RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9353
(543 letters)
>gnl|CDD|185706 cd07895, Adenylation_mRNA_capping, Adenylation domain of
GTP-dependent mRNA capping enzymes. RNA capping enzymes
transfer GMP from GTP to the 5'-diphosphate end of
nascent mRNAs to form a G(5')ppp(5')RNA cap structure.
The RNA cap is found only in eukarya. RNA capping is
chemically analogous to the first two steps of
polynucleotide ligation. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation of nicked
nucleic acid substrates using the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
Structural studies reveal a shared structure for DNA
ligases and capping enzymes, with a common catalytic
core composed of an adenylation or
nucleotidyltransferase domain and a C-terminal OB-fold
domain containing conserved sequence motifs. The
adenylation domain binds ATP and contains many active
site residues.
Length = 215
Score = 264 bits (678), Expect = 6e-86
Identities = 98/215 (45%), Positives = 136/215 (63%), Gaps = 2/215 (0%)
Query: 242 DKIVQLQNEIKDLC-NYERVGFPGSQPVSMDRNNIGYLAEKKYMVSWKADGTRYMMYIKN 300
+K+ +L+ ++ +LC +ER GFPGSQPVS R N+ L + Y V K+DG RY++ I
Sbjct: 1 EKLSELRRKVAELCPGWERGGFPGSQPVSFSRKNLELLKQNDYFVCEKSDGVRYLLLITG 60
Query: 301 ADEIYFTDRDFSMYKISGLTFPHRKDPNKRLTNTLLDGEMVIDRVQGQNIPRYLVYDIIR 360
E+Y DR ++K+ GL FP RK+ TLLDGE+VID+V G+ PRYL++DI+
Sbjct: 61 RGEVYLIDRKNDVFKVPGLFFPRRKNLEPHHQGTLLDGELVIDKVPGKKRPRYLIFDILA 120
Query: 361 FDNNDVTRQKFTTRIQIIKVEIIEPRHRAMENSRINKLAEPFSVRVKDFWSVDKAGYLLS 420
F+ VT + + R++ IK E+IEPR+ ++ I+K EPFSVR+KDF+ + K L
Sbjct: 121 FNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPLYKIEKLFE 180
Query: 421 DKF-TLCHEPDGLIFQPVDEPYVMGKAVDTLKWKP 454
L HE DGLIF P DEPYV G + LKWKP
Sbjct: 181 KIIPKLPHENDGLIFTPNDEPYVPGTDKNLLKWKP 215
>gnl|CDD|216438 pfam01331, mRNA_cap_enzyme, mRNA capping enzyme, catalytic domain.
This family represents the ATP binding catalytic domain
of the mRNA capping enzyme.
Length = 193
Score = 201 bits (512), Expect = 1e-61
Identities = 84/196 (42%), Positives = 108/196 (55%), Gaps = 11/196 (5%)
Query: 266 QPVSMDRNNIGYLAEKKYMVSWKADGTRYMMYIKNADEIYFTDRDFSMYKISGLTFPHRK 325
QPVS R N+ L +K Y V KADG RYMM I + D +Y DRD + + L FP +
Sbjct: 1 QPVSFSRENLKLLEQKDYYVCEKADGIRYMMLITD-DGVYLIDRDNEYFLVENLRFPLKL 59
Query: 326 DPN--KRLTNTLLDGEMVIDRV-QGQNIPRYLVYDIIRFDNNDVTRQKFTTRIQIIKVEI 382
+ K TLLDGE+VID V + RYL+YDI+ + V+++ F+ R++I+K EI
Sbjct: 60 NGEGDKVHHGTLLDGELVIDTVPGTEQKLRYLIYDIVAINGVSVSQRPFSKRLEILKKEI 119
Query: 383 IEPRHRAMENSRINKLA-EPFSVRVKDFW----SVDKAGYLLSDKFTLCHEPDGLIFQPV 437
I+PR + I + PFSVR K FW S TL HE DGLIFQP
Sbjct: 120 IKPRAANKFKTHIIRYDLFPFSVRFKSFWLLSASEKLLSKKKIK--TLSHEIDGLIFQPW 177
Query: 438 DEPYVMGKAVDTLKWK 453
D PYV G + LKWK
Sbjct: 178 DTPYVPGTDQNLLKWK 193
>gnl|CDD|227551 COG5226, CEG1, mRNA capping enzyme, guanylyltransferase (alpha)
subunit [RNA processing and modification].
Length = 404
Score = 139 bits (351), Expect = 3e-36
Identities = 101/317 (31%), Positives = 148/317 (46%), Gaps = 39/317 (12%)
Query: 252 KDLCNYE-RVGFPGSQPVSMDRNNIGYLAEKKYMVSWKADGTRYMMYI-----KNADEIY 305
K LC E R FPGSQPVS +NIG L Y+V K+DG R ++ + A Y
Sbjct: 32 KLLCITEPRETFPGSQPVSFTLDNIGLLLNNDYLVCEKSDGVRALLLVTEEPVTGAFRGY 91
Query: 306 FTDRDFSMYKISGLTFP---HRKDPNKRLTNTLLDGEMVIDRVQGQNIP--RYLVYDIIR 360
F DR + Y++ P KD L +TLLDGE+V D + + +P RYL++D +
Sbjct: 92 FYDRRNNFYEVHTSFPPCSTVLKDGEVLLEDTLLDGELVFDCLPYEKVPQLRYLLFDCLA 151
Query: 361 FDNNDVTRQKFTTRIQIIKVEIIEPRHRAMENSRINKLAEPFSVRVKD------FWSVDK 414
+ V R + + R++ ++ E +PR R + I+ + PF VK FW + K
Sbjct: 152 YAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFHFSVKQMLKSYGFWKIYK 211
Query: 415 AGYLLSDKFTLCHEPDGLIFQPVDEPYVMGKAVDTLKWKPHTMNSIDFLMKIETRS---- 470
+ L H DGLIF P DEPY +GK LKWKP ++N+IDF + + +
Sbjct: 212 K----IPE--LKHGNDGLIFTPADEPYSVGKDGALLKWKPASLNTIDFRLVLHKKWSEVD 265
Query: 471 --GLGILPTKVGKLYAGSNRSQQQFAEM-----KITKATKD---LDGKIVEC-KWENNQW 519
P ++ G + + FA + + D L +IVEC + W
Sbjct: 266 DYNYVCSPKFGLDVWFGRK-TYRFFASGEVIDGEWCELKYDCDPLYWRIVECVLKKEGAW 324
Query: 520 VFMRERTDKSFPNAVET 536
+R R DK PN +
Sbjct: 325 KLLRFRDDKDTPNHISV 341
>gnl|CDD|217793 pfam03919, mRNA_cap_C, mRNA capping enzyme, C-terminal domain.
Length = 105
Score = 88.7 bits (220), Expect = 3e-21
Identities = 39/88 (44%), Positives = 53/88 (60%), Gaps = 5/88 (5%)
Query: 456 TMNSIDFLMKIETRSGLGILPTKVGKL---YAGSNRSQQQFAEMKITKATKDLDGKIVEC 512
+N++DFL+KIE G G+L +VGKL G N +F K+T K +GKIVEC
Sbjct: 1 ELNTVDFLLKIEKEEGRGMLLPEVGKLDYVAGGYNVEFAKFEWEKLTSDLKPYNGKIVEC 60
Query: 513 KWEN--NQWVFMRERTDKSFPNAVETAM 538
+++ WVFMR R DKS PN++ TA
Sbjct: 61 SFDDDKGVWVFMRIRVDKSNPNSINTAR 88
>gnl|CDD|185704 cd06846, Adenylation_DNA_ligase_like, Adenylation domain of
proteins similar to ATP-dependent polynucleotide
ligases. ATP-dependent polynucleotide ligases catalyze
the phosphodiester bond formation of nicked nucleic acid
substrates using ATP as a cofactor in a three step
reaction mechanism. This family includes ATP-dependent
DNA and RNA ligases. DNA ligases play a vital role in
the diverse processes of DNA replication, recombination
and repair. ATP-dependent DNA ligases have a highly
modular architecture, consisting of a unique arrangement
of two or more discrete domains, including a DNA-binding
domain, an adenylation or nucleotidyltransferase (NTase)
domain, and an oligonucleotide/oligosaccharide binding
(OB)-fold domain. The adenylation domain binds ATP and
contains many active site residues. Together with the
C-terminal OB-fold domain, it comprises a catalytic core
unit that is common to most members of the ATP-dependent
DNA ligase family. The catalytic core contains six
conserved sequence motifs (I, III, IIIa, IV, V and VI)
that define this family of related
nucleotidyltransferases including eukaryotic
GRP-dependent mRNA-capping enzymes. The catalytic core
contains both the active site as well as many
DNA-binding residues. The RNA circularization protein
from archaea and bacteria contains the minimal catalytic
unit, the adenylation domain, but does not contain an
OB-fold domain. This family also includes the m3G-cap
binding domain of snurportin, a nuclear import adaptor
that binds m3G-capped spliceosomal U small
nucleoproteins (snRNPs), but doesn't have enzymatic
activity.
Length = 182
Score = 65.5 bits (160), Expect = 2e-12
Identities = 39/195 (20%), Positives = 72/195 (36%), Gaps = 16/195 (8%)
Query: 263 PGSQPVSMDRNNIGYLAEKKYMVSWKADGTRYMMYIKNADEIYFTDRDFSMYKISGLTFP 322
P ++ Y + +Y V K DG R ++ N ++ R + + P
Sbjct: 1 PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALN-GGVFAISRTGLEVPLPSILIP 59
Query: 323 HRKDPNKRLTNTLLDGEMVIDRVQGQNI-PRYLVYDIIRFDNNDVTRQKFTTRIQIIKVE 381
++ +LDGE+V++ + N P Y +D++ + ++ R +K
Sbjct: 60 -GRELLTLKPGFILDGELVVENREVANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSL 118
Query: 382 IIEPRHRAMENSRINKLAEPFSVRVKDFWSVDKAGYLLSDKFTLCHEPDGLIFQPVDEPY 441
+ E L V +++ S D+ L +K +GL+F+ D PY
Sbjct: 119 LKEFEG----------LDPVKLVPLENAPSYDETLDDLLEKLK-KKGKEGLVFKHPDAPY 167
Query: 442 VMGKAVD--TLKWKP 454
LK KP
Sbjct: 168 KGRPGSSGNQLKLKP 182
>gnl|CDD|216117 pfam00782, DSPc, Dual specificity phosphatase, catalytic domain.
Ser/Thr and Tyr protein phosphatases. The enzyme's
tertiary fold is highly similar to that of
tyrosine-specific phosphatases, except for a
"recognition" region.
Length = 131
Score = 51.5 bits (124), Expect = 5e-08
Identities = 28/119 (23%), Positives = 50/119 (42%), Gaps = 13/119 (10%)
Query: 46 CEGHKEAPNEKQTRLKIGLWIDLTKTSRFYDKSEVEENDIAYIKIQCEGHKEAPNEKQTR 105
+A EK L I I++T+ + + I Y+ I E + E
Sbjct: 6 YPTASKAFLEK---LGITHVINVTREVPNSNL----NSGILYLGIPVEDNHET----NIS 54
Query: 106 VFINLCSKFISKSPLE--KIGVHCTHGFNRTGFLLISYLVEEMNFDVSAAIFAFSMARP 162
++ +FI + + K+ VHC G +R+ L+I+YL++ N ++ A RP
Sbjct: 55 KYLPEAVEFIDDAIQKGGKVLVHCQAGISRSATLIIAYLMKTRNLSLNEAYSFVKERRP 113
>gnl|CDD|214551 smart00195, DSPc, Dual specificity phosphatase, catalytic domain.
Length = 138
Score = 49.6 bits (119), Expect = 3e-07
Identities = 24/110 (21%), Positives = 46/110 (41%), Gaps = 11/110 (10%)
Query: 55 EKQTRLKIGLWIDLTKTSRFYDKSEVEENDIAYIKIQCEGHKEAPNEKQTRVFINLCSKF 114
+L I I++T Y+ S+ Y+ + + + E + +F
Sbjct: 20 ALLKKLGITHVINVTNEVPNYNGSDFT-----YLGVPIDDNTETKISP----YFPEAVEF 70
Query: 115 ISKSPLE--KIGVHCTHGFNRTGFLLISYLVEEMNFDVSAAIFAFSMARP 162
I + + K+ VHC G +R+ L+I+YL++ N ++ A RP
Sbjct: 71 IEDAESKGGKVLVHCQAGVSRSATLIIAYLMKTRNMSLNDAYDFVKDRRP 120
>gnl|CDD|216280 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligase domain. This
domain belongs to a more diverse superfamily, including
pfam01331 and pfam01653.
Length = 195
Score = 43.1 bits (102), Expect = 1e-04
Identities = 38/189 (20%), Positives = 67/189 (35%), Gaps = 43/189 (22%)
Query: 280 EKKYMVSWKADGTRYMMYIKNADEIYFTDR---DFSMYKISGLTFPHRKDPNKRLTNTLL 336
++V K DG R ++ K+ E+ R + L F + + +L
Sbjct: 18 GGAFIVEEKYDGERVQIH-KDGGEVKLLSRNGKPITATYPELLEFLDEAFF-PDVKSFIL 75
Query: 337 DGEMVIDRVQGQNIPR-----------------YLVYDIIRFDNNDVTRQKFTTRIQIIK 379
DGE+V G+ +P + V+D++ D +T + R +++
Sbjct: 76 DGEIVAVDPTGRILPFQTLTTRKKKKVKKEPLCFFVFDVLYLDGESLTDEPLKERRELL- 134
Query: 380 VEIIEPRHR--AMENSRINKLAEPFSVRVKDFWS-VDKAGYLLSDKFTLCHEPDGLIFQP 436
E + R E N + E +K+F K G E G++ +
Sbjct: 135 EEYFKIPVRIEIAETIETNDIEE-----LKEFLEEAIKEG----------LE--GVVVKD 177
Query: 437 VDEPYVMGK 445
D PY GK
Sbjct: 178 PDSPYEPGK 186
>gnl|CDD|225297 COG2453, CDC14, Predicted protein-tyrosine phosphatase [Signal
transduction mechanisms].
Length = 180
Score = 38.2 bits (89), Expect = 0.003
Identities = 26/122 (21%), Positives = 49/122 (40%), Gaps = 8/122 (6%)
Query: 48 GHKEAPNEK--QTRL-KIGLWI--DLTKTSRFYDKSEVEENDIAYIKIQCEGHKEAPNEK 102
G + E QT L I + +L Y+ + E + I + + P+ +
Sbjct: 31 GVRPLGYELGIQTILSLINALVIEELELLGALYNVAIEENDGIQVLHLPIL-DGTVPDLE 89
Query: 103 QTRVFINLCSKFISKSPLEKIGVHCTHGFNRTGFLLISYLVEEMNFDVSAAIFAFSMARP 162
++ + +SK +K+ VHC G R+G ++ +YL+ ++ A R
Sbjct: 90 DLDKIVDFIEEALSKG--KKVVVHCQGGIGRSGTVIAAYLMLYGGLSLADEAIAVKRRRR 147
Query: 163 PG 164
PG
Sbjct: 148 PG 149
>gnl|CDD|214649 smart00404, PTPc_motif, Protein tyrosine phosphatase, catalytic
domain motif.
Length = 105
Score = 35.8 bits (83), Expect = 0.009
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 107 FINLCSKFISKSPLEK-IGVHCTHGFNRTG-FLLISYLV-----EEMNFDVSAAIFAFSM 159
+ K +++S + VHC+ G RTG F+ I L+ E D+ +
Sbjct: 25 LLRAVKKNLNQSESSGPVVVHCSAGVGRTGTFVAIDILLQQLEAEAGEVDIFDTVKELRS 84
Query: 160 ARP 162
RP
Sbjct: 85 QRP 87
>gnl|CDD|214469 smart00012, PTPc_DSPc, Protein tyrosine phosphatase, catalytic
domain, undefined specificity. Protein tyrosine
phosphatases. Homologues detected by this profile and
not by those of "PTPc" or "DSPc" are predicted to be
protein phosphatases with a similar fold to DSPs and
PTPs, yet with unpredicted specificities.
Length = 105
Score = 35.8 bits (83), Expect = 0.009
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 107 FINLCSKFISKSPLEK-IGVHCTHGFNRTG-FLLISYLV-----EEMNFDVSAAIFAFSM 159
+ K +++S + VHC+ G RTG F+ I L+ E D+ +
Sbjct: 25 LLRAVKKNLNQSESSGPVVVHCSAGVGRTGTFVAIDILLQQLEAEAGEVDIFDTVKELRS 84
Query: 160 ARP 162
RP
Sbjct: 85 QRP 87
>gnl|CDD|221526 pfam12316, Dsh_C, Segment polarity protein dishevelled (Dsh) C
terminal. This domain family is found in eukaryotes,
and is typically between 177 and 207 amino acids in
length. The family is found in association with
pfam00778, pfam02377, pfam00610, pfam00595. The segment
polarity gene dishevelled (dsh) is required for pattern
formation of the embryonic segments. It is involved in
the determination of body organisation through the
Wingless pathway (analogous to the Wnt-1 pathway).
Length = 202
Score = 35.7 bits (82), Expect = 0.033
Identities = 17/54 (31%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 182 PCNLPAPPSYDDSEASSSSKSHHSNNSSHSNS-RNRNNKSRIAKNPTFMPGVSG 234
P PA S S S+ S HS S S S R+ +SR A G
Sbjct: 48 PYFPPAYQDPGYSYGSGSAGSQHSEGSRSSGSNRSDGERSRAADGREGGRKSGG 101
>gnl|CDD|183473 PRK12361, PRK12361, hypothetical protein; Provisional.
Length = 547
Score = 31.1 bits (71), Expect = 1.9
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 80 VEENDIAYIKIQCEGHKEAPNEKQTRVFINLCSKFISKSPLEKIGVHCTHGFNRTGFLLI 139
+ E DI Y+ I H P Q IN + + + + + VHC G R+ +L
Sbjct: 138 LTEEDIDYLNIPILDHS-VPTLAQLNQAINWIHRQVRAN--KSVVVHCALGRGRSVLVLA 194
Query: 140 SYLV 143
+YL+
Sbjct: 195 AYLL 198
>gnl|CDD|220378 pfam09749, HVSL, Uncharacterized conserved protein. This entry is
of proteins of approximately 300 residues conserved from
plants to humans. It contains two conserved motifs, HxSL
and FHVSL. The function is unknown.
Length = 238
Score = 30.0 bits (68), Expect = 2.3
Identities = 29/135 (21%), Positives = 50/135 (37%), Gaps = 23/135 (17%)
Query: 65 WIDLTKTSRFYD--KSEVEENDIAYIKIQCEGHKEAPNEKQTRVFINLCSKFISKSPLEK 122
ID F D + + I K+Q G K NE++TR F+ L SK+ L +
Sbjct: 103 QID-----PFVDSLRQALRSAGIRRFKVQFSGLKVYSNEEKTRTFLVLEVSESSKNALNR 157
Query: 123 IGVH----CTHGFNRTGFLLISYLVEEMNFDVSAAIFAFSMARPPGI---YKQDYLNELF 175
+ + F Y ++ +F VS A+ + P L E+
Sbjct: 158 L-LDAINEALREFGLPPL----Y-DDDPSFHVS---IAWCLGDPSEELKEKSLSELQEIL 208
Query: 176 RRYDDVPCNLPAPPS 190
+++ +L P +
Sbjct: 209 DALEELIFDLQFPVN 223
>gnl|CDD|185524 PTZ00242, PTZ00242, protein tyrosine phosphatase; Provisional.
Length = 166
Score = 29.6 bits (67), Expect = 2.3
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 75 YDKSEVEENDIAYIKIQCEGHKEAPNEKQTRVFINLCSKFISK--SPLEKIGVHCTHGFN 132
YD +E+N I + P + ++ L + +K +P E I VHC G
Sbjct: 52 YDAELLEKNGIE-VHDWPFDDGAPPPKAVIDNWLRLLDQEFAKQSTPPETIAVHCVAGLG 110
Query: 133 RTGFLLISYLVE 144
R L+ LVE
Sbjct: 111 RAPILVALALVE 122
>gnl|CDD|165098 PHA02730, PHA02730, ankyrin-like protein; Provisional.
Length = 672
Score = 30.0 bits (67), Expect = 3.7
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 13/75 (17%)
Query: 184 NLPAPPSYDDSEASSSSKSHHSNNSSHSNS-------------RNRNNKSRIAKNPTFMP 230
+ P+ YD + K + ++ + N+ RNR ++ R AKNPTF+
Sbjct: 556 DFPSKVKYDIAGRHKELKRYRADINRMKNAYISGVSMFDILFKRNRRHRLRYAKNPTFIN 615
Query: 231 GVSGVKALYDEDKIV 245
VS +K E +
Sbjct: 616 FVSNIKWYKKELTSI 630
>gnl|CDD|111998 pfam03162, Y_phosphatase2, Tyrosine phosphatase family. This
family is closely related to the pfam00102 and pfam00782
families.
Length = 150
Score = 28.5 bits (64), Expect = 4.9
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 9/87 (10%)
Query: 81 EENDIAYIKIQCEGHKEAP-NEKQTRVFINLCSKFISKSPLEKIGVHCTHGFNRTGFLLI 139
E I I EG+K+ N + K + + +HC G +RTG L+I
Sbjct: 53 ESEHIKLYHIHMEGNKDPFVNIPSHL--LRRALKLLLNKDNYPVLIHCNRGKHRTG-LVI 109
Query: 140 SYLVEEMNFDVSAAI-----FAFSMAR 161
L + + +++ + F+ S AR
Sbjct: 110 GCLRKLQKWSLASILNEYRRFSGSKAR 136
>gnl|CDD|217492 pfam03321, GH3, GH3 auxin-responsive promoter.
Length = 513
Score = 29.5 bits (67), Expect = 5.1
Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 12/67 (17%)
Query: 352 RYLVYDIIRFDN--NDVTRQKFTTRIQ-IIKVE----IIEPRHRAMENSRINKLAEPFSV 404
RY + D++R N + +F R + ++ + E +A++N E +
Sbjct: 357 RYRIGDVVRVTGFYNYTPQFEFVGRTKHVLSLFGEKLTEEELEKAVKN-----ALESTGL 411
Query: 405 RVKDFWS 411
+ ++ S
Sbjct: 412 EIVEYTS 418
>gnl|CDD|185713 cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA
Ligase IV. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriophages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligase in eukaryotic cells (I, III and IV). DNA ligase
IV is required for DNA non-homologous end joining
pathways, including recombination of the V(D)J
immunoglobulin gene segments in cells of the mammalian
immune system. DNA ligase IV is stabilized by forming a
complex with XRCC4, a nuclear phosphoprotein, which is
phosphorylated by DNA-dependent protein kinase. DNA
ligases have a highly modular architecture consisting of
a unique arrangement of two or more discrete domains.
The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
all members of the ATP-dependent DNA ligase family. The
adenylation domain binds ATP and contains many of the
active-site residues. The common catalytic unit
comprises six conserved sequence motifs (I, III, IIIa,
IV, V and VI) that define this family of related
nucleotidyltransferases.
Length = 225
Score = 29.1 bits (66), Expect = 5.7
Identities = 33/153 (21%), Positives = 62/153 (40%), Gaps = 34/153 (22%)
Query: 272 RNNIGYLAEK-----KYMVSWKADGTRYMMYIKNADEIYFTDR--DFS-----MYKISGL 319
R NIGY+ K + + K DG R ++ + YF+ D++ L
Sbjct: 19 RLNIGYVEIKLLKGKPFYIETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYGASLTPGSL 78
Query: 320 TFPHRKDPNKRLTNTLLDGEMVI-DRVQGQNIPR--------------------YLVYDI 358
T N ++ + +LDGEMV+ D+ + +P ++V+DI
Sbjct: 79 TPYIHLAFNPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLREVEDSDLQPCFVVFDI 138
Query: 359 IRFDNNDVTRQKFTTRIQIIKVEIIEPRHRAME 391
+ + +T R ++++ +II P +E
Sbjct: 139 LYLNGKSLTNLPLHERKKLLE-KIITPIPGRLE 170
>gnl|CDD|113869 pfam05114, DUF692, Protein of unknown function (DUF692). This
family consists of several uncharacterized bacterial
proteins.
Length = 275
Score = 28.9 bits (65), Expect = 6.7
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 450 LKWKPHTMNSIDFLMKIETRSGLGIL 475
L MN ++FL + + G+L
Sbjct: 144 LHLPDEEMNEVEFLNAVADEADCGLL 169
>gnl|CDD|215717 pfam00102, Y_phosphatase, Protein-tyrosine phosphatase.
Length = 233
Score = 28.8 bits (65), Expect = 7.1
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 125 VHCTHGFNRTG-FLLISYLVEEM 146
VHC+ G RTG F+ I L++++
Sbjct: 173 VHCSAGVGRTGTFIAIDILLQQL 195
>gnl|CDD|223030 PHA03271, PHA03271, envelope glycoprotein C; Provisional.
Length = 490
Score = 28.8 bits (64), Expect = 7.5
Identities = 8/45 (17%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 179 DDVP-CNLPAPPSYDDSEASSSSKSHHSNNSSHSNSRNRNNKSRI 222
D P +PA P + S ++ + + + +N N+ ++
Sbjct: 50 DGGPLAEVPASPPTELSTTVATKTAVPTTGEKSESHKNANDAHKM 94
>gnl|CDD|211368 cd09257, AP_muniscins_like_MHD, Mu-homology domain (MHD) of
muniscins adaptor proteins (AP) and similar proteins.
This family corresponds to the MHD found in muniscins, a
novel family of endocytic adaptor proteins. The term,
muniscins, has been assigned to name the MHD of proteins
with both EFC/F-BAR domain and MHD. These two domains
are responsible for the membrane-tubulation activity
associated with transmembrane cargo proteins. Members in
this family include an endocytic adaptor Syp1, the
mammalian FCH domain only proteins (FCHo1/2),
SH3-containing GRB2-like protein 3-interacting protein 1
(SGIP1), and related uncharacterized proteins. Syp1 is a
poorly characterized yeast protein with multiple
biological functions. Syp1 contains an N-terminal
EFC/F-BAR domain that induces membrane tabulation, a
proline-rich domain (PRD) in the middle region, and a
C-terminal MHD that can directly binds to the endocytic
adaptor/scaffold protein Ede1 or a transmembrane stress
sensor cargo protein Mid2. Thus, Syp1 represents a novel
type of endocytic adaptor protein that participates in
endocytosis, promotes vesicle tabulation, and
contributes to cell polarity and stress response. Syp1
shares the same domain architecture with its two
ubiquitously expressed mammalian counterparts, the
membrane-sculpting F-BAR domain-containing Fer/Cip4
homology domain-only proteins 1 and 2 (FCHo1/2). FCHo1/2
represent key initial proteins ultimately controlling
cellular nutrient uptake, receptor regulation, and
synaptic vesicle retrieval. They are required for plasma
membrane clathrin-coated vesicle (CCV) budding and
marked sites of CCV formation. They bind specifically to
the plasma membrane and recruit the scaffold proteins
eps15 and intersectin, which subsequently engage the
adaptor complex AP2 and clathrin, leading to coated
vesicle formation. Another mammalian neuronal-specific
protein, neuronal-specific transcript Scr homology 3
(SH3)-domain growth factor receptor-bound 2 (GRB2)-like
(endophilin) interacting protein 1 [SGIP1] does not
contain EFC/F-BAR domain, but does have a PRD and a
C-terminal MHD and has been classified into this family
as well. SGIP1 is an endophilin-interacting protein that
plays an obligatory role in the regulation of energy
homeostasis. It is also involved in clathrin-mediated
endocytosis by interacting with phospholipids and eps15.
Length = 246
Score = 28.5 bits (64), Expect = 7.7
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 2/43 (4%)
Query: 246 QLQNEIKDLCNYERVGFPGSQPVSMDRNNIGYLAEKKYMVSWK 288
L + ++ V PG S+ + +K ++WK
Sbjct: 134 SLPGPLSNVTVI--VNVPGGAGTSLKSSPSAIWDREKRELTWK 174
>gnl|CDD|214550 smart00194, PTPc, Protein tyrosine phosphatase, catalytic domain.
Length = 259
Score = 28.4 bits (64), Expect = 8.6
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 125 VHCTHGFNRTG-FLLISYLVEEMN----FDVSAAIFAFSMARP 162
VHC+ G RTG F+ I L++++ D+ + RP
Sbjct: 199 VHCSAGVGRTGTFIAIDILLQQLEAGKEVDIFEIVKELRSQRP 241
>gnl|CDD|238006 cd00047, PTPc, Protein tyrosine phosphatases (PTP) catalyze the
dephosphorylation of phosphotyrosine peptides; they
regulate phosphotyrosine levels in signal transduction
pathways. The depth of the active site cleft renders the
enzyme specific for phosphorylated Tyr (pTyr) residues,
instead of pSer or pThr. This family has a distinctive
active site signature motif, HCSAGxGRxG. Characterized
as either transmembrane, receptor-like or
non-transmembrane (soluble) PTPs. Receptor-like PTP
domains tend to occur in two copies in the cytoplasmic
region of the transmembrane proteins, only one copy may
be active.
Length = 231
Score = 28.3 bits (64), Expect = 9.5
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 125 VHCTHGFNRTG-FLLISYLVEEM 146
VHC+ G RTG F+ I L++ +
Sbjct: 171 VHCSAGVGRTGTFIAIDILLQRL 193
>gnl|CDD|143596 cd07572, nit, Nit1, Nit 2, and related proteins, and the Nit1-like
domain of NitFhit (class 10 nitrilases). This subgroup
includes mammalian Nit1 and Nit2, the Nit1-like domain
of the invertebrate NitFhit, and various uncharacterized
bacterial and archaeal Nit-like proteins. Nit1 and Nit2
are candidate tumor suppressor proteins. In NitFhit, the
Nit1-like domain is encoded as a fusion protein with the
non-homologous tumor suppressor, fragile histidine triad
(Fhit). Mammalian Nit1 and Fhit may affect distinct
signal pathways, and both may participate in DNA
damage-induced apoptosis. Nit1 is a negative regulator
in T cells. Overexpression of Nit2 in HeLa cells leads
to a suppression of cell growth through cell cycle
arrest in G2. These Nit proteins and the Nit1-like
domain of NitFhit belong to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to class 10.
Length = 265
Score = 28.2 bits (64), Expect = 9.7
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 309 RDFSMYKISGLTFPHRKDPNKRLTNTLLDGEMVIDRVQGQNIPRY 353
++ ++ + G + P R D + ++ NT L V D G+ + RY
Sbjct: 72 KEHGIWLVGG-SIPERDDDDGKVYNTSL----VFDP-DGELVARY 110
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
0.316 0.133 0.391
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,093,243
Number of extensions: 2612618
Number of successful extensions: 2168
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2148
Number of HSP's successfully gapped: 39
Length of query: 543
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 441
Effective length of database: 6,413,494
Effective search space: 2828350854
Effective search space used: 2828350854
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.3 bits)