BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy3437
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor
Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77
A RESOLUTION
Length = 106
Score = 113 bits (282), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 56/93 (60%), Positives = 65/93 (69%), Gaps = 20/93 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWAQAARR LA+QYP LHNAELSKTLG LW+ L++
Sbjct: 34 MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRL--------------------LNE 73
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKC 93
S+K+PF+EEAERLR HK +HP+YKYQPRRRK
Sbjct: 74 SEKRPFVEEAERLRVQHKKDHPDYKYQPRRRKS 106
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 93.6 bits (231), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 48/92 (52%), Positives = 57/92 (61%), Gaps = 20/92 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ R+ LA Q P LHNAELSK LG WK L +
Sbjct: 11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTL-------------------- 50
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
++K+PF+EEAERLR H +HPNYKY+PRRRK
Sbjct: 51 AEKRPFVEEAERLRVQHMQDHPNYKYRPRRRK 82
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 89.0 bits (219), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 41/91 (45%), Positives = 58/91 (63%), Gaps = 20/91 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVW++ RR +A + P +HN+E+SK LG WK L S+
Sbjct: 8 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLL--------------------SE 47
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRR 91
++K+PFI+EA+RLR +H EHP+YKY+PRR+
Sbjct: 48 TEKRPFIDEAKRLRALHMKEHPDYKYRPRRK 78
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1
And Sox2 Transcription Factors With A 19mer
Oligonucleotide From The Hoxb1 Regulatory Element
Length = 88
Score = 89.0 bits (219), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 41/91 (45%), Positives = 58/91 (63%), Gaps = 20/91 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVW++ RR +A + P +HN+E+SK LG WK L S+
Sbjct: 12 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLL--------------------SE 51
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRR 91
++K+PFI+EA+RLR +H EHP+YKY+PRR+
Sbjct: 52 TEKRPFIDEAKRLRALHMKEHPDYKYRPRRK 82
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 89.0 bits (219), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 41/91 (45%), Positives = 58/91 (63%), Gaps = 20/91 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVW++ RR +A + P +HN+E+SK LG WK L S+
Sbjct: 7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLL--------------------SE 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRR 91
++K+PFI+EA+RLR +H EHP+YKY+PRR+
Sbjct: 47 TEKRPFIDEAKRLRALHMKEHPDYKYRPRRK 77
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 88.6 bits (218), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 44/91 (48%), Positives = 56/91 (61%), Gaps = 20/91 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVW+Q RR + Q P +HNAE+SK LG WK LK D
Sbjct: 7 MNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLK--------------------D 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRR 91
SDK PFI+EAERLR H +++P+YKY+PR++
Sbjct: 47 SDKIPFIQEAERLRLKHMADYPDYKYRPRKK 77
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 83.6 bits (205), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 43/88 (48%), Positives = 51/88 (57%), Gaps = 20/88 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ R+ LA Q P LHNAELSK LG WK L +
Sbjct: 12 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTL-------------------- 51
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQP 88
++K+PF+EEAERLR H +HPNYK P
Sbjct: 52 AEKRPFVEEAERLRVQHMQDHPNYKSGP 79
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 42/85 (49%), Positives = 50/85 (58%), Gaps = 20/85 (23%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ R+ LA Q P LHNAELSK LG WK L +
Sbjct: 7 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTL-------------------- 46
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYK 85
++K+PF+EEAERLR H +HPNYK
Sbjct: 47 AEKRPFVEEAERLRVQHMQDHPNYK 71
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box
Domain Of The Human Male Sex Determining Factor Sry
Complexed To Dna
Length = 85
Score = 72.8 bits (177), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 34/91 (37%), Positives = 56/91 (61%), Gaps = 20/91 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+VW++ RR +A + P + N+E+SK LG WK L ++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKML--------------------TE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRR 91
++K PF +EA++L+ +H+ ++PNYKY+PRR+
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYRPRRK 79
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The
Hmg-Box Domain Of The Human Male Sex Determining Factor
Sry Complexed To Dna
Length = 85
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 56/91 (61%), Gaps = 20/91 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
+NAF+VW++ RR +A + P + N+E+SK LG WK L ++
Sbjct: 9 INAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKML--------------------TE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRR 91
++K PF +EA++L+ +H+ ++PNYKY+PRR+
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYRPRRK 79
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr
pdb|1HRY|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multid-Dimensional Heteronuclear-Edited And-Filtered
Nmr
Length = 76
Score = 68.6 bits (166), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 53/88 (60%), Gaps = 20/88 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+VW++ RR +A + P + N+E+SK LG WK L++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKM--------------------LTE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQP 88
++K PF +EA++L+ +H+ ++PNYKY+P
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYRP 76
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 66.6 bits (161), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 32/93 (34%), Positives = 51/93 (54%), Gaps = 20/93 (21%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAFMVWA+ RR + +P +HN+ +SK LG WK +++
Sbjct: 9 MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKA--------------------MTN 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKC 93
+K+P+ EE RL + H ++P+YKY+PR ++
Sbjct: 49 LEKQPYYEEQARLSKQHLEKYPDYKYKPRPKRT 81
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 52/87 (59%), Gaps = 20/87 (22%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
MNAF+VW++ RR +A + P + N+E+SK LG WK L++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKM--------------------LTE 48
Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQ 87
++K PF +EA++L+ +H+ ++PNYKY+
Sbjct: 49 AEKWPFFQEAQKLQAMHREKYPNYKYR 75
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLW 35
+AF ++ R + ++P L +++K LG +W
Sbjct: 94 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 127
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna
pdb|1QRV|B Chain B, Crystal Structure Of The Complex Of Hmg-D And Dna
Length = 73
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 33/57 (57%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTK 57
++A+M+W +AR ++ + P + E++K G LW+ +K ++ + + +D Y +
Sbjct: 8 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDR 64
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 33/57 (57%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTK 57
++A+M+W +AR ++ + P + E++K G LW+ +K ++ + + +D Y +
Sbjct: 8 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDR 64
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 38.9 bits (89), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 33/57 (57%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTK 57
++A+M+W +AR ++ + P + E++K G LW+ +K ++ + + +D Y +
Sbjct: 9 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDR 65
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex
pdb|3NM9|D Chain D, Hmgd(M13a)-Dna Complex
pdb|3NM9|G Chain G, Hmgd(M13a)-Dna Complex
pdb|3NM9|J Chain J, Hmgd(M13a)-Dna Complex
pdb|3NM9|M Chain M, Hmgd(M13a)-Dna Complex
pdb|3NM9|P Chain P, Hmgd(M13a)-Dna Complex
Length = 73
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 32/57 (56%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTK 57
++A+ +W +AR ++ + P + E++K G LW+ +K ++ + + +D Y +
Sbjct: 8 LSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDR 64
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVM 48
MNAFM++A+ R YP N +S LG WK +K E + +
Sbjct: 22 MNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTL 69
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 3 AFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMS 49
AFM+W R ++ + P + E++K G +WK LK ++ + +
Sbjct: 10 AFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWEDAAA 56
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 32.3 bits (72), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 20/83 (24%)
Query: 3 AFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSD 62
F ++ R + + P + +++K LG +W L +DS+
Sbjct: 16 GFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNL--------------------NDSE 55
Query: 63 KKPFIEEAERLRQIHKSEHPNYK 85
K+P+I +A +L++ ++ + +YK
Sbjct: 56 KQPYITKAAKLKEKYEKDVADYK 78
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTL 38
++A ++++ RR L + P L +EL++ L +W L
Sbjct: 25 VSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDL 62
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTL--KVETHYHHVMSPFEDTYTK 57
MNAF+++ + R + ++P L N +K L W L K + Y + ++D + K
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMK 70
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVE 41
++A+M +A R + ++ P + ++ K LG WK L E
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPE 65
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLW 35
+AF ++ R + ++P L +++K LG +W
Sbjct: 107 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 140
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
Protein Nhp6a In Complex With Sry Dna
pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
Protein Nhp6a
Length = 93
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVE 41
++A+M +A R + ++ P + ++ K LG WK L E
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPE 65
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 20/84 (23%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDS 61
+AF ++ R + +++P L + +K LG +W ++ S
Sbjct: 14 SAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMW--------------------SEQSAK 53
Query: 62 DKKPFIEEAERLRQIHKSEHPNYK 85
DK+P+ ++A +L++ ++ + Y+
Sbjct: 54 DKQPYEQKAAKLKEKYEKDIAAYR 77
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
Length = 77
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLW 35
+AF ++ R + ++P L +++K LG +W
Sbjct: 12 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 45
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
pdb|1HSN|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
Length = 79
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLW 35
+AF ++ R + ++P L +++K LG +W
Sbjct: 8 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 41
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 20/84 (23%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDS 61
+AF ++ R + +++P L + +K LG +W ++ S
Sbjct: 13 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMW--------------------SEQSAK 52
Query: 62 DKKPFIEEAERLRQIHKSEHPNYK 85
DK+P+ ++A +L++ ++ + Y+
Sbjct: 53 DKQPYEQKAAKLKEKYEKDIAAYR 76
>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
pdb|1NHN|A Chain A, The Structure Of The Hmg Box And Its Interaction With
Dna
Length = 81
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 2 NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLW 35
+AF ++ R + ++P L +++K LG +W
Sbjct: 10 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 43
>pdb|3I33|A Chain A, Crystal Structure Of The Human 70kda Heat Shock Protein 2
(Hsp70-2) Atpase Domain In Complex With Adp And
Inorganic Phosphate
Length = 404
Score = 26.6 bits (57), Expect = 4.7, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 38 LKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSE-HPNYKYQPRRRKCSKN 96
L +E V S DT+ D D + AE ++ HK + PN + R R +
Sbjct: 231 LTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACER 290
Query: 97 LGTSANNLSKSTSSINSLKKG 117
+ ++ ++++ I+SL +G
Sbjct: 291 AKRTLSSSTQASIEIDSLYEG 311
>pdb|3BTS|A Chain A, Crystal Structure Of A Ternary Complex Of The
Transcriptional Repressor Gal80p (Gal80s0 [g301r]) And
The Acidic Activation Domain Of Gal4p (Aa 854-874) From
Saccharomyces Cerevisiae With Nad
pdb|3BTS|B Chain B, Crystal Structure Of A Ternary Complex Of The
Transcriptional Repressor Gal80p (Gal80s0 [g301r]) And
The Acidic Activation Domain Of Gal4p (Aa 854-874) From
Saccharomyces Cerevisiae With Nad
pdb|3BTV|A Chain A, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S0)-[g301r]
pdb|3BTV|B Chain B, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S0)-[g301r]
Length = 438
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 16 ANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEA 70
A +P+L + S T+ ++ ++V +HY VM E ++K + + K F+E A
Sbjct: 75 ATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLE--FSKNNPNLKYLFVEWA 127
>pdb|3BTU|A Chain A, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S2) [e351k]
pdb|3BTU|B Chain B, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S2) [e351k]
pdb|3BTU|C Chain C, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S2) [e351k]
pdb|3BTU|D Chain D, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S2) [e351k]
pdb|3BTU|E Chain E, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S2) [e351k]
pdb|3BTU|F Chain F, Crystal Structure Of The Super-Repressor Mutant Of Gal80p
From Saccharomyces Cerevisiae; Gal80(S2) [e351k]
Length = 438
Score = 26.2 bits (56), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 16 ANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEA 70
A +P+L + S T+ ++ ++V +HY VM E ++K + + K F+E A
Sbjct: 75 ATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLE--FSKNNPNLKYLFVEWA 127
>pdb|3V2U|A Chain A, Crystal Structure Of The Yeast Gal Regulon Complex Of The
Repressor, Gal80p, And The Transducer, Gal3p, With
Galactose And Atp
pdb|3V2U|B Chain B, Crystal Structure Of The Yeast Gal Regulon Complex Of The
Repressor, Gal80p, And The Transducer, Gal3p, With
Galactose And Atp
Length = 438
Score = 26.2 bits (56), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 16 ANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEA 70
A +P+L + S T+ ++ ++V +HY VM E ++K + + K F+E A
Sbjct: 75 ATAFPTLESFASSSTIDMIVIAIQVASHYEVVMPLLE--FSKNNPNLKYLFVEWA 127
>pdb|3AFH|A Chain A, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With A Glutamyl-Amp
Analog
Length = 488
Score = 25.8 bits (55), Expect = 7.2, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 4 FMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPF-EDTYTKLSDSD 62
F+ WA+ A + PS+ S+TL + + + + + +M PF D Y D
Sbjct: 341 FIEWAKYA----GKEIPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEKDYV 396
Query: 63 KKPFI--EEAERL 73
+K F+ EEAER+
Sbjct: 397 EK-FLKREEAERV 408
>pdb|3AL0|C Chain C, Crystal Structure Of The Glutamine Transamidosome From
Thermotoga Maritima In The Glutamylation State
Length = 592
Score = 25.8 bits (55), Expect = 7.5, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 4 FMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPF-EDTYTKLSDSD 62
F+ WA+ A + PS+ S+TL + + + + + +M PF D Y D
Sbjct: 445 FIEWAKYA----GKEIPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEKDYV 500
Query: 63 KKPFI--EEAERL 73
+K F+ EEAER+
Sbjct: 501 EK-FLKREEAERV 512
>pdb|3AKZ|B Chain B, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
pdb|3AKZ|D Chain D, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
pdb|3AKZ|C Chain C, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
pdb|3AKZ|A Chain A, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
Length = 487
Score = 25.8 bits (55), Expect = 7.5, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 4 FMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPF-EDTYTKLSDSD 62
F+ WA+ A + PS+ S+TL + + + + + +M PF D Y D
Sbjct: 340 FIEWAKYA----GKEIPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEKDYV 395
Query: 63 KKPFI--EEAERL 73
+K F+ EEAER+
Sbjct: 396 EK-FLKREEAERV 407
>pdb|3OOS|A Chain A, The Structure Of An AlphaBETA FOLD FAMILY HYDROLASE FROM
BACILLUS Anthracis Str. Sterne
Length = 278
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 54 TYTKLSDSDKKPFIEEAERLRQI 76
T TK +S+ PF+EE ++ Q
Sbjct: 251 TLTKFEESNHNPFVEEIDKFNQF 273
>pdb|2YFH|A Chain A, Structure Of A Chimeric Glutamate Dehydrogenase
pdb|2YFH|B Chain B, Structure Of A Chimeric Glutamate Dehydrogenase
pdb|2YFH|C Chain C, Structure Of A Chimeric Glutamate Dehydrogenase
pdb|2YFH|D Chain D, Structure Of A Chimeric Glutamate Dehydrogenase
pdb|2YFH|E Chain E, Structure Of A Chimeric Glutamate Dehydrogenase
pdb|2YFH|F Chain F, Structure Of A Chimeric Glutamate Dehydrogenase
Length = 448
Score = 25.4 bits (54), Expect = 9.1, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 22 LHNAELSKTLGVLWKTLKVETHYHHVMSPFED 53
L A+ + LG WK KV+ HH+M+ D
Sbjct: 381 LEMAQNAARLG--WKAEKVDARLHHIMTDIHD 410
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.313 0.126 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,690,719
Number of Sequences: 62578
Number of extensions: 132036
Number of successful extensions: 406
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 360
Number of HSP's gapped (non-prelim): 53
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 46 (22.3 bits)