RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 036996
(214 letters)
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 258 bits (661), Expect = 1e-84
Identities = 105/181 (58%), Positives = 140/181 (77%), Gaps = 2/181 (1%)
Query: 33 VIDFIADYYKNIEKYPVQSKVEPGYLSARLPDTAPHSPESLDDILKDVTDCILPGLTHWQ 92
++DFIADYYK+IE +PV S+V+PGYL LPD+AP+ PE+LD +L DV ILPG+THWQ
Sbjct: 22 MVDFIADYYKSIENFPVLSQVQPGYLRELLPDSAPNQPETLDQVLDDVQAKILPGVTHWQ 81
Query: 93 SPNFFGYFQANASTAGFLGEMLCSGFNVVGFNWLASPVATELESIVMDWMGKMLKLPSSF 152
SPN+F Y+ +N+S AGFLGEML +G N+VGF+W+ SP ATELE IV+DW+ K+L LP F
Sbjct: 82 SPNYFAYYPSNSSVAGFLGEMLSAGLNIVGFSWITSPAATELEMIVLDWLAKLLNLPEQF 141
Query: 153 LFSGTGGGVLHGSTCESLVCTLAAARDKALEKLGGGFDNITKLAVYASDQTHFALQKSAK 212
L +G GGGV+ G+ E+++ L AARD+ L K+G + + KL VYASDQTH ALQK+ +
Sbjct: 142 LSTGNGGGVIQGTASEAVLVVLLAARDRVLRKVGK--NALEKLVVYASDQTHSALQKACQ 199
Query: 213 L 213
+
Sbjct: 200 I 200
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 215 bits (548), Expect = 2e-67
Identities = 97/194 (50%), Positives = 141/194 (72%), Gaps = 6/194 (3%)
Query: 21 LEPKSFSDESKAVIDFIADYYKNIEK----YPVQSKVEPGYLSARLPDTAPHSPESLDDI 76
++ + ++ ++DFIADYYKN++ +PV S+V+PGYL LPD+AP PESL ++
Sbjct: 54 MDSELLREQGHIMVDFIADYYKNLQDSPQDFPVLSQVQPGYLRDMLPDSAPERPESLKEL 113
Query: 77 LKDVTDCILPGLTHWQSPNFFGYFQANASTAGFLGEMLCSGFNVVGFNWLASPVATELES 136
L DV+ I+PG+THWQSP++F Y+ ++ S AGFLGEML +G +VVGF WL SP ATELE
Sbjct: 114 LDDVSKKIMPGITHWQSPSYFAYYASSTSVAGFLGEMLNAGLSVVGFTWLTSPAATELEI 173
Query: 137 IVMDWMGKMLKLPSSFLFSGTGGGVLHGSTCESLVCTLAAARDKALEKLGGGFDNITKLA 196
IV+DW+ K+L+LP FL +G GGGV+ G+ CE+++ + AARD+ L+K+G + +L
Sbjct: 174 IVLDWLAKLLQLPDHFLSTGNGGGVIQGTGCEAVLVVVLAARDRILKKVGKTL--LPQLV 231
Query: 197 VYASDQTHFALQKS 210
VY SDQTH + +K+
Sbjct: 232 VYGSDQTHSSFRKA 245
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 198 bits (506), Expect = 1e-62
Identities = 78/160 (48%), Positives = 99/160 (61%), Gaps = 1/160 (0%)
Query: 55 PGYLSARLPDTAPHSPESLDDILKDVTDCILPGLTHWQSPNFFGYFQANASTAGFLGEML 114
PGYL LP+ AP PE L DIL D+ I+PG+T W SPNF YF A S LG+ML
Sbjct: 1 PGYLRPLLPEAAPIIPEPLLDILGDIRKNIMPGVTTWHSPNFHAYFPAGNSYPSLLGDML 60
Query: 115 CSGFNVVGFNWLASPVATELESIVMDWMGKMLKLPSSFLFSGTGGGVLHGSTCESLVCTL 174
N GF W +SP TELE++VMDW+ KML LP FL SG GGGVL G + ES + L
Sbjct: 61 SDAINCNGFTWESSPACTELENVVMDWLAKMLGLPKEFLGSGEGGGVLQGGSSESNLLAL 120
Query: 175 AAARDKALEKLGG-GFDNITKLAVYASDQTHFALQKSAKL 213
AAR K + ++ G ++ KL Y SDQ H +++K+A +
Sbjct: 121 LAARTKWIRRMKAAGKPSLGKLVAYTSDQAHSSIEKAALI 160
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 107 bits (270), Expect = 6e-28
Identities = 44/119 (36%), Positives = 60/119 (50%), Gaps = 6/119 (5%)
Query: 96 FFGYFQANASTAGFLGEMLCSGFNVVGFNWLASPVATELESIVMDWMGKMLKLPSSFLFS 155
F F L EML S N + F W SP ATE+E+ V++W+ K+ LPS
Sbjct: 1 FLAGFVTTMDPPALLLEMLTSAKNAIDFTWDESPAATEMEAEVVNWLAKLFGLPSE---- 56
Query: 156 GTGGGVLHGSTCESLVCTLAAARDKALEKL-GGGFDNITKLAVYASDQTHFALQKSAKL 213
GV ES + L AARD+A ++L GG I KL + SDQ H +++K+A
Sbjct: 57 -DADGVFTSGGSESNLLALLAARDRARKRLKAGGGRGIDKLVIVCSDQAHVSVEKAAAY 114
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 85.1 bits (211), Expect = 2e-19
Identities = 41/180 (22%), Positives = 68/180 (37%), Gaps = 8/180 (4%)
Query: 34 IDFIADYYKNIEKYPVQSKVEPGYLSARLPDTAPHSPESLDDILKDVTD-CILPGLTHWQ 92
ID + D K + P + + AP E L+++L ++ + I L
Sbjct: 1 IDGLIDKDMLNSKRYSGDSLSPLFGALSDSRMAPEKGEPLEEVLDELAELLIKDELYLDG 60
Query: 93 SPNFFGYFQANASTAGFLGEMLCSGFNVVGFNWLASPVATELESIVMDWMGKMLKLPSSF 152
P E+L S N + SP A ELE V++ + +L P
Sbjct: 61 HPRANLAGFCPTRVPPVAAELLVSALNKNLGDPDESPAAAELEERVVNMLSDLLGAPEEA 120
Query: 153 LFSGTGGGVLHGSTCESLVCTLAAARDKALEK-LGGGFDNITKLAVYASDQTHFALQKSA 211
G G T E+ + L AAR++ ++ L K + S+ HF+ +K+A
Sbjct: 121 S-----GTFTSGGT-EANLLALLAARERWRKRALAESGKPGGKPNIVCSETAHFSFEKAA 174
>gnl|CDD|216262 pfam01042, Ribonuc_L-PSP, Endoribonuclease L-PSP. Endoribonuclease
active on single-stranded mRNA. Inhibits protein
synthesis by cleavage of mRNA. Previously thought to
inhibit protein synthesis initiation. This protein may
also be involved in the regulation of purine
biosynthesis.
Length = 120
Score = 32.2 bits (74), Expect = 0.071
Identities = 6/33 (18%), Positives = 11/33 (33%)
Query: 179 DKALEKLGGGFDNITKLAVYASDQTHFALQKSA 211
L G ++ K ++ +D FA
Sbjct: 53 KAVLAAAGASLSDVVKTTIFLADMNDFAEVNEV 85
>gnl|CDD|223329 COG0251, TdcF, Putative translation initiation inhibitor, yjgF
family [Translation, ribosomal structure and
biogenesis].
Length = 130
Score = 29.9 bits (68), Expect = 0.39
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 179 DKALEKLGGGFDNITKLAVYASDQTHFA 206
LE G D++ K+ V+ +D FA
Sbjct: 61 KAVLEAAGSTLDDVVKVTVFLTDMNDFA 88
>gnl|CDD|237836 PRK14855, nhaA, pH-dependent sodium/proton antiporter; Provisional.
Length = 423
Score = 31.0 bits (70), Expect = 0.49
Identities = 30/103 (29%), Positives = 41/103 (39%), Gaps = 23/103 (22%)
Query: 48 PVQSKVEPGYLSARLPDTAPHSPESLDDILKDVTDCI------LPGLTHWQSP------- 94
P++ + YL++ L AP PE + L+D+ D + L L H P
Sbjct: 241 PIRRRDPLPYLASLLDAAAPGRPEVVGARLRDLEDLLERAQSPLHRLEHALHPWSTFLIL 300
Query: 95 NFFGYFQANASTAG----------FLGEMLCSGFNVVGFNWLA 127
F F A S +G FLG +L VVG WLA
Sbjct: 301 PVFALFNAGVSVSGGGLGTVSLGVFLGLLLGKPLGVVGGAWLA 343
>gnl|CDD|100004 cd00448, YjgF_YER057c_UK114_family, YjgF, YER057c, and UK114 belong
to a large family of proteins present in bacteria,
archaea, and eukaryotes with no definitive function. The
conserved domain is similar in structure to chorismate
mutase but there is no sequence similarity and no
functional connection. Members of this family have been
implicated in isoleucine (Yeo7, Ibm1, aldR) and purine
(YjgF) biosynthesis, as well as threonine anaerobic
degradation (tdcF) and mitochondrial DNA maintenance
(Ibm1). This domain homotrimerizes forming a distinct
intersubunit cavity that may serve as a small molecule
binding site.
Length = 107
Score = 28.3 bits (64), Expect = 1.1
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 179 DKALEKLGGGFDNITKLAVYASDQTHFA 206
+ LE GG D++ K+ VY +D FA
Sbjct: 42 EAVLEAAGGSLDDVVKVTVYLTDMADFA 69
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 29.0 bits (65), Expect = 2.0
Identities = 17/43 (39%), Positives = 18/43 (41%), Gaps = 10/43 (23%)
Query: 156 GTGGGVLHGSTCESLVCTLAAARDKALEKLGGG----FDNITK 194
GT G V HG T TL AA L K GG +D I
Sbjct: 16 GTIGHVDHGKT------TLTAAITTVLAKEGGAAARAYDQIDN 52
>gnl|CDD|220978 pfam11099, M11L, Apoptosis regulator M11L like. Apoptosis
regulators function to modulate the apoptotic cascades
and thereby favour productive viral replication. M11L
inhibits mitochondrial-dependant apoptosis by mimicking
and competing with host proteins for the binding and
blocking of Bak and Bax, two executioner proteins.
Length = 167
Score = 28.5 bits (64), Expect = 2.0
Identities = 9/34 (26%), Positives = 11/34 (32%)
Query: 26 FSDESKAVIDFIADYYKNIEKYPVQSKVEPGYLS 59
S+ K IDFI + K S L
Sbjct: 117 ISENGKDFIDFIDEKDKYNTTNYNISTRCVIKLF 150
>gnl|CDD|129116 TIGR00004, TIGR00004, reactive intermediate/imine deaminase. This
protein was described initially as an inhibitor of
protein synthesis intiation, then as an endoribonuclease
active on single-stranded mRNA, endoribonuclease L-PSP.
Members of this family, conserved in all domains of life
and often with several members per bacterial genome,
appear to catalyze a reaction that minimizes toxic
by-products from reactions catalyzed by pyridoxal
phosphate-dependent enzymes [Cellular processes, Other].
Length = 124
Score = 27.6 bits (62), Expect = 2.8
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 182 LEKLGGGFDNITKLAVYASDQTHFA 206
LE G D++ K V+ +D FA
Sbjct: 61 LEAAGLSLDDVVKTTVFLTDLNDFA 85
>gnl|CDD|176376 cd01781, AF6_RA_repeat2, Ubiquitin domain of AT-6, second repeat.
The AF-6 protein (also known as afadin and canoe) is a
multidomain cell junction protein that contains two
N-terminal Ras-associating (RA) domains in addition to
FHA (forkhead-associated), DIL (class V myosin homology
region), and PDZ domains and a proline-rich region. AF6
acts downstream of the Egfr (Epidermal Growth
Factor-receptor)/Ras signalling pathway and provides a
link from Egfr to cytoskeletal elements.
Length = 100
Score = 27.2 bits (60), Expect = 2.9
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 44 IEKYPVQSKVEPGYLSAR--LPDTAPHSPE-SLDDILKDVTDCILPGLTHWQSPNFFGYF 100
+EKY ++ Y D S +D+ + D +C L +T N F F
Sbjct: 36 LEKYGLEKSDPDDYCLVEVSNDDDRKSSDLREIDERILDDDECPLFIMTAGPGENGFDSF 95
Query: 101 QA 102
A
Sbjct: 96 LA 97
>gnl|CDD|234865 PRK00923, PRK00923, sirohydrochlorin cobaltochelatase; Reviewed.
Length = 126
Score = 27.2 bits (61), Expect = 4.0
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 28 DESKAVIDFIADYYKNIEKYPVQSKVEPGYLSARLPDTAPHSPESLDD 75
+K V+ IA+ K + + VE G++ P T P + + L
Sbjct: 14 PYNKEVVTKIAEKIKEKHPFYI---VEVGFMEFNEP-TIPEALKKLIG 57
>gnl|CDD|200501 cd11240, Sema_4, The Sema domain, a protein interacting module, of
class 4 semaphorins (Sema4). Class 4 semaphorins
(Sema4s) are transmembrane regulator molecules involved
in the development of the nervous system, immune
response, cytoskeletal organization, angiogenesis, and
cell-cell interactions. There are 7 distinct subfamilies
in class 4 semaphorins, named 4A to 4G. Several class 4
subfamilies play important roles in the immune system
and are called "immune semaphorins". Sema4A plays
critical roles in T cell-DC interactions in the immune
response. Sema4D/CD100, expressed by lymphocytes,
promotes the aggregation and survival of B lymphocytes
and inhibits cytokine-induced migration of immune cells
in vitro. It is required for normal activation of B and
T lymphocytes. Sema4B negatively regulates basophil
functions through T cell-basophil contacts and
significantly inhibits IL-4 and IL-6 production from
basophils in response to various stimuli, including IL-3
and papain. Sema4s not only influence the activation
state of cells but also modulate their migration and
survival. The effects of Sema4s on nonlymphoid cells are
mediated by plexin D1 and plexin Bs. The Sema4G and
Sema4C genes are expressed in the developing cerebellar
cortex and are involved in neural tube closure and
development of cerebellar granules cells through
receptor plexin B2. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 456
Score = 27.4 bits (61), Expect = 5.9
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 57 YLSARLPDTAPHSPESLDDILKDVTDCILPGLTHWQSPNFFGYFQANASTAG 108
+L A+L + P S ++L+DV +L W + F+G F + + +G
Sbjct: 236 FLKAQLVCSQPDS-GLPFNVLRDVF--VLSPD-SWDATIFYGVFTSQWNVSG 283
>gnl|CDD|226087 COG3557, COG3557, Uncharacterized domain/protein associated with
RNAses G and E [Translation, ribosomal structure and
biogenesis].
Length = 177
Score = 27.0 bits (60), Expect = 6.9
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 21/75 (28%)
Query: 20 DLEPKSFSDESKAVIDFIADYYKNIEKYPVQSKVEPGYLSARLPDTAPHSPESLDDILKD 79
DL+ K F D K ++D + +Y ++ +K H P +D ILK+
Sbjct: 105 DLDIKVFPDGEKKLLD-VDEYEEHRKKM--------------------HYPPDIDRILKE 143
Query: 80 VTDCILPGLTHWQSP 94
D ++ + ++ P
Sbjct: 144 NVDILVDWIEEYKGP 158
>gnl|CDD|199844 cd03860, M14_CP_A-B_like, Peptidase M14 carboxypeptidase subfamily
A/B-like. The Peptidase M14 Carboxypeptidase (CP) A/B
subfamily is one of two main M14 CP subfamilies defined
by sequence and structural homology, the other being the
N/E subfamily. CPs hydrolyze single, C-terminal amino
acids from polypeptide chains. They have a recognition
site for the free C-terminal carboxyl group, which is a
key determinant of specificity. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by a globular N-terminal pro-region linked to the
enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. There are nine members in the A/B family:
CPA1, CPA2, CPA3, CPA4, CPA5, CPA6, CPB, CPO and CPU.
CPA1, CPA2 and CPB are produced by the pancreas. The A
forms have slightly different specificities, with CPA1
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulkier aromatic side chains. CPA3
is found in secretory granules of mast cells and
functions in inflammatory processes. CPA4 is detected in
hormone-regulated tissues, and is thought to play a role
in prostate cancer. CPA5 is present in discrete regions
of pituitary and other tissues, and cleaves aliphatic
C-terminal residues. CPA6 is highly expressed in
embryonic brain and optic muscle, suggesting that it may
play a specific role in cell migration and axonal
guidance. CPU (also called CPB2) is produced and
secreted by the liver as the inactive precursor, PCPU,
commonly referred to as thrombin-activatable
fibrinolysis inhibitor (TAFI). Little is known about CPO
but it has been suggested to have specificity for acidic
residues.
Length = 293
Score = 27.1 bits (61), Expect = 7.6
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 2 GSFGLSAN---NITHGTS-FSADLEPKSFSDESKAVIDFIADYYKNIEKY 47
G G S+N G S FS EP E++AV DF+ I+ Y
Sbjct: 139 GGEGASSNPCSETYAGPSAFS---EP-----ETRAVRDFLLSLAGRIKLY 180
>gnl|CDD|237246 PRK12881, acnA, aconitate hydratase; Provisional.
Length = 889
Score = 27.2 bits (61), Expect = 7.8
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 161 VLHGSTCESLVCTLAAARDKALEKLGG 187
V+ T + LAA RD A + GG
Sbjct: 87 VMQDFTGVPALVDLAAMRD-AAAEAGG 112
>gnl|CDD|221945 pfam13158, DUF3993, Protein of unknown function (DUF3993). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 160 amino acids in length.
Length = 122
Score = 26.0 bits (57), Expect = 8.7
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 3 SFGLSANNITHGTSFSADLEPK-SFSDESKAVID 35
SF I +GT F P SF+ E+K V D
Sbjct: 78 SFEEKQGWIFYGTDFGEYYIPFFSFTSETKVVGD 111
>gnl|CDD|233662 TIGR01973, NuoG, NADH-quinone oxidoreductase, chain G. This model
represents the G subunit (one of 14: A->N) of the
NADH-quinone oxidoreductase complex I which generally
couples NADH and ubiquinone oxidation/reduction in
bacteria and mammalian mitochondria while translocating
protons, but may act on NADPH and/or plastoquinone in
cyanobacteria and plant chloroplasts. This model
excludes related subunits from formate dehydrogenase
complexes [Energy metabolism, Electron transport].
Length = 603
Score = 26.9 bits (60), Expect = 9.0
Identities = 7/40 (17%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 179 DKALEKLGGGFDNITKLAVYASDQTH----FALQKSAKLI 214
+AL +++ A ++ FAL+K + +
Sbjct: 289 AEALAIAAEKLKASSRIGGIAGPRSSLEELFALKKLVRKL 328
>gnl|CDD|235601 PRK05773, PRK05773, 3,4-dihydroxy-2-butanone 4-phosphate
synthase; Validated.
Length = 219
Score = 26.6 bits (59), Expect = 9.1
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 34 IDFIADYYKNIEKYPVQSKVEPGY 57
++F+A+ K E Y K +P Y
Sbjct: 67 LNFLAEILKRHELYRKLVK-KPSY 89
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
0.318 0.134 0.404
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,897,776
Number of extensions: 1006075
Number of successful extensions: 942
Number of sequences better than 10.0: 1
Number of HSP's gapped: 933
Number of HSP's successfully gapped: 27
Length of query: 214
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 121
Effective length of database: 6,812,680
Effective search space: 824334280
Effective search space used: 824334280
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 (21.7 bits)
S2: 57 (26.0 bits)