RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12430
(146 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 = 113 bits (286), Expect = 4e-34
Identities = 40/67 (59%), Positives = 52/67 (77%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFM+++K RRK+L+ P N ISKILG RWKA+SN EKQPYYEE +L +LHM+
Sbjct: 6 MNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKL 65
Query: 61 HPDYRYR 67
+PDY++R
Sbjct: 66 YPDYKWR 72
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 78.0 bits (193), Expect = 4e-20
Identities = 22/65 (33%), Positives = 42/65 (64%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++AF ++++++R K+ P + N+ ISKILG +WK +S EK+PY E+ + + +
Sbjct: 5 LSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKA 64
Query: 61 HPDYR 65
+P Y+
Sbjct: 65 YPAYK 69
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 76.6 bits (189), Expect = 2e-19
Identities = 27/65 (41%), Positives = 43/65 (66%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
M+AFM+++++ R KI PD+ N+ ISK LG RWK +S EK PY E+ + + + E+
Sbjct: 6 MSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEE 65
Query: 61 HPDYR 65
P+Y+
Sbjct: 66 MPEYK 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 = 72.7 bits (179), Expect = 5e-18
Identities = 17/62 (27%), Positives = 37/62 (59%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++A+ +++++ R ++ P + ISKILG WK++S EK+ Y E+ + + + ++
Sbjct: 5 LSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKE 64
Query: 61 HP 62
P
Sbjct: 65 MP 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 = 63.4 bits (155), Expect = 2e-14
Identities = 22/72 (30%), Positives = 39/72 (54%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
NAF+++ +D+ ++ P + N+ IS+I+G W++ S K Y E + H +
Sbjct: 6 RNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHARE 65
Query: 61 HPDYRYRPRPKR 72
+PDY+Y PR
Sbjct: 66 YPDYKYTPRKSS 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 = 55.7 bits (135), Expect = 2e-11
Identities = 17/49 (34%), Positives = 34/49 (69%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEE 49
++A+ ++++++R K+ K PD + ++KILG +WK +S EK+ Y E+
Sbjct: 5 LSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEK 53
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 47.9 bits (114), Expect = 2e-07
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEE-QSRLSKLHME 59
++A+ +++ + R +I K P + + K+L +WK +++ EK+PYY+E S + E
Sbjct: 75 LSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQRE 134
Query: 60 KHPD 63
K
Sbjct: 135 KEEY 138
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 40.2 bits (94), Expect = 3e-05
Identities = 19/62 (30%), Positives = 39/62 (62%), Gaps = 3/62 (4%)
Query: 1 MNAFMVWAKDERRKILKACPDMHN--SNISKILGARWKAMSNAEKQPYYEEQSRLSKLHM 58
++A+M +AK++R +I+ P++ + + K++G W +S EK P YE++++ K+
Sbjct: 27 LSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAP-YEKKAQEDKVRY 85
Query: 59 EK 60
EK
Sbjct: 86 EK 87
>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 = 35.1 bits (81), Expect = 0.002
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 1 MNAFMVWAKDERRKILKACPDMHN-SNISKILGARWKAMSNAEKQPYYEE 49
NA+ + + R ++ + P + + SK+ +WKAMS EK+ Y E+
Sbjct: 8 RNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEK 57
>gnl|CDD|235636 PRK05886, yajC, preprotein translocase subunit YajC; Validated.
Length = 109
Score = 29.4 bits (66), Expect = 0.27
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNS 25
M FM +A +RK ++A D+H S
Sbjct: 14 MGGFMYFASRRQRKAMQATIDLHES 38
>gnl|CDD|225347 COG2733, COG2733, Predicted membrane protein [Function unknown].
Length = 415
Score = 29.3 bits (66), Expect = 0.69
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 22 MHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKL 56
+ I+ G W ++S K+ Y E S L K
Sbjct: 286 KEDEAIATAAGDMWTSLSEWLKEDYESEDSMLRKR 320
>gnl|CDD|215808 pfam00231, ATP-synt, ATP synthase.
Length = 288
Score = 28.3 bits (64), Expect = 1.4
Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 32/88 (36%)
Query: 9 KDERRKILKACPDMHNS--NISKILGARWKAMS--------NAEKQ-----PYYEEQSR- 52
K+ +R+I S N KI KAM A+++ PY E+
Sbjct: 4 KEIKRRI--------KSVKNTQKIT----KAMKMVAASKLRKAQERLEAARPYAEKIREV 51
Query: 53 ----LSKLHMEKHPDYRYRPRPKRTCIV 76
+ KHP R K+ ++
Sbjct: 52 LAELAAASEDIKHPLLEQREVVKKVLLI 79
>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 28.2 bits (63), Expect = 1.7
Identities = 19/84 (22%), Positives = 26/84 (30%), Gaps = 8/84 (9%)
Query: 63 DYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEAGPSGSGGPAFPFPGDG 122
D R+R RT D + ++R E R+ E GG P
Sbjct: 360 DDRFRADMLRTW--DDWDAFALWHARVLRGEFAERRRPRGPPENEDEADGGGGLAPP--- 414
Query: 123 SLSPSDMMPFSPGSPGSMDSHDED 146
P P P P D D++
Sbjct: 415 ---PEPPRPPPPPFPDDDDEGDDE 435
>gnl|CDD|221794 pfam12825, DUF3818, Domain of unknown function in PX-proteins
(DUF3818). This domain is found on proteins carrying a
PX domain. Its function is unknown.
Length = 340
Score = 27.7 bits (62), Expect = 2.6
Identities = 6/20 (30%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 87 KTLMRQR-RNEMRQLWCRGE 105
+ +R+R ++ M++LW E
Sbjct: 215 QLYLRERDKDLMKKLWQEPE 234
>gnl|CDD|148384 pfam06748, DUF1217, Protein of unknown function (DUF1217). This
family represents a conserved region that is found
within bacterial proteins, most of which are
hypothetical. Some members contain multiple copies.
Length = 150
Score = 26.4 bits (59), Expect = 4.2
Identities = 9/37 (24%), Positives = 21/37 (56%)
Query: 5 MVWAKDERRKILKACPDMHNSNISKILGARWKAMSNA 41
M++AK +K+L++ +S +K+ R++ + A
Sbjct: 7 MIYAKAFIKKVLESDLSDPDSFANKLSDKRYREFAAA 43
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 26.8 bits (59), Expect = 4.9
Identities = 12/53 (22%), Positives = 17/53 (32%), Gaps = 10/53 (18%)
Query: 103 RGEAGPSGSGGPAFP----------FPGDGSLSPSDMMPFSPGSPGSMDSHDE 145
+G GP G GG G GS P + + +M D+
Sbjct: 34 QGMGGPVGGGGGPGAGGGAPGGPVGGGGGGSGGPPGGGEVAGEAEDAMSEFDD 86
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 27.0 bits (59), Expect = 5.2
Identities = 14/42 (33%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 101 WCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPGSMDS 142
W P SG P P P SP PG+P S+ S
Sbjct: 436 WDDAPPAPPRSGIPPRPAPRMPEASP------VPGAPDSVAS 471
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 26.5 bits (59), Expect = 5.3
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 14/52 (26%)
Query: 36 KAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYK 87
KAMS EK+ E+ +L + +Y + CI+DG K ++ ++
Sbjct: 102 KAMSKEEKKAIKAEKEKLEE-------EYGF-------CILDGHKEKVGNFR 139
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 26.1 bits (58), Expect = 6.1
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 16/90 (17%)
Query: 2 NAFMVWAKDERRKILKACPDMHNSNISKI----LGARWKAMSNAEKQPYYEEQSRLSKLH 57
N F + RKIL +SK + ++ +K EE+ + +
Sbjct: 62 NFFKDF-----RKILTKEEKHIIKKLSKCDFTPIYQYFEEEKEKKKAMSKEEKKAIKEEK 116
Query: 58 MEKHPDYRYRPRPKRTCIVDGKKMRISEYK 87
+ Y Y C+VDG K ++ ++
Sbjct: 117 EKLEEPYGY-------CLVDGHKEKVGNFR 139
>gnl|CDD|237458 PRK13654, PRK13654, magnesium-protoporphyrin IX monomethyl ester
cyclase; Provisional.
Length = 355
Score = 26.0 bits (58), Expect = 8.8
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 57 HMEKHPDYRYRP 68
H+EKHP++R+ P
Sbjct: 185 HLEKHPEHRFHP 196
>gnl|CDD|220320 pfam09623, Cas_NE0113, CRISPR-associated protein NE0113
(Cas_NE0113). Members of this minor CRISPR-associated
(Cas) protein family are encoded in cas gene clusters in
Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC
19718, Mannheimia succiniciproducens MBEL55E, and
Verrucomicrobium spinosum.
Length = 225
Score = 25.8 bits (57), Expect = 8.8
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 11/52 (21%)
Query: 44 QPYYEEQSRLSKLH----MEKHPDYRYRPR-------PKRTCIVDGKKMRIS 84
Q Y Q RLS + E HPD+ Y P+ IVD ++ R++
Sbjct: 135 QLYGRPQDRLSHVLVPPEFESHPDFFYPPKEPRQLHLKPEDGIVDTREARVT 186
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 0.419
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: 7,545,020
Number of extensions: 645334
Number of successful extensions: 685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 678
Number of HSP's successfully gapped: 38
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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 (21.7 bits)
S2: 54 (24.6 bits)