RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15633
(129 letters)
>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 = 115 bits (291), Expect = 3e-35
Identities = 41/72 (56%), Positives = 54/72 (75%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
HIKRPMNAFM++S+ RRK+ Q+ P N ISK LG WK L+ EK+PY +EAK+L+
Sbjct: 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKE 60
Query: 83 MHMKDHPDYKYR 94
+HMK +PDYK+R
Sbjct: 61 LHMKLYPDYKWR 72
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 90.7 bits (226), Expect = 2e-25
Identities = 32/69 (46%), Positives = 51/69 (73%)
Query: 24 IKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAM 83
KRP++AF ++S+ QR K+ +NP + N+EISK LG +WK L+E EK+PY ++A++ +A
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKAR 60
Query: 84 HMKDHPDYK 92
+ K +P YK
Sbjct: 61 YEKAYPAYK 69
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 83.5 bits (207), Expect = 2e-22
Identities = 34/70 (48%), Positives = 51/70 (72%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
KRPM+AFM++S+ R KI +NP + N+EISK+LG WKLL+E EK PY ++AK+ +
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
Query: 83 MHMKDHPDYK 92
+ ++ P+YK
Sbjct: 61 RYEEEMPEYK 70
>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 = 77.7 bits (192), Expect = 3e-20
Identities = 24/66 (36%), Positives = 43/66 (65%)
Query: 24 IKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRAM 83
KRP++A+ ++S+ R ++ +NP + EISK LG WK L+E EK+ Y ++A++ +
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKER 60
Query: 84 HMKDHP 89
+ K+ P
Sbjct: 61 YEKEMP 66
>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 = 73.8 bits (182), Expect = 1e-18
Identities = 25/77 (32%), Positives = 46/77 (59%)
Query: 23 HIKRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
I RP NAF+++ + + ++ +NP + N+EIS+ +G W+ + K Y + A+ +
Sbjct: 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKE 60
Query: 83 MHMKDHPDYKYRPRRKP 99
H +++PDYKY PR+
Sbjct: 61 RHAREYPDYKYTPRKSS 77
>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 = 61.1 bits (149), Expect = 7e-14
Identities = 22/58 (37%), Positives = 42/58 (72%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
KRP++A+ ++S+ QR K+ ++NP +E++K LG +WK L+E EK+ Y ++A++ +
Sbjct: 2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKE 59
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 56.4 bits (136), Expect = 1e-10
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHNSEISKRLGAEWKLLTENEKRPYIDEAKRLR 81
KRP++A+ ++S R +I ++NPK+ E+ K L +WK LT+ EK PY EA R
Sbjct: 72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDR 128
>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 = 37.4 bits (87), Expect = 1e-04
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHN-SEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
K NA+ + + R ++ ++ P++ +E SK +WK ++E EK Y ++A+ +
Sbjct: 5 KAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKAREDKK 63
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 34.1 bits (78), Expect = 0.004
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 25 KRPMNAFMVWSRLQRRKIAQDNPKMHN--SEISKRLGAEWKLLTENEKRPYIDEAKRLRA 82
KR ++A+M +++ +R +I +NP++ + + K +G W L+E EK PY +A+ +
Sbjct: 24 KRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKV 83
Query: 83 MHMKDHPDY 91
+ K+ +Y
Sbjct: 84 RYEKEKAEY 92
>gnl|CDD|152771 pfam12336, SOXp, SOX transcription factor. This domain family is
found in eukaryotes, and is approximately 80 amino acids
in length. The family is found in association with
pfam00505. There are two conserved sequence motifs: KKDK
and LPG. This family is made up of SOX transcription
factors. These are involved in upregulation of nestin, a
neural promoter.
Length = 84
Score = 32.2 bits (73), Expect = 0.014
Identities = 16/30 (53%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 93 YRPRRKPKTL-RKDGYTYPAVSVPYQSVPV 121
YRPRRK KTL +KD Y+ P +P PV
Sbjct: 1 YRPRRKTKTLLKKDKYSLPGGLLPANGAPV 30
>gnl|CDD|226154 COG3627, PhnJ, Uncharacterized enzyme of phosphonate metabolism
[Inorganic ion transport and metabolism].
Length = 291
Score = 28.6 bits (64), Expect = 0.81
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 45 DNPKMHNSEISKRLGAEWKLLTENEKRPY-IDEAKRLRAMHMKDHP 89
DNPKM S + GA EKR Y + R+ ++ DHP
Sbjct: 197 DNPKMDMSPALQLFGA------GREKRIYAVPPFTRVESLDFDDHP 236
>gnl|CDD|235989 PRK07324, PRK07324, transaminase; Validated.
Length = 373
Score = 27.2 bits (61), Expect = 2.6
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 53 EISKRLGAE---WKLLTENEKRPYIDEAKRL 80
+I + LGAE W+L EN P +DE +RL
Sbjct: 119 DIPESLGAEVDYWQLKEENGWLPDLDELRRL 149
>gnl|CDD|226297 COG3774, OCH1, Mannosyltransferase OCH1 and related enzymes [Cell
envelope biogenesis, outer membrane].
Length = 347
Score = 26.3 bits (58), Expect = 5.6
Identities = 20/96 (20%), Positives = 31/96 (32%), Gaps = 14/96 (14%)
Query: 6 GGTYPNTLLSPEKKIDDHIK--------RPMNAFMVWSRLQRRKIAQDNPKMHNSEISKR 57
G L +DD K P + + + P+ ++ I K
Sbjct: 26 IGNIKKLLSQLFLWLDDREKDLLTEEEFSPKADMRRSKKQYQEEDDSIFPRDSHAAIPKI 85
Query: 58 LGAEWKLLTENEKRPYIDEAKRLRAMHMKDHPDYKY 93
+ W NEK P + +L HPDY+Y
Sbjct: 86 IWQTWS----NEKFP--EYVNKLFNRWRSLHPDYRY 115
>gnl|CDD|234495 TIGR04192, GRASP_w_spasm, ATP-GRASP peptide maturase,
grasp-with-spasm system. Members of this protein family
are ATP-GRASP proteins that occur in a peptide
maturation cassette with a SPASM domain protein. SPASM
(TIGR04085) usually occurs as a C-terminal extension to
radical SAM enzymes that act as peptide maturases,
although it can occur independently.
Length = 318
Score = 25.9 bits (57), Expect = 6.2
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 33 VWSRLQRRKIAQDNPKMHNSEI-------SKRLGAEWKLLTE 67
VW R R I+ N + HN E+ K L EWK L E
Sbjct: 66 VWYR--RGGISFKNFRFHNQELDRYLFDVQKSLLREWKDLKE 105
>gnl|CDD|225134 COG2224, AceA, Isocitrate lyase [Energy production and
conversion].
Length = 433
Score = 26.2 bits (58), Expect = 6.7
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 34 WSRLQRRKIAQDNPKMHNS----EISKRLGAE--WKLLTENEKRPYI 74
W ++R A+D K+ S RLGA W+LL E K Y+
Sbjct: 21 WKGIKRPYSAEDVVKLRGSVPIEYTLARLGAAKLWELLHELFKEKYV 67
>gnl|CDD|130050 TIGR00977, LeuA_rel, 2-isopropylmalate synthase/homocitrate
synthase family protein. This model represents
uncharacterized proteins related to 2-isopropylmalate
synthases and homocitrate synthases but phylogenetically
distint. Each species represented in the seed alignment
also has a member of a known family of 2-isopropylmalate
synthases [Unknown function, General].
Length = 526
Score = 26.0 bits (57), Expect = 8.0
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 1 MCENSGGTYPNTLLSPEKKIDDHIKRP 27
+C+ +GGT P+ + K+ +K+P
Sbjct: 173 LCDTNGGTLPHEISEITTKVKRSLKQP 199
>gnl|CDD|205590 pfam13412, HTH_24, Winged helix-turn-helix DNA-binding.
Length = 48
Score = 23.9 bits (53), Expect = 8.2
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 44 QDNPKMHNSEISKRLG 59
Q+NP++ E+++RLG
Sbjct: 13 QENPRISQRELAERLG 28
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 334
Score = 25.7 bits (57), Expect = 9.7
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 77 AKRLRAMHMKDHPDYKYRPRRKPKTLRKDGYTYPAVSVPYQSVPV 121
A+ +A+ M+ + Y PR P++ + DGY P P S+P
Sbjct: 149 ARLAQALGMEVYA-YTRSPRPTPESRKDDGYIVPGTGDPDGSIPS 192
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 0.133 0.406
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,889,637
Number of extensions: 596253
Number of successful extensions: 585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 33
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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 (24.3 bits)