (67), Expect = 1.6
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 116 FTGDSTVTLDNHK--TINIT-DLNIGDKVLT 143
F G V + K IN + DL GDKV+T
Sbjct: 193 FDGGGGVVPEWSKVGQINPSMDLKAGDKVMT 223
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 29.4 bits (67), Expect = 1.8
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 24 TLAISVMNEWPGVRLRV 40
+ MNE PG R+RV
Sbjct: 204 VMVYGQMNEPPGARMRV 220
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 29.5 bits (66), Expect = 2.0
Identities = 28/119 (23%), Positives = 49/119 (41%), Gaps = 17/119 (14%)
Query: 115 CFTGDSTVTLDNHKTINITDLNIGDK--VLTLNTITGEMEYSEVLLFLHRDPNLVHNFVQ 172
C T D+ V+L + + I ++ G + VL LN + + + ++ L F D N
Sbjct: 890 CVTPDTYVSLHDGRIKEIDEIVEGSERNVLGLNGL--KPKEAKALKFWEIDYN--GPIKV 945
Query: 173 ITTESGSLIKMTPSH--LILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKNGKARNG 229
IT ++ IK TP H L++R + + A+ +R D + N
Sbjct: 946 ITLKNNYEIKATPDHGLLVMR---------DGKLGWVSAKNIREGDYVAFAFNTGVEGR 995
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 29.1 bits (66), Expect = 2.3
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 6/23 (26%)
Query: 78 ARMAVEAGFDWVYYESRNHIHCS 100
AR A EAGFD V IH +
Sbjct: 155 ARRAKEAGFDGVE------IHGA 171
>gnl|CDD|239242 cd02932, OYE_YqiM_FMN, Old yellow enzyme (OYE) YqjM-like FMN
binding domain. YqjM is involved in the oxidative stress
response of Bacillus subtilis. Like the other OYE
members, each monomer of YqjM contains FMN as a
non-covalently bound cofactor and uses NADPH as a
reducing agent. The YqjM enzyme exists as a
homotetramer that is assembled as a dimer of
catalytically dependent dimers, while other OYE members
exist only as monomers or dimers. Moreover, the protein
displays a shared active site architecture where an
arginine finger at the COOH terminus of one monomer
extends into the active site of the adjacent monomer and
is directly involved in substrate recognition. Another
remarkable difference in the binding of the ligand in
YqjM is represented by the contribution of the
NH2-terminal tyrosine instead of a COOH-terminal
tyrosine in OYE and its homologs.
Length = 336
Score = 28.6 bits (65), Expect = 2.8
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 6/22 (27%)
Query: 78 ARMAVEAGFDWVYYESRNHIHC 99
AR AVEAGFD + E IH
Sbjct: 160 ARRAVEAGFDVI--E----IHA 175
>gnl|CDD|215241 PLN02440, PLN02440, amidophosphoribosyltransferase.
Length = 479
Score = 28.9 bits (65), Expect = 2.9
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 201 LNDIEYTYAERVRVNDSIIVHKNGKARNGIQRGAPIPPPRPKPC 244
L+ I TY V + I+V K+ G+ +P P PKPC
Sbjct: 199 LDLIGATYEREVNPGEVIVVDKD----KGVSSQCLMPHPEPKPC 238
>gnl|CDD|216083 pfam00724, Oxidored_FMN, NADH:flavin oxidoreductase / NADH oxidase
family.
Length = 336
Score = 28.5 bits (64), Expect = 2.9
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 6/28 (21%)
Query: 73 KYGLLARMAVEAGFDWVYYESRNHIHCS 100
++ A+ AVEAGFD V IH +
Sbjct: 144 EFVQAAKRAVEAGFDGVE------IHGA 165
>gnl|CDD|220887 pfam10844, DUF2577, Protein of unknown function (DUF2577). This
family of proteins has no known function.
Length = 101
Score = 27.2 bits (61), Expect = 3.0
Identities = 12/30 (40%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 116 FTGDSTVTLDNHKTINITD-LNIGDKVLTL 144
T + N I TD L GDKVL L
Sbjct: 58 ITVEGNTETSNRGKITFTDGLKKGDKVLVL 87
>gnl|CDD|178754 PLN03215, PLN03215, ascorbic acid mannose pathway regulator 1;
Provisional.
Length = 373
Score = 28.8 bits (64), Expect = 3.0
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 12/70 (17%)
Query: 30 MNEWPGVRLRVIEGWDEEGHHASDSLHYEGRA--------VDITTSDRDSSKYGLLARMA 81
+N W G V++ + G+H SD + ++G+ V SD + S++G
Sbjct: 184 INYWDG---NVLKALKQMGYHFSDIIVHKGQTYALDSIGIVYWINSDLEFSRFGTSLDEN 240
Query: 82 VEAGFDWVYY 91
+ G W
Sbjct: 241 ITDG-CWTGD 249
>gnl|CDD|114701 pfam05993, Reovirus_M2, Reovirus major virion structural protein
Mu-1/Mu-1C (M2). This family consists of several
Reovirus major virion structural protein Mu-1/Mu-1C (M2)
sequences. This family is family is thought to play a
role in host cell membrane penetration.
Length = 648
Score = 28.6 bits (63), Expect = 3.2
Identities = 17/83 (20%), Positives = 25/83 (30%), Gaps = 3/83 (3%)
Query: 103 TETTHVNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSEVLLFLHR 162
T VN AG D + L + +N I E+ Y + F+
Sbjct: 383 GAATVVNA--AGASAEDLAFNARGQPIFAMLHLAANFEPEQINGIDPEINYYGLATFIDP 440
Query: 163 DPNLVHNFVQITTESGSLIKMTP 185
NF L+ M+P
Sbjct: 441 AAISPSNFSNPDLMDA-LLTMSP 462
>gnl|CDD|223133 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 28.3 bits (64), Expect = 3.6
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 24 TLAISVMNEWPGVRLRV 40
L MNE PG R+RV
Sbjct: 208 ALVFGQMNEPPGARMRV 224
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 28.5 bits (64), Expect = 4.2
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 161 HRDPNLVHNFVQITTESGSLIKMTPSHLILRW 192
H P+ + ++ TE G + +TP H +L W
Sbjct: 990 HPAPD---HLIRFETERGRSLTVTPDHAMLVW 1018
>gnl|CDD|219057 pfam06487, SAP18, Sin3 associated polypeptide p18 (SAP18). This
family consists of several eukaryotic Sin3 associated
polypeptide p18 (SAP18) sequences. SAP18 is known to be
a component of the Sin3-containing complex which is
responsible for the repression of transcription via the
modification of histone polypeptides. SAP18 is also
present in the ASAP complex which is thought to be
involved in the regulation of splicing during the
execution of programmed cell death.
Length = 121
Score = 26.8 bits (60), Expect = 4.9
Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 11/58 (18%)
Query: 86 FDWVYYESRNHIHCSVKTETTHVNGKGAGCFTGDSTVTLDNHKTINITDLNIGDKVLT 143
F VY + + + S + KG D TL + K IGD +
Sbjct: 73 FRLVYPDKKRGRYLSKDLGSVISGQKGP-----DDNKTLQDAK------FVIGDYLDV 119
>gnl|CDD|238553 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
nucleotide-binding domain. The F-ATPase is found in
bacterial plasma membranes, mitochondrial inner
membranes and in chloroplast thylakoid membranes. It has
also been found in the archaea Methanosarcina barkeri.
It uses a proton gradient to drive ATP synthesis and
hydrolyzes ATP to build the proton gradient. The
extrinisic membrane domain, F1, is composed of alpha,
beta, gamma, delta and epsilon subunits with a
stoichiometry of 3:3:1:1:1. The beta subunit of ATP
synthase is catalytic.
Length = 274
Score = 28.0 bits (63), Expect = 5.0
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 24 TLAISVMNEWPGVRLRV 40
L MNE PG R RV
Sbjct: 130 ALVYGQMNEPPGARARV 146
>gnl|CDD|237236 PRK12858, PRK12858, tagatose 1,6-diphosphate aldolase; Reviewed.
Length = 340
Score = 27.7 bits (62), Expect = 5.7
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 189 ILRWHRPNAKSILNDIEYTYAERV 212
+L ++RP+ +ND ++ + ERV
Sbjct: 125 LLLYYRPDEDDAINDRKHAFVERV 148
>gnl|CDD|236447 PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated.
Length = 463
Score = 27.4 bits (62), Expect = 7.4
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 30 MNEWPGVRLRV 40
MNE PG RLRV
Sbjct: 211 MNEPPGARLRV 221
>gnl|CDD|239548 cd03465, URO-D_like, The URO-D _like protein superfamily includes
bacterial and eukaryotic uroporphyrinogen decarboxylases
(URO-D), coenzyme M methyltransferases and other
putative bacterial methyltransferases. Uroporphyrinogen
decarboxylase (URO-D) decarboxylates the four acetate
side chains of uroporphyrinogen III (uro-III) to create
coproporphyrinogen III, an important branching point of
the tetrapyrrole biosynthetic pathway. The
methyltransferases represented here are important for
ability of methanogenic organisms to use other compounds
than carbon dioxide for reduction to methane.
Length = 330
Score = 27.3 bits (61), Expect = 8.1
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 127 HKTINITDLNIGDKVLTLNTITGE-------MEYSEVLLFLHRDPNLVHNFVQITTES 177
+ I + +GD+V + + G M S+ L+ L+ DP LVH ++ TE
Sbjct: 112 LEAIRLLKEELGDRVPVIGAVGGPFTLASLLMGASKFLMLLYTDPELVHKLLEKCTEF 169
>gnl|CDD|184795 PRK14698, PRK14698, V-type ATP synthase subunit A; Provisional.
Length = 1017
Score = 27.7 bits (61), Expect = 8.3
Identities = 32/128 (25%), Positives = 53/128 (41%), Gaps = 20/128 (15%)
Query: 112 GAG-CFTGDSTVTLDNHKTINITDLNIGDKVLTLNTITGEMEYSE----VLLFLHRDPNL 166
G+G C GD+ + I I DL T+ G E++E + L+ ++D +
Sbjct: 237 GSGKCVDGDTLILTKEFGLIKIKDLYEILDGKGKKTVEGNEEWTELEEPITLYGYKDGKI 296
Query: 167 VH------------NFVQITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRV 214
V ++I T +G IK+TP H + R + +IE A+ ++
Sbjct: 297 VEIKATHVYKGASAGMIEIKTRTGRKIKVTPIHKLFT-GRVTKDGL--EIEEVMAKDIKK 353
Query: 215 NDSIIVHK 222
D I V K
Sbjct: 354 GDRIAVAK 361
>gnl|CDD|237344 PRK13306, ulaD, 3-keto-L-gulonate-6-phosphate decarboxylase;
Provisional.
Length = 216
Score = 26.8 bits (60), Expect = 8.6
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 75 GLLARMAVEAGFDWV 89
+LA+MA EAG DWV
Sbjct: 70 KILAKMAFEAGADWV 84
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 27.3 bits (60), Expect = 9.7
Identities = 31/124 (25%), Positives = 50/124 (40%), Gaps = 25/124 (20%)
Query: 116 FTGDSTVTLDNHKTINITDLNIGDKVLTL---NTITGEMEYSEVLLFLHRDPNLVHNFVQ 172
FT + LDN K NI D I VL N + E+ LV N++
Sbjct: 1175 FTKFAAAYLDNKKIENIDDDEITASVLNTPNKNALNDELN------------ELVENYLN 1222
Query: 173 ITTESGSLIKMTPSHLILRWHRPNAKSILNDIEYTYAERVRVNDSIIVHKNGKARNGIQR 232
+ S ++ + LI + + SI N+I ++D+ ++ K R+GI
Sbjct: 1223 SCKSAYSNLR---NFLIEVYSCGSNVSICNNIR-------DISDNNLIEFARKLRDGIPV 1272
Query: 233 GAPI 236
AP+
Sbjct: 1273 AAPV 1276
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 0.136 0.416
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,316,053
Number of extensions: 1132871
Number of successful extensions: 1116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1106
Number of HSP's successfully gapped: 37
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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: 58 (26.1 bits)