RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15636
(101 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 = 90.1 bits (224), Expect = 2e-25
Identities = 31/59 (52%), Positives = 42/59 (71%)
Query: 43 HIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
HIKRPMNAFM++S+ RRK+ + P N ISK LG WK L+ EK+P+ +EAK+L+
Sbjct: 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLK 59
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 75.7 bits (187), Expect = 7e-20
Identities = 26/58 (44%), Positives = 44/58 (75%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP++AF ++S+ QR K+ +NP + N+EISK LG +WK L+E EK+P+ ++A++ +
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEK 58
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 72.3 bits (178), Expect = 1e-18
Identities = 29/59 (49%), Positives = 44/59 (74%)
Query: 43 HIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRPM+AFM++S+ R K+ +NP + N+EISK+LG WKLL+E EK P+ ++AK+ +
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59
>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 = 69.2 bits (170), Expect = 2e-17
Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP++A+ ++S+ R ++ +NP + EISK LG WK L+E EK+ + ++A++ +
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDK 58
>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 = 62.3 bits (152), Expect = 1e-14
Identities = 21/57 (36%), Positives = 41/57 (71%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP++A+ ++S+ QR K+ +NP +E++K LG +WK L+E EK+ + ++A++ +
Sbjct: 2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDK 58
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 53.7 bits (129), Expect = 4e-10
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP++A+ ++S R ++ +NPK+ E+ K L +WK LT+ EK P+ 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 = 44.0 bits (104), Expect = 2e-07
Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHN-SEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
K NA+ + + R ++ + P++ +E SK +WK ++E EK + ++A+ +
Sbjct: 5 KAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKAREDK 62
>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 = 43.0 bits (102), Expect = 5e-07
Identities = 16/59 (27%), Positives = 34/59 (57%)
Query: 43 HIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
I RP NAF+++ + + ++ +NP + N+EIS+ +G W+ + K + + A+ +
Sbjct: 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEK 59
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 32.9 bits (75), Expect = 0.007
Identities = 15/51 (29%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHN--SEISKRLGAEWKLLTEMEKRPF 93
KR ++A+M +++ +R ++ +NP++ + + K +G W L+E EK P+
Sbjct: 24 KRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPY 74
>gnl|CDD|223778 COG0706, YidC, Preprotein translocase subunit YidC [Intracellular
trafficking and secretion].
Length = 314
Score = 27.4 bits (61), Expect = 1.2
Identities = 10/55 (18%), Positives = 18/55 (32%), Gaps = 2/55 (3%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAK 98
++ + S KM PK+ EI ++ K + E + K
Sbjct: 121 VRLLIFPLSQKSTRSMAKMQELQPKI--KEIQEKYKGTDKQKQQQEMMKLYKKHK 173
>gnl|CDD|219822 pfam08401, DUF1738, Domain of unknown function (DUF1738). This
region is found in a number of bacterial hypothetical
proteins. Some members are annotated as being similar
to replication primases, and in fact this region is
often found together with the Toprim domain
(pfam01751).
Length = 123
Score = 26.8 bits (60), Expect = 1.4
Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 12/45 (26%)
Query: 16 HSEGHIKRPMNALSLHSLHLGHHHSEGHIKRPMNAFMVWSRGQRR 60
+ G + P NA++ G +N ++W + +
Sbjct: 28 SAGGGLGLPRNAVT------------GRPYSGINVLLLWMAAEEQ 60
>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 = 27.1 bits (60), Expect = 1.6
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 53 VWSRGQRRKMALDNPKMHNSEI-------SKRLGAEWKLLTE 87
VW R R ++ N + HN E+ K L EWK L E
Sbjct: 66 VWYR--RGGISFKNFRFHNQELDRYLFDVQKSLLREWKDLKE 105
>gnl|CDD|177283 PHA00451, PHA00451, protein kinase.
Length = 362
Score = 26.3 bits (58), Expect = 2.7
Identities = 6/41 (14%), Positives = 15/41 (36%)
Query: 48 MNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEM 88
A M+ L N + +++ +R W++ +
Sbjct: 302 PRARMLMGDKHWHNAWLHNNNLDFAKLEERAALAWQMADGL 342
>gnl|CDD|237434 PRK13578, PRK13578, ornithine decarboxylase; Provisional.
Length = 720
Score = 25.7 bits (57), Expect = 5.7
Identities = 28/89 (31%), Positives = 31/89 (34%), Gaps = 41/89 (46%)
Query: 38 HHSEGHI---------KRPMNAFMVWSRGQRRKM------------ALD-NPKMHNSEIS 75
H + HI KR NAFM + ALD N KMH E
Sbjct: 367 HKKDNHIKGQARYCPHKRLNNAFM---------LHASTSPFYPLFAALDVNAKMHEGESG 417
Query: 76 KRLGAEW-KLLTEMEK---------RPFI 94
+RL E KL E K RPFI
Sbjct: 418 RRLWMECVKLGIEARKLILARCKLIRPFI 446
>gnl|CDD|213914 TIGR04301, ODC_inducible, ornithine decarboxylase SpeF. Members of
this family are known or trusted examples of ornithine
decarboxylase, all encoded in the immediate vicinity of
an ornithine-putrescine antiporter. Decarboxylation of
ornithine to putrescine, followed by exchange of a
putrescine for a new ornithine, is a proton-motive cycle
that can be induced by low pH and protect a bacterium
against transient exposure to acidic conditions.
Length = 719
Score = 25.5 bits (56), Expect = 6.0
Identities = 28/82 (34%), Positives = 32/82 (39%), Gaps = 23/82 (28%)
Query: 38 HHSEGHIK---------RPMNAFMVW---SRGQRRKMALD-NPKMHNSEISKRLGAEW-K 83
H + HIK R NAFM+ S ALD N KMH E +RL + K
Sbjct: 367 HKKDSHIKGQARYCNHKRFNNAFMMHASTSPFYPLFAALDVNAKMHEGESGRRLWMDCVK 426
Query: 84 LLTEMEK---------RPFIDE 96
E K RPFI E
Sbjct: 427 TGIEARKLLLKNCKYIRPFIPE 448
>gnl|CDD|183711 PRK12738, kbaY, tagatose-bisphosphate aldolase; Reviewed.
Length = 286
Score = 25.4 bits (55), Expect = 6.3
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 9 SLHLGHHHSEGHIKRPMNA 27
+LHL HH S I+R ++A
Sbjct: 78 ALHLDHHESLDDIRRKVHA 96
Score = 25.4 bits (55), Expect = 6.3
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 32 SLHLGHHHSEGHIKRPMNA 50
+LHL HH S I+R ++A
Sbjct: 78 ALHLDHHESLDDIRRKVHA 96
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 0.133 0.415
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: 5,070,550
Number of extensions: 401705
Number of successful extensions: 399
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 31
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 53 (24.2 bits)