RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5930
(2426 letters)
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.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 = 1172
Score = 34.3 bits (78), Expect = 1.2
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 1934 LDLVKTRFCSMSQETRKQFIGTIILGLIDKTPDIKVMKAIIKMTEEWLKVNKVEQNNVP 1992
LD+V+ + +++ET K+ + TI L DK + V + + ++ E+ K V VP
Sbjct: 1023 LDIVRRDWSPLAKETGKKVLDTI---LSDKDVEEAV-EEVQEVLEKIGK--NVLNGEVP 1075
>gnl|CDD|184446 PRK14000, PRK14000, potassium-transporting ATPase subunit C;
Provisional.
Length = 185
Score = 32.7 bits (74), Expect = 1.3
Identities = 19/82 (23%), Positives = 32/82 (39%)
Query: 200 VKTVTMGLAASKVNASGGEGPTTPPFGQFQPKDTKVYIRLVKWALKALDVYTLNPSSSSL 259
+ V + A++V SGG +G P+ K +K K + + S S L
Sbjct: 69 ISAVNYNMNANEVKESGGPASGGSNYGNSNPELKKRVQETIKQEGKKISSDAVTASGSGL 128
Query: 260 LPNNLQRTPLQQASRTKEEKEV 281
P+ QQ R +E+ +
Sbjct: 129 DPDITVDNAKQQVKRIAKERNI 150
>gnl|CDD|143444 cd07126, ALDH_F12_P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, ALDH family 12.
Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH,
EC=1.5.1.12), family 12: a proline catabolic enzyme of
the aldehyde dehydrogenase (ALDH) protein superfamily.
P5CDH is a mitochondrial enzyme involved in proline
degradation and catalyzes the NAD + -dependent conversion
of P5C to glutamate. The P5CDH, ALDH12A1 gene, in
Arabidopsis, has been identified as an
osmotic-stress-inducible ALDH gene. This CD contains both
Viridiplantae and Alveolata P5CDH sequences.
Length = 489
Score = 32.9 bits (75), Expect = 2.5
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 1834 TEPISSNVASKREELDHLYVCVSKVIYEGLSNYEKNPTATCSTLYGTVMMLKAACMNHPA 1893
+ S + +E++ + + GL N KNP LYG V A + P
Sbjct: 22 GDKFISVPDTDEDEINEFVDSLRQCPKSGLHNPLKNPERY--LLYGDVSHRVAHELRKPE 79
Query: 1894 YVDRFILEFMRVIQRMA 1910
V+ F F R+IQR+A
Sbjct: 80 -VEDF---FARLIQRVA 92
>gnl|CDD|227365 COG5032, TEL1, Phosphatidylinositol kinase and protein kinases of the
PI-3 kinase family [Signal transduction mechanisms / Cell
division and chromosome partitioning / Chromatin
structure and dynamics / DNA replication, recombination,
and repair / Intracellular trafficking and secretion].
Length = 2105
Score = 32.4 bits (74), Expect = 4.1
Identities = 45/189 (23%), Positives = 70/189 (37%), Gaps = 37/189 (19%)
Query: 2211 AQLCHLDTHLAEKVWLDMFPQMWSILSETQQQNLTDEIIPFIVSGIHVVQKDVHPSSINT 2270
LC L L FP ++ + + H+ Q D+ P+ I
Sbjct: 1028 ESLCSFLAKLLHDEELYFFPLLFVSS-----------LETLLSVNYHINQLDLRPN-ILK 1075
Query: 2271 IYESLAHCNPPLPIKPAIMTYLGKAQGLWHRVTLSLEKMAVEGLLKQNRMQNRAPSVADC 2330
+ S +KP ++ YL + +R E L K +R+ + +
Sbjct: 1076 HFGSFVRFQ----LKPHLVKYLQRWYEALNRY--------FELLSKGDRLFAISFTKLRN 1123
Query: 2331 YDFEPDHAPQQQDIIDQLAEMYSALREEDMWFGLWQKNAKHKETLYALAYEQQGFYEQAL 2390
D E+YS+L E DM+ L + K ETL A AYEQ G + +A
Sbjct: 1124 VD------------ALGKLELYSSLAEIDMFLSLH-RRRKLLETLVATAYEQVGEWYKAQ 1170
Query: 2391 KAYEVTIKK 2399
+ YEV +K
Sbjct: 1171 QLYEVAQRK 1179
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 32.1 bits (74), Expect = 4.4
Identities = 28/132 (21%), Positives = 46/132 (34%), Gaps = 13/132 (9%)
Query: 1645 KEEAEGTSGGKAIQEPPRKKMALESFAPGESSMKYDIPTASKPIEKVHAD--AVINFLAR 1702
+EE + A E + LE F K K +E A +
Sbjct: 199 EEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVEGRLAQHKKYAKLREK 258
Query: 1703 LSCQVSDLPPN------LSSSMQS---QVIQTPGEMLARRCVSLIRMALKPEVWSHQNTE 1753
L ++ L L ++ +V E+L R V ++M K + Q E
Sbjct: 259 LKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELL--RLVERLKMPRKDFLKLFQGNE 316
Query: 1754 FKLTWLDKVLSS 1765
+TWL+K ++S
Sbjct: 317 LDITWLEKEIAS 328
>gnl|CDD|224915 COG2004, RPS24A, Ribosomal protein S24E [Translation, ribosomal
structure and biogenesis].
Length = 107
Score = 30.0 bits (68), Expect = 4.7
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 2316 KQNRMQNRAPSVADCYDFEPDHAPQQQDIIDQLAEMYSALREEDMWFGLWQKNAKHKETL 2375
+ N + R V Y E P ++++ ++LA M A +E + + + K +
Sbjct: 10 RDNPLLKRKEIVFVVY-HEGSPTPSRKEVREKLAAMLGADKELVVVDYIKTEFGKGRSKG 68
Query: 2376 YALAYE 2381
YA Y+
Sbjct: 69 YAKIYD 74
>gnl|CDD|133211 cd05080, PTKc_Tyk2_rpt2, Catalytic (repeat 2) domain of the Protein
Tyrosine Kinase, Tyrosine kinase 2. Protein Tyrosine
Kinase (PTK) family; Tyrosine kinase 2 (Tyk2); catalytic
(c) domain (repeat 2). 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.
Tyk2 is a member of the Janus kinase (Jak) subfamily of
proteins, which are cytoplasmic (or nonreceptor) tyr
kinases containing an N-terminal FERM domain, followed by
a Src homology 2 (SH2) domain, a pseudokinase domain, and
a C-terminal tyr kinase catalytic domain. Jaks are
crucial for cytokine receptor signaling. They are
activated by autophosphorylation upon cytokine-induced
receptor aggregation, and subsequently trigger downstream
signaling events such as the phosphorylation of signal
transducers and activators of transcription (STATs). Tyk2
is widely expressed in many tissues. It is involved in
signaling via the cytokine receptors IFN-alphabeta, IL-6,
IL-10, IL-12, IL-13, and IL-23. It mediates cell surface
urokinase receptor (uPAR) signaling and plays a role in
modulating vascular smooth muscle cell (VSMC) functional
behavior in response to injury. Tyk2 is also important in
dendritic cell function and T helper (Th)1 cell
differentiation. A homozygous mutation of Tyk2 was found
in a patient with hyper-IgE syndrome (HIES), a primary
immunodeficiency characterized by recurrent skin
abscesses, pneumonia, and elevated serum IgE. This
suggests that Tyk2 may play important roles in multiple
cytokine signaling involved in innate and adaptive
immunity.
Length = 283
Score = 31.4 bits (71), Expect = 4.9
Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 13/90 (14%)
Query: 2270 TIYESLAHCNPPLPIKPAIMTYLGKAQGLWHRVTLSLEKMAVEGLLKQNRM--QNRAPS- 2326
T+YE L HC+ +G QG V L +E L + R+ P
Sbjct: 199 TLYELLTHCDSKQSPPKKFEEMIGPKQGQMTVVRL------IELLERGMRLPCPKNCPQE 252
Query: 2327 ----VADCYDFEPDHAPQQQDIIDQLAEMY 2352
+ +C++ E P + +I L EM+
Sbjct: 253 VYILMKNCWETEAKFRPTFRSLIPILKEMH 282
>gnl|CDD|197854 smart00745, MIT, Microtubule Interacting and Trafficking molecule
domain.
Length = 77
Score = 28.4 bits (64), Expect = 7.9
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 2377 ALAYEQQGFYEQALKAYEVTIKKGLEEY---ANSPAPISHNSELRLREKQWLR 2426
AL ++ G YE+AL+ Y KK +E + L+ + ++L
Sbjct: 15 ALKADEAGNYEEALELY----KKAIEYLLEGIKVESDSKRREALKAKAAEYLD 63
>gnl|CDD|224705 COG1792, MreC, Cell shape-determining protein [Cell envelope
biogenesis, outer membrane].
Length = 284
Score = 30.8 bits (70), Expect = 8.0
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 9/89 (10%)
Query: 1306 PKLLVKILLHYFSHHRHIIDLLFFILRAVTERLLPDFTFLREFLETTVAQTYSI-----E 1360
P + LL F ++ +L +L + + +R+ + T ++ S+ E
Sbjct: 1 PIFSLNKLLKIFL----VLIILLLLLLLFADSRGQVSSIIRQVVGTVLSPVQSVVAAPFE 56
Query: 1361 WKRKAFLRFLELFKLALVSQELKAKILQL 1389
+ L LAL ++ELK ++ +L
Sbjct: 57 FVDGVLEFLKSLKDLALENEELKKELAEL 85
>gnl|CDD|214938 smart00958, SecA_PP_bind, SecA preprotein cross-linking domain.
The SecA ATPase is involved in the insertion and
retraction of preproteins through the plasma membrane.
This domain has been found to cross-link to
preproteins, thought to indicate a role in preprotein
binding. The pre-protein cross-linking domain is
comprised of two sub domains that are inserted within
the ATPase domain.
Length = 114
Score = 29.3 bits (67), Expect = 8.6
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 23 PLVYSTLADLVHHVRQLLPMSDLIKAVHLFSKNIH 57
L +LVHHV Q L +A LF +++
Sbjct: 53 NLYDPENIELVHHVNQAL------RAHKLFKRDVD 81
>gnl|CDD|222285 pfam13646, HEAT_2, HEAT repeats. This family includes multiple HEAT
repeats.
Length = 88
Score = 28.8 bits (65), Expect = 8.8
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 999 LRKAAMRALASWHYVPNCSQKIFNTLFAALERPNPELQEAAFQA 1042
+R AA RAL + L L+ P+PE++ AA +A
Sbjct: 16 VRAAAARALGELG-----DPEALPALLELLKDPDPEVRRAAAEA 54
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
0.321 0.136 0.396
Gapped
Lambda K H
0.267 0.0863 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 123,312,538
Number of extensions: 12471436
Number of successful extensions: 10063
Number of sequences better than 10.0: 1
Number of HSP's gapped: 10059
Number of HSP's successfully gapped: 24
Length of query: 2426
Length of database: 10,937,602
Length adjustment: 113
Effective length of query: 2313
Effective length of database: 5,925,600
Effective search space: 13705912800
Effective search space used: 13705912800
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: 67 (29.3 bits)