RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10825
(140 letters)
>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 = 61.6 bits (150), Expect = 2e-13
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 4/81 (4%)
Query: 27 IIGYLPFEVLGT--SGYDYYHVDDLDSVVTCH-EALMQKGEGTSCYYRFLTKGQQWIWLQ 83
I+GY P E+ + D H +D + V E ++KGE S YR K ++ W++
Sbjct: 11 ILGYTPEELKSSYEGWLDLVHPEDRERVRRALQEFSLKKGEPYSGEYRIRRKDGEYRWVE 70
Query: 84 TRFYITYHQWNSKPEFIVCTH 104
R N KP ++
Sbjct: 71 ARGRPIR-DENGKPVRVIGVA 90
>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 = 60.0 bits (145), Expect = 8e-13
Identities = 18/83 (21%), Positives = 31/83 (37%)
Query: 24 APPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQ 83
A ++GY P E++G S D H +D + + E L+ GE + R K IW+
Sbjct: 21 AEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80
Query: 84 TRFYITYHQWNSKPEFIVCTHRV 106
+ + +
Sbjct: 81 VSLTPIRDEGGEVIGLLGVVRDI 103
>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to
contribute to PAS structural domain). PAC motif occurs
C-terminal to a subset of all known PAS motifs. It is
proposed to contribute to the PAS domain fold.
Length = 43
Score = 41.0 bits (97), Expect = 4e-06
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 67 SCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVS 108
+ YR K +IW+ + + E I+ R ++
Sbjct: 1 TVEYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDIT 41
>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 = 33.4 bits (77), Expect = 0.013
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 3/80 (3%)
Query: 27 IIGYLPFEVLGTSGYDYYHVDDLDSVVTCHE-ALMQKGEGTSCYYRFLTKGQQWIWLQTR 85
I GY E++G + + +D + V E L + E S R K IW++
Sbjct: 35 IFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEREPVSEERRVRRKDGSEIWVEVS 94
Query: 86 FYITYHQWNSKPEFIVCTHR 105
++ + N +V R
Sbjct: 95 --VSPIRTNGGELGVVGIVR 112
>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 = 31.6 bits (72), Expect = 0.025
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 27 IIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQ 61
++GY P E++G S + H +D + V + L+
Sbjct: 33 LLGYSPEELIGKSLLELIHPEDRERVQEALQRLLS 67
>gnl|CDD|234409 TIGR03945, PLP_SbnA_fam, 2,3-diaminopropionate biosynthesis protein
SbnA. Members of this family include SbnA, a protein of
the staphyloferrin B biosynthesis operon of
Staphylococcus aureus. SbnA and SbnB together appear to
synthesize 2,3-diaminopropionate, a precursor of certain
siderophores and other secondary metabolites. SbnA is a
pyridoxal phosphate-dependent enzyme [Cellular
processes, Biosynthesis of natural products].
Length = 304
Score = 30.6 bits (70), Expect = 0.20
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 41 YDYYHVDDLDSVVTCHEALMQKG 63
D HV + D+V C ++G
Sbjct: 234 DDVVHVPEYDTVAGCRRLARREG 256
>gnl|CDD|213963 TIGR04350, C_S_lyase_PatB, putative C-S lyase. Members of this
subfamily are probable C-S lyases from a family of
pyridoxal phosphate-dependent enzymes that tend to be
(mis)annotated as probable aminotransferases. One member
is PatB of Bacillus subtilis, a proven C-S-lyase.
Another is the virulence factor cystalysin from
Treponema denticola, whose hemolysin activity may stem
from H2S production. Members of the seed alignment occur
next to examples of the enzyme 5-histidylcysteine
sulfoxide synthase, from ovothiol A biosynthesis, and
would be expected to perform a C-S cleavage of
5-histidylcysteine sulfoxide to leave
1-methyl-4-mercaptohistidine (ovothiol A).
Length = 384
Score = 30.7 bits (70), Expect = 0.21
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 5/27 (18%)
Query: 81 WLQTRFYITYHQWNSKPEFIVCTHRVV 107
WL R H W PE+IV VV
Sbjct: 72 WLAQR-----HGWQIDPEWIVFLPGVV 93
>gnl|CDD|222120 pfam13426, PAS_9, PAS domain.
Length = 101
Score = 29.6 bits (67), Expect = 0.22
Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 1/82 (1%)
Query: 27 IIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRF 86
++GY E+LG S D + D + V ++ G K + +
Sbjct: 20 LLGYTREELLGKSIRDLFGPGDDEEAVARLREALRNGGEVEVELELRRKDGEPFPVLVSA 79
Query: 87 YITYHQWNSKPEFIVCTHRVVS 108
+ + + IV R ++
Sbjct: 80 SPVRDE-DGEVVGIVGILRDIT 100
>gnl|CDD|163696 cd08065, MPN_eIF3h, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF2h.
Eukaryotic translation initiation factor 3 (eIF3)
subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma;
eIF3-p40) is an evolutionarily non-conserved subunit of
the functional core that comprises eIF3a, eIF3b, eIF3c,
eIF3e, eIF3f, and eIF3h, and contains the MPN domain.
However, it lacks the canonical JAMM motif, and
therefore does not show catalytic isopeptidase
activity.Together with eIF3e and eIF3f, eIF3h stabilizes
the eIF3 complex. Results suggest that eIF3h regulates
cell growth and viability, and that over-expression of
the gene may provide growth advantage to prostate,
breast, and liver cancer cells. For example, EIF3h gene
amplification is common in late-stage prostate cancer
suggesting that it may be functionally involved in the
progression of the disease. It has been shown that
coamplification of MYC, a well characterized oncogene
involved in cell growth, differentiation, and apoptosis,
and EIF3h in patients with non-small cell lung cancer
(NSCLC) improves survival if treated with the Epidermal
Growth Factor Receptor Tyrosine Kinase Inhibitor
(EGFR-TKI), Gefitinib. Plant eIF3h is implicated in
translation of specific mRNAs.
Length = 266
Score = 27.6 bits (62), Expect = 2.1
Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 7/84 (8%)
Query: 6 PVTFCMSDLMNSTIYDLVAPPIIGYLPFE--VLGTSGYDYYHVDDLDSVVTCHEALMQKG 63
PV S L+N+ + +L F+ L T+ + +++ L V K
Sbjct: 167 PVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKF 226
Query: 64 EGTSCYYRFLTKGQQWI--WLQTR 85
+ Y R L + Q I WLQ R
Sbjct: 227 ---NYYQRNLARQQAQIQQWLQKR 247
>gnl|CDD|177351 PHA02117, PHA02117, glutathionylspermidine synthase
domain-containing protein.
Length = 397
Score = 27.5 bits (61), Expect = 2.8
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 78 QWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRDNNQVPDSE 124
QW WL + Q+N E +V + +N L N V +
Sbjct: 141 QWNWLDDA-HPRRQQFNEIHEALVNHWADMKKLNALNGCLNIVATGQ 186
>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 = 26.6 bits (59), Expect = 2.9
Identities = 17/80 (21%), Positives = 25/80 (31%), Gaps = 2/80 (2%)
Query: 29 GYLPFEVLGTSGYDYYHVDDLDSVVTC-HEALMQKGEGTSCYYRFLTKGQQWIWLQTRFY 87
G EV+G S D DD V +AL+Q E F + ++ R
Sbjct: 35 GLSREEVIGKSLLDLIPEDDDAEVAELLRQALLQGEESRGFEVSFRVPDGRPRHVEVRAS 94
Query: 88 ITYHQWNSKPEFIVCTHRVV 107
F+ R +
Sbjct: 95 PVRDAGGEVRGFL-GVLRDI 113
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 27.2 bits (61), Expect = 3.2
Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 5/52 (9%)
Query: 13 DLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGE 64
D ++ V + G LP G G + V D V H A M+KG
Sbjct: 172 DEGPTSTGLDVLDYLNGKLPAYPPG--GTSFVDVRD---VAEGHIAAMEKGR 218
>gnl|CDD|221842 pfam12902, Ferritin-like, Ferritin-like. This is a family of
bacterial ferritin-like substances that also includes a
C-terminal domain of VioB, polyketide synthase enzymes,
that make up one of the key components of the violacein
biosynthesis pathway. Violacein is a purple-coloured,
broad-spectrum antibacterial pigment.
Length = 217
Score = 26.6 bits (59), Expect = 3.9
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 22/72 (30%)
Query: 20 YDLVAPPIIGYLPFEVLGTSGYDYYH-------VDDLDSVVTCHEALMQKGEGT------ 66
+ G ++ G ++Y+ V DL S + + + ++GEGT
Sbjct: 146 GNKGFGGFEGDPLRQI----GNEHYYPPDELFPVTDLASALRAIDEITEQGEGTDLSPED 201
Query: 67 -----SCYYRFL 73
S YYRF
Sbjct: 202 DEDELSHYYRFR 213
>gnl|CDD|168292 PRK05906, PRK05906, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 454
Score = 26.7 bits (59), Expect = 4.6
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 5/21 (23%)
Query: 71 RFLTKG-----QQWIWLQTRF 86
RFL KG +QW+WL R+
Sbjct: 292 RFLEKGIACKPEQWMWLHKRW 312
>gnl|CDD|227660 COG5362, COG5362, Phage-related terminase [General function
prediction only].
Length = 202
Score = 26.5 bits (58), Expect = 5.1
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 44 YHVDDLDSVVTCHEALMQKGEGT 66
H DD+DSV + LM +
Sbjct: 176 KHDDDVDSVSSALVKLMIGQQSL 198
>gnl|CDD|215305 PLN02562, PLN02562, UDP-glycosyltransferase.
Length = 448
Score = 26.0 bits (57), Expect = 7.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 87 YITYHQWNSKPEFIVCTHRVVSY 109
Y+T+ WNS E I C R++ Y
Sbjct: 350 YLTHCGWNSTMEAIQCQKRLLCY 372
>gnl|CDD|143454 cd07136, ALDH_YwdH-P39616, Bacillus subtilis aldehyde dehydrogenase
ywdH-like. Uncharacterized Bacillus subtilis ywdH
aldehyde dehydrogenase (locus P39616) most closely
related to the ALDHs and fatty ALDHs of families 3 and
14, and similar sequences, are included in this CD.
Length = 449
Score = 25.9 bits (58), Expect = 8.5
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 15 MNSTIYDLVAPPIIGYLPFEVLGTSGYDYYH 45
+N TI L P YLPF +G SG YH
Sbjct: 384 INDTIMHLANP----YLPFGGVGNSGMGSYH 410
>gnl|CDD|191545 pfam06507, Auxin_resp, Auxin response factor. A conserved region
of auxin-responsive transcription factors.
Length = 83
Score = 24.5 bits (54), Expect = 9.6
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 84 TRFYITYHQWNSKPEFIVCTHRVVSYVNV 112
+ F++ Y+ S EF+V + + +N
Sbjct: 9 SPFHVFYNPRASTSEFVVPYAKYLKAMNN 37
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 0.137 0.442
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: 7,147,526
Number of extensions: 612257
Number of successful extensions: 418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 416
Number of HSP's successfully gapped: 30
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.7 bits)