RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5907
(56 letters)
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA
in a non-sequence specific fashion and contain two or
more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 52.2 bits (126), Expect = 2e-11
Identities = 17/52 (32%), Positives = 34/52 (65%)
Query: 2 PYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
Y +S++ ++K +N D + E+ KI+G+ W++L E++K +Y E E++K
Sbjct: 7 AYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDK 58
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding
preferences. Two phylogenically distinct groups of
Class I proteins bind DNA in a sequence specific
fashion and contain a single HMG box. One group
(SOX-TCF) includes transcription factors, TCF-1, -3,
-4; and also SRY and LEF-1, which bind four-way DNA
junctions and duplex DNA targets. The second group
(MATA) includes fungal mating type gene products MC,
MATA1 and Ste11. Class II and III proteins (HMGB-UBF)
bind DNA in a non-sequence specific fashion and contain
two or more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 52.2 bits (126), Expect = 2e-11
Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 2 PYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
Y +S++ +VKA+N L + EI KI+G+MW+ L E++K +Y E E++K
Sbjct: 7 AYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDK 58
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 46.1 bits (110), Expect = 6e-09
Identities = 20/53 (37%), Positives = 34/53 (64%)
Query: 1 MPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
+ +S++ ++KA+N LK EI KI+G+ W++L E++K Y E E+EK
Sbjct: 6 SAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEK 58
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 39.6 bits (93), Expect = 2e-06
Identities = 18/52 (34%), Positives = 33/52 (63%)
Query: 2 PYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
+M +S++ ++KA+N DL EI K +G+ W+ L E++K Y E +++K
Sbjct: 8 AFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include the fungal mating type gene products
MC, MATA1 and Ste11.
Length = 77
Score = 34.9 bits (81), Expect = 2e-04
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
++ Y + Q+K +N L EI +IIG+MWR + K Y E E+EK
Sbjct: 9 FILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEK 59
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 35.2 bits (81), Expect = 4e-04
Identities = 13/53 (24%), Positives = 31/53 (58%)
Query: 1 MPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
Y YS + D+++ +N L E+GK++ + W++L +++K Y ++ ++
Sbjct: 76 SAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDR 128
Score = 29.1 bits (65), Expect = 0.063
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 2 PYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
P++ K+ +V+ + D L E KII + W +L E +K +Y++ Y++ K
Sbjct: 150 PFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLK 201
>gnl|CDD|187665 cd09805, type2_17beta_HSD-like_SDR_c, human 17beta-hydroxysteroid
dehydrogenase type 2 (type 2 17beta-HSD)-like, classical
(c) SDRs. 17beta-hydroxysteroid dehydrogenases are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. This
classical-SDR subgroup includes the human proteins: type
2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD,
dehydrogenase/reductase SDR family member 9,
short-chain dehydrogenase/reductase family 9C member 7,
3-hydroxybutyrate dehydrogenase type 1, and retinol
dehydrogenase 5. SDRs are a functionally diverse family
of oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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 (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 281
Score = 31.1 bits (71), Expect = 0.014
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 22 KLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKIYK 56
+LWE K ++W LP + K +Y EDY E K
Sbjct: 192 ELWE--KQAKKLWERLPPEVKKDYGEDYIDELKNK 224
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 26.9 bits (60), Expect = 0.19
Identities = 13/51 (25%), Positives = 27/51 (52%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
+M +S++ +V + + I KI+G W+ L ++K Y E+ ++ K
Sbjct: 9 FMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLK 59
>gnl|CDD|236562 PRK09552, mtnX, 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate
phosphatase; Reviewed.
Length = 219
Score = 26.5 bits (59), Expect = 0.61
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 11 WDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVE 47
W+++K L +L I + +GQM++ LP + K E ++
Sbjct: 32 WEELKDDILSQEL-SIQEGVGQMFQLLPSNLKEEIIQ 67
>gnl|CDD|235101 PRK03059, PRK03059, PII uridylyl-transferase; Provisional.
Length = 856
Score = 26.4 bits (59), Expect = 0.69
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 23 LWEIGKIIGQMWRDL 37
L +I+GQM DL
Sbjct: 421 LPNFRRIVGQMQHDL 435
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 25.6 bits (56), Expect = 0.80
Identities = 14/54 (25%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 3 YMRYSRKVWDQVKAQNLDLK--LWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKI 54
YM ++++ ++ A+N +L + +GK++G+ W L E++K Y + +++K+
Sbjct: 30 YMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKV 83
>gnl|CDD|192522 pfam10296, DUF2404, Putative integral membrane protein conserved
region (DUF2404). This domain is conserved from plants
to humans. The function is not known.
Length = 91
Score = 25.6 bits (57), Expect = 0.96
Identities = 11/28 (39%), Positives = 20/28 (71%), Gaps = 3/28 (10%)
Query: 29 IIGQMWRDLPEDQKTEYVEDYEQEKIYK 56
+IG+++ DL +TE +E++ +EKI K
Sbjct: 3 LIGRLFFDL---LRTEALENFIREKIQK 27
>gnl|CDD|218369 pfam04994, TfoX_C, TfoX C-terminal domain. TfoX may play a key
role in the development of genetic competence by
regulating the expression of late competence-specific
genes. This family corresponds to the C-terminal
presumed domain of TfoX. The domain is found associated
with pfam00383 in a member from Neisseria meningitidis
serogroup B. It is also found as an isolated domain in
some proteins suggesting this is an autonomous domain.
Length = 77
Score = 24.8 bits (55), Expect = 1.4
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 8 RKVWDQVKAQNLDLKLWEI-GKIIGQMWRDLPEDQKTE 44
K+ + +L+L L+ + G + G+ W LPE++K E
Sbjct: 36 LKLKRSGSSVSLNL-LYALEGALEGKHWNVLPEERKEE 72
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 25.0 bits (54), Expect = 2.3
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 8 RKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVE 47
K DQ + +K+ EI KII +WR Q EY+E
Sbjct: 1124 YKTLDQAIMKFHSMKMEEINKIIRDLWRSTYRGQDIEYIE 1163
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b
and Arl10c have been solved.
Length = 159
Score = 24.6 bits (54), Expect = 2.9
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 8/27 (29%)
Query: 13 QVKAQNLDLKLWEIGKIIGQ-----MW 34
+V N+ +K+W++G GQ MW
Sbjct: 38 KVTKGNVTIKVWDLG---GQPRFRSMW 61
>gnl|CDD|234709 PRK00275, glnD, PII uridylyl-transferase; Provisional.
Length = 895
Score = 24.2 bits (53), Expect = 4.5
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 19 LDLKLWEIGKIIGQMWRDL 37
L L E G I+GQM DL
Sbjct: 437 LGRYLPEFGHIVGQMQHDL 455
>gnl|CDD|221558 pfam12395, DUF3658, Protein of unknown function. This domain
family is found in bacteria, and is approximately 110
amino acids in length. The family is found in
association with pfam08874. There are two completely
conserved residues (D and R) that may be functionally
important.
Length = 111
Score = 23.7 bits (52), Expect = 5.7
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 9 KVWDQVKAQNLDLKLWEIGKIIG 31
K W+Q+ +N L++W+ GKI+
Sbjct: 21 KEWEQLSNENAPLRIWKDGKIVS 43
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 22.8 bits (49), Expect = 9.0
Identities = 9/46 (19%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 3 YMRYSRKVWDQVKAQNLDL-KLWEIGKIIGQMWRDLPEDQKTEYVE 47
Y + + + ++K + + + E K+ + W+ + E++K +Y E
Sbjct: 11 YFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEE 56
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
0.317 0.136 0.428
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,875,449
Number of extensions: 184364
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 271
Number of HSP's successfully gapped: 22
Length of query: 56
Length of database: 10,937,602
Length adjustment: 28
Effective length of query: 28
Effective length of database: 9,695,690
Effective search space: 271479320
Effective search space used: 271479320
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: 53 (24.2 bits)