RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6003
(109 letters)
>gnl|CDD|222120 pfam13426, PAS_9, PAS domain.
Length = 101
Score = 63.5 bits (155), Expect = 1e-14
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAA 70
LV + I+Y +D RL G++R E++ + + L GP + AV ++EAL
Sbjct: 1 ILVLDPD---GRIVYANDAALRLLGYTREELLGKS--IRDLFGPGDDEEAVARLREALRN 55
Query: 71 GVEKHFEILYYKKDGKY 87
G E E+ +KDG+
Sbjct: 56 GGEVEVELELRRKDGEP 72
>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional.
Length = 361
Score = 64.8 bits (158), Expect = 1e-13
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 13 VANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGV 72
+ + H I+ + F LTG++ EV+ ++ C+FL G T AV ++ A+AA
Sbjct: 58 ITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRN--CRFLQGAATDPIAVAKIRAAIAAER 115
Query: 73 EKHFEILYYKKDG 85
E E+L Y+KDG
Sbjct: 116 EIVVELLNYRKDG 128
>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional.
Length = 540
Score = 59.3 bits (144), Expect = 1e-11
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 8/81 (9%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
I++ + F +TG++ E++ + C+FL GP T + V V++A+A E EIL Y+
Sbjct: 55 IVFANRAFLEMTGYAAEEIIGNN--CRFLQGPETDRATVAEVRDAIAERREIATEILNYR 112
Query: 83 KDGKYSSVGGSYGDITPVSPV 103
KD G S+ + VSPV
Sbjct: 113 KD------GSSFWNALFVSPV 127
>gnl|CDD|237426 PRK13558, PRK13558, bacterio-opsin activator; Provisional.
Length = 665
Score = 49.1 bits (117), Expect = 4e-08
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 9/81 (11%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
+IY +D F R+TG+S EV+ ++ C+FL G T++ V ++EA+ E+ Y+
Sbjct: 173 LIYINDAFERITGYSPDEVLGRN--CRFLQGEDTNEERVAELREAIDEERPTSVELRNYR 230
Query: 83 KDGK--YSSVGGSYGDITPVS 101
KDG ++ V DI P+
Sbjct: 231 KDGSTFWNQV-----DIAPIR 246
>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea,
eubacteria and eukarya. Probably the most surprising
identification of a PAS domain was that in EAG-like
K+-channels. PAS domains have been found to bind
ligands, and to act as sensors for light and oxygen in
signal transduction.
Length = 103
Score = 40.3 bits (94), Expect = 1e-05
Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
I+Y + +L G+S E++ + + +H + + ++ L+ G E+ +
Sbjct: 14 ILYANPAAEQLLGYSPEELIGKSLL-DLIHPEDREEL-RERLENLLSGGEPVTLEVRLRR 71
Query: 83 KDGKY 87
KDG
Sbjct: 72 KDGSV 76
>gnl|CDD|216228 pfam00989, PAS, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 113
Score = 37.0 bits (86), Expect = 3e-04
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
I+Y + L G SR EV+ + + + ++ A + + L + FE+ +
Sbjct: 23 ILYVNAAAEELLGLSREEVIGKSLL-DLIPEDDDAEVAELLRQALLQGEESRGFEVSFRV 81
Query: 83 KDGKY 87
DG+
Sbjct: 82 PDGRP 86
>gnl|CDD|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction
mechanisms].
Length = 232
Score = 36.0 bits (81), Expect = 0.001
Identities = 12/66 (18%), Positives = 20/66 (30%)
Query: 22 HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81
I+Y + L G+S E + + + A G E
Sbjct: 133 RILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYRVR 192
Query: 82 KKDGKY 87
+KDG+
Sbjct: 193 RKDGER 198
>gnl|CDD|214512 smart00091, PAS, PAS domain. PAS motifs appear in archaea,
eubacteria and eukarya. Probably the most surprising
identification of a PAS domain was that in EAG-like
K+-channels.
Length = 67
Score = 33.9 bits (78), Expect = 0.002
Identities = 8/49 (16%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 12 LVANSHLGLC------HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGP 54
++ + G+ I+Y + L G+S E++ + + + +H
Sbjct: 6 ILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKS-LLELIHPE 53
>gnl|CDD|232884 TIGR00229, sensory_box, PAS domain S-box. The PAS domain was
previously described. This sensory box, or S-box domain
occupies the central portion of the PAS domain but is
more widely distributed. It is often tandemly repeated.
Known prosthetic groups bound in the S-box domain
include heme in the oxygen sensor FixL, FAD in the
redox potential sensor NifL, and a 4-hydroxycinnamyl
chromophore in photoactive yellow protein. Proteins
containing the domain often contain other regulatory
domains such as response regulator or sensor histidine
kinase domains. Other S-box proteins include
phytochromes and the aryl hydrocarbon receptor nuclear
translocator [Regulatory functions, Small molecule
interactions].
Length = 124
Score = 33.8 bits (78), Expect = 0.004
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 22 HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKH-FEILY 80
+I+Y + F + G+S E++ ++ + + + + + ++ L E E
Sbjct: 24 NILYVNPAFEEIFGYSAEELIGRNVL-ELIPEEDREEVR-ERIERRLEGEREPVSEERRV 81
Query: 81 YKKDGKY 87
+KDG
Sbjct: 82 RRKDGSE 88
>gnl|CDD|219844 pfam08447, PAS_3, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 90
Score = 32.7 bits (75), Expect = 0.009
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 23 IIYCSDGFCRLTGFSRAEVM-QQDAICKFLHGPLTSQHAVQVVKEALAAGVEK-HFEILY 80
IIY S F + G++ E+ + +H P + + ++E E E
Sbjct: 1 IIYWSPRFEEILGYTPEELKSSYEGWLDLVH-PEDRERVRRALQEFSLKKGEPYSGEYRI 59
Query: 81 YKKDGKY 87
+KDG+Y
Sbjct: 60 RRKDGEY 66
>gnl|CDD|221967 pfam13188, PAS_8, PAS domain.
Length = 64
Score = 29.1 bits (65), Expect = 0.11
Identities = 7/59 (11%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 12 LVANSHLGLC-----HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVK 65
L N+ G+ I+Y + L G+ + + + + ++ ++
Sbjct: 6 LFENAPDGILVLDGDRILYANPAALELLGYELLGELLGELLDDLEALAEEALELLEELR 64
>gnl|CDD|143448 cd07130, ALDH_F7_AASADH, NAD+-dependent alpha-aminoadipic
semialdehyde dehydrogenase, ALDH family members 7A1 and
7B. Alpha-aminoadipic semialdehyde dehydrogenase
(AASADH, EC=1.2.1.31), also known as ALDH7A1,
Antiquitin-1, ALDH7B, or
delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH),
is a NAD+-dependent ALDH. Human ALDH7A1 is involved in
the pipecolic acid pathway of lysine catabolism,
catalyzing the oxidation of alpha-aminoadipic
semialdehyde to alpha-aminoadipate. Arabidopsis
thaliana ALDH7B4 appears to be an
osmotic-stress-inducible ALDH gene encoding a
turgor-responsive or stress-inducible ALDH. The
Streptomyces clavuligerus P6CDH appears to be involved
in cephamycin biosynthesis, catalyzing the second stage
of the two-step conversion of lysine to
alpha-aminoadipic acid. The ALDH7A1 enzyme and others
in this group have been observed as tetramers, yet the
bacterial P6CDH enzyme has been reported as a monomer.
Length = 474
Score = 28.7 bits (65), Expect = 0.47
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 51 LHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSVGGSY 94
L GPL ++ AV A+ + +L+ GK G+Y
Sbjct: 316 LVGPLHTKAAVDNYLAAIEEAKSQGGTVLF---GGKVIDGPGNY 356
>gnl|CDD|106506 PRK13560, PRK13560, hypothetical protein; Provisional.
Length = 807
Score = 28.5 bits (63), Expect = 0.62
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 23 IIYCSDGFCRLTGFSRAEVM 42
+ C+D C GF R E++
Sbjct: 226 VFGCNDAACLACGFRREEII 245
>gnl|CDD|218819 pfam05942, PaREP1, Archaeal PaREP1/PaREP8 family. This family
consists of several archaeal PaREP1 and PaREP8 proteins
the function of this family is unknown.
Length = 114
Score = 27.5 bits (62), Expect = 0.71
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 62 QVVKEALAAGVEKHFEILYYKKDGK 86
Q K L A K+ L K GK
Sbjct: 31 QAWKALLKALAAKNRLKLAEKARGK 55
>gnl|CDD|183097 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Provisional.
Length = 799
Score = 27.8 bits (62), Expect = 1.4
Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 4/81 (4%)
Query: 6 HTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVK 65
H +R +V + I+ C+ F + G+ +E L+ P ++
Sbjct: 144 HLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQ-PDTLLNIPEFPADNRIRLQ 199
Query: 66 EALAAGVEKHFEILYYKKDGK 86
+ L E L + G+
Sbjct: 200 QLLWKTARDQDEFLLLTRTGE 220
>gnl|CDD|183050 PRK11241, gabD, succinate-semialdehyde dehydrogenase I;
Provisional.
Length = 482
Score = 26.8 bits (59), Expect = 2.4
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 53 GPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSVGGSY 94
GPL + AV V+E +A +EK ++ GK +GG++
Sbjct: 329 GPLIDEKAVAKVEEHIADALEKGARVV---CGGKAHELGGNF 367
>gnl|CDD|143405 cd07086, ALDH_F7_AASADH-like, NAD+-dependent alpha-aminoadipic
semialdehyde dehydrogenase and related proteins. ALDH
subfamily which includes the NAD+-dependent,
alpha-aminoadipic semialdehyde dehydrogenase (AASADH,
EC=1.2.1.31), also known as Antiquitin-1, ALDH7A1,
ALDH7B or delta-1-piperideine-6-carboxylate
dehydrogenase (P6CDH), and other similar sequences, such
as the uncharacterized aldehyde dehydrogenase of
Candidatus kuenenia AldH (locus CAJ73105).
Length = 478
Score = 26.8 bits (60), Expect = 2.5
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 51 LHGPLTSQHAVQVVKEALAAGVEKHFEILY 80
L GPL +Q AV+ A+ + +L
Sbjct: 317 LVGPLINQAAVEKYLNAIEIAKSQGGTVLT 346
>gnl|CDD|221296 pfam11894, DUF3414, Protein of unknown function (DUF3414). This
family of proteins are functionally uncharacterized. This
protein is found in eukaryotes. Proteins in this family
are typically between 764 to 2011 amino acids in length.
This protein has a conserved LLG sequence motif.
Length = 1612
Score = 26.9 bits (60), Expect = 2.9
Identities = 8/39 (20%), Positives = 14/39 (35%), Gaps = 2/39 (5%)
Query: 1 MTLKHHTNRSFLVANSHL--GLCHIIYCSDGFCRLTGFS 37
M+L T + L +C+ +G CR+
Sbjct: 1373 MSLSRETLQIIKSYGERLIEVICNDAIDGEGTCRILALL 1411
>gnl|CDD|226107 COG3579, PepC, Aminopeptidase C [Amino acid transport and
metabolism].
Length = 444
Score = 26.3 bits (58), Expect = 3.6
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 40 EVMQQDA-ICKFLHGPLTSQHAVQVVKEALAAGV-----------EKHFEILYYKKDGKY 87
++++QDA I + V+ +KE L + + F+ Y KD KY
Sbjct: 177 KLLRQDAQILRDALKEGADDDTVEALKEELLQEIFNFLAMTLGLPPEKFDFAYRDKDNKY 236
Query: 88 SSVGGSYGDITP 99
G +TP
Sbjct: 237 HKEKG----LTP 244
>gnl|CDD|206023 pfam13852, DUF4197, Protein of unknown function (DUF4197). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 228 and 249 amino
acids in length.
Length = 203
Score = 26.0 bits (58), Expect = 4.3
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 53 GPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSS 89
L+ + +KEAL+ G E+ L K DG +
Sbjct: 3 SGLSDSEIAEGLKEALSLGAERAVARL-GKPDGFLGN 38
>gnl|CDD|202517 pfam03051, Peptidase_C1_2, Peptidase C1-like family. This family
is closely related to the Peptidase_C1 family pfam00112,
containing several prokaryotic and eukaryotic
aminopeptidases and bleomycin hydrolases.
Length = 438
Score = 25.8 bits (57), Expect = 5.2
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 16/72 (22%)
Query: 42 MQQDA-ICKFLHGPLTSQHAVQVVKE----------ALAAGV-EKHFEILYYKKDGKYSS 89
+++DA I + L +Q KE A+A G + F+ Y KD Y
Sbjct: 177 LRKDALILRRLVEEGADDEEIQAKKEEMLSEIFRVLAIALGEPPETFDFEYRDKDKNYHK 236
Query: 90 VGGSYGDITPVS 101
+ DITP+
Sbjct: 237 I----KDITPLE 244
>gnl|CDD|234850 PRK00861, PRK00861, putative lipid kinase; Reviewed.
Length = 300
Score = 25.7 bits (57), Expect = 5.9
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 51 LHGPLTSQ--HAVQVVKEALAAGVEKHFEILYYKKDGKYSSVGG 92
L LT+ A Q+ +EA+ G E I+ DG S+V G
Sbjct: 35 LDIYLTTPEIGADQLAQEAIERGAEL---IIASGGDGTLSAVAG 75
>gnl|CDD|182556 PRK10568, PRK10568, periplasmic protein; Provisional.
Length = 203
Score = 25.5 bits (56), Expect = 6.5
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 51 LHGPLTSQ-HAVQVVKEALAAGVE--KHFEILYYKKDGKYSSVGGSYGDITPVSPV 103
L G + SQ A + VK +A GVE + +D K SV G GD S +
Sbjct: 91 LSGFVESQAQAEEAVK--VAKGVEGVTSVSDKLHVRDAKEQSVKGYAGDTATTSEI 144
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 25.4 bits (56), Expect = 6.7
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 88 SSVGGSYGDITPVSPVVPVHTI 109
S+VG YGDI PVS + TI
Sbjct: 181 STVG--YGDIVPVSESARLFTI 200
>gnl|CDD|233479 TIGR01578, MiaB-like-B, MiaB-like tRNA modifying enzyme,
archaeal-type. This clade of sequences is closely
related to MiaB, a modifier of isopentenylated
adenosine-37 of certain eukaryotic and bacterial tRNAs
(see TIGR01574). Sequence alignments suggest that this
equivalog performs the same chemical transformation as
MiaB, perhaps on a different (or differently modified)
tRNA base substrate. This clade is a member of a
subfamily (TIGR00089) and spans the archaea and
eukaryotes. The only archaeal miaB-like genes are in
this clade, while eukaryotes have sequences described by
This model as well as ones falling within the scope of
the MiaB equivalog model [Protein synthesis, tRNA and
rRNA base modification].
Length = 420
Score = 25.5 bits (56), Expect = 7.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 39 AEVMQQDAICKFLHGPLTS 57
A V Q + + KFLH P+ S
Sbjct: 234 ANVYQHEKVYKFLHLPVQS 252
>gnl|CDD|241488 cd13334, FERM_C_JAK3, Janus kinase (JAK) FERM domain C-lobe. JAK3
functions in signal transduction and interacts with
members of the STAT (signal transduction and activators
of transcription) family. It is required for signaling
of the type I receptors that use the common gamma chain:
IL-2, IL-4, IL-7, IL-9, IL-15 and IL-21. Cytokine
binding induces the association of separate cytokine
receptor subunits and the activation of the
receptor-associated JAKs. In the absence of cytokine,
JAKs lack protein tyrosine kinase activity. Once
activated, the JAKs create docking sites for the STAT
transcription factors by phosphorylation of specific
tyrosine residues on the cytokine receptor subunits.
Unlike the ubiquitous expression of JAK1, JAK2 and Tyk2,
JAK3 is predominantly expressed in hematopoietic cells,
such as NK cells, T cells and B cells. Mutations of
JAK3 result in severe combined immunodeficiency (SCID).
In addition to its well-known roles in T cells and NK
cells, JAK3 has recently been found to inhibits
IL-8-mediated chemotaxis. JAK3 interacts with CD247,
TIAF1, and IL2RG. JAK (also called Just Another Kinase)
is a family of intracellular, non-receptor tyrosine
kinases that transduce cytokine-mediated signals via the
JAK-STAT pathway. The JAK family in mammals consists of
4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed
of seven JAK homology (JH) domains (JH1-JH7) . The
C-terminal JH1 domain is the main catalytic domain,
followed by JH2, which is often referred to as a
pseudokinase domain, followed by JH3-JH4 which is
homologous to the SH2 domain, and lastly JH5-JH7 which
is a FERM domain. Named after Janus, the two-faced
Roman god of doorways, JAKs possess two near-identical
phosphate-transferring domains; one which displays the
kinase activity (JH1), while the other negatively
regulates the kinase activity of the first (JH2). The
FERM domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe,A-lobe,
B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3 within the
FERM domain is part of the PH domain family. The FERM
domain is found in the cytoskeletal-associated proteins
such as ezrin, moesin, radixin, 4.1R, and merlin. These
proteins provide a link between the membrane and
cytoskeleton and are involved in signal transduction
pathways. The FERM domain is also found in protein
tyrosine phosphatases (PTPs) , the tyrosine kinases FAK
and JAK, in addition to other proteins involved in
signaling. This domain is structurally similar to the PH
and PTB domains and consequently is capable of binding
to both peptides and phospholipids at different sites.
Length = 174
Score = 25.1 bits (55), Expect = 8.5
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 28 DGFCRLTGFSRAEVMQQDAICKFL-------HGPLTSQHAVQVVK 65
DG+ RLT S ++ A + L HGP+TS+ AV +K
Sbjct: 130 DGYFRLTTDSHHYFCKEVAPPRLLEDIENQCHGPITSEFAVHKLK 174
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
0.323 0.137 0.424
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,440,074
Number of extensions: 445542
Number of successful extensions: 472
Number of sequences better than 10.0: 1
Number of HSP's gapped: 468
Number of HSP's successfully gapped: 27
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.3 bits)