RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3760
(306 letters)
>1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine
biosynthesis, transcription regulation; 1.80A
{Klebsiella aerogenes} SCOP: c.94.1.1
Length = 324
Score = 362 bits (931), Expect = e-126
Identities = 128/304 (42%), Positives = 193/304 (63%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLT 60
M L Q R++ E V N N++ A+ LYTSQPG+SK + LE+EL I IF R GK + +T
Sbjct: 1 MKLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVT 60
Query: 61 KPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
GQ I+R ++ +++ +K + E + D G+L +ATTHTQARYALP +IK F ++P
Sbjct: 61 PAGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYP 120
Query: 121 KVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLL 180
+V L + QG+P QI E + AD AI TE L D L+ +PCY W I+V +HPL
Sbjct: 121 RVSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLAT 180
Query: 181 LNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGI 240
S+S++E++ YPL+TY F+GR +LD F+ LTP IV ++D+IKTYV L +G+
Sbjct: 181 KGSVSIEELAQYPLVTYTFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGLGV 240
Query: 241 GIIASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFI 300
G+IAS+A D D +L + A+ +F + +++ ++ T+LRSY+Y FI+ +P L R +
Sbjct: 241 GVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRFAPHLTRDVV 300
Query: 301 NKIL 304
+ +
Sbjct: 301 DTAV 304
>2fyi_A HTH-type transcriptional regulator CBL; Lys-R family,
cofactor-binding DO cysteine biosynthesis; 2.80A
{Escherichia coli K12} SCOP: c.94.1.1
Length = 228
Score = 255 bits (654), Expect = 1e-85
Identities = 87/227 (38%), Positives = 143/227 (62%)
Query: 80 LKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIR 139
L G + +G LTIATTHTQARY+LP++IK F FP+V+L L+QG P++I +++
Sbjct: 1 LVPRGSHMTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQ 60
Query: 140 NDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDL 199
N +ADI I +E LS +L++ P ++W + ++VP DHPL ++ ++L+ I+ +PLITY
Sbjct: 61 NGEADIGIASERLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQ 120
Query: 200 SFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSI 259
+GR ++D F+ + L IVL +SD+IKTYV L +GIG++A + ++NL +
Sbjct: 121 GITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEEENLIRL 180
Query: 260 SASHLFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRKFINKILNN 306
HLF + +K+G R+YV+ F++L + L+ + I + +
Sbjct: 181 DTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVME 227
>3fzv_A Probable transcriptional regulator; LYSR, structural genomics,
PSI-2, structure initiative; 2.71A {Pseudomonas
aeruginosa PA01}
Length = 306
Score = 163 bits (415), Expect = 1e-48
Identities = 55/245 (22%), Positives = 108/245 (44%), Gaps = 6/245 (2%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
L Q + FV + ++ EA++ LY +QP +S A+ LEE + +FIRH + L
Sbjct: 4 YTLRQLKYFV--TTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSL 61
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T G R + +++ ++ + G + I T A LP +I F +
Sbjct: 62 TPAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAY 121
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWE-YVIIVPLDHPL 178
P V++ + G +++ + + + + D+A + E S + + P + ++P H
Sbjct: 122 PGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDST-IETEPLMPPQRPHALLPEGHRF 180
Query: 179 LLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238
+SL+++ P+I D+ S R F LTP I + + ++++ V
Sbjct: 181 AGQAQVSLRDLCLEPMILLDVQPS-RTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGF 239
Query: 239 GIGII 243
G ++
Sbjct: 240 GFSLL 244
>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR,
TSAR, WHTH, DNA- transcription, transcription
regulation; 1.85A {Comamonas testosteroni} PDB: 3fxr_A*
3fxu_A* 3fzj_A 3n6t_A 3n6u_A*
Length = 305
Score = 157 bits (399), Expect = 3e-46
Identities = 56/263 (21%), Positives = 107/263 (40%), Gaps = 9/263 (3%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
+ L + + + + +L AA+ L+ SQP +S AI +LE+EL + +R + + L
Sbjct: 2 LKLQTLQALI--CIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVS-L 58
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T GQA ++ +I+ E ++ + G++T A + A ALP + F +F
Sbjct: 59 TSFGQAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREF 118
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVT-EILSPSDKLISIPCYQWEYVIIVPLDHPL 178
P V +++ G ++ +R+ D A+ L + P Y + VI+ HP
Sbjct: 119 PDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHP- 177
Query: 179 LLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL-TPYIVLETINSDIIKTYVELR 237
+ N+ L E+ + F+ L P + L + + V
Sbjct: 178 -MANATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHS 236
Query: 238 MGIGII-ASIAFDSNRDKNLRSI 259
+ + ++ + L SI
Sbjct: 237 DLLTTMPRTLYERNAFKDQLCSI 259
>2hxr_A HTH-type transcriptional regulator CYNR; CYNR transcriptional
regulator LYSR struc genomics, PSI-2, protein structure
initiative; 2.05A {Escherichia coli} PDB: 3hfu_A
Length = 238
Score = 122 bits (309), Expect = 8e-34
Identities = 39/217 (17%), Positives = 93/217 (42%), Gaps = 9/217 (4%)
Query: 67 LRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSL 126
+ +QE+ K+ + + G+L IA T T Y + ++ +F ++P + L L
Sbjct: 4 RQYASRALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQL 63
Query: 127 LQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISL 186
+ + ++I +M+ D+ D+ I + + L +IP ++V HPL + ++L
Sbjct: 64 QEMSQEKIEDMLCRDELDVGIAFAPVHSPE-LEAIPLLTESLALVVAQHHPLAVHEQVAL 122
Query: 187 KEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASI 246
+ + L+ F+ R ++D L P +V+E + + + ++ +
Sbjct: 123 SRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAA 182
Query: 247 AFDSNRDKNLRSISASHLFGTTISR---VIIKQGTYL 280
+ L++I L + R ++ ++ ++
Sbjct: 183 IAT--QHDGLKAI---SLAPPLLERTAVLLRRKNSWQ 214
>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA
binding and regulatory domai binding protein; 2.20A
{Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB:
1iz1_A
Length = 294
Score = 123 bits (311), Expect = 2e-33
Identities = 47/251 (18%), Positives = 89/251 (35%), Gaps = 8/251 (3%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
M Q + F+ AV + N+ AAK L+ SQP +++ + LE +L + + R + I L
Sbjct: 1 MEFRQLKYFI--AVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIE-L 57
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T G A L I++ + + D G L++A T +LP +++ F
Sbjct: 58 TAAGHAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTST 117
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
P +SL + E + + + + Q + + V
Sbjct: 118 PTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPG-IEIVNIAQEDLYLAVHRSQSGK 176
Query: 180 LLNSISLKEISNYPLITYDLSFSGRI--KLDREFSLQKLTPYIVLETINSDIIKTYVELR 237
+ L ++ L + ++ F + P I ++
Sbjct: 177 FGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG 236
Query: 238 MGIGII-ASIA 247
I+ AS+A
Sbjct: 237 AASSIVPASVA 247
>4ab5_A Transcriptional regulator, LYSR family; transcription factors;
2.51A {Neisseria meningitidis serogroup B} PDB: 4ab6_A
Length = 222
Score = 118 bits (298), Expect = 2e-32
Identities = 41/204 (20%), Positives = 78/204 (38%), Gaps = 7/204 (3%)
Query: 91 DTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTE 150
+ G L IA L + EF +P+V+L ++ G ++ +AD+AIV+E
Sbjct: 6 EAGELRIAVECHTCFDWLMPAMGEFRPMWPQVELDIVSGFQADPVGLLLQHRADLAIVSE 65
Query: 151 ILSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDRE 210
+ + P + +E V I DHPL N + ++ LITY + +
Sbjct: 66 AEKQNG-ISFQPLFAYEMVGICAPDHPLAAKNVWTAEDFIGETLITYPVPDEMLDLPKKI 124
Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGIIASIAFDSNRDKNLRSISASHLFGTTIS 270
+ + P + + I V R GI + +K + + +
Sbjct: 125 LIPKNINP-PRRHSELTIAIIQLVASRRGIAALPYWTVMPYLEK--GYVVHRQITADGLQ 181
Query: 271 R---VIIKQGTYLRSYVYSFIKLL 291
I+ +SY+ +F +++
Sbjct: 182 SKLYAAIRTEDTDKSYLNNFCQII 205
>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A
{Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A*
3m1e_A
Length = 313
Score = 115 bits (290), Expect = 3e-30
Identities = 54/253 (21%), Positives = 105/253 (41%), Gaps = 11/253 (4%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
M L R FV V + ++++AA+ L +QP +S+ I +LEEEL I +F R + + +
Sbjct: 1 MELRHLRYFV--TVVEEQSISKAAEKLCIAQPPLSRQIQKLEEELGIQLFERGFRPAK-V 57
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T+ G + I+ + K + + L I + LP+II F Q
Sbjct: 58 TEAGMFFYQHAVQILTHTAQASSMAKRIAT-VSQTLRIGYVSSLLYGLLPEIIYLFRQQN 116
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
P++ + L++ K ++ + D+ ++ + I ++ + + + H L
Sbjct: 117 PEIHIELIECGTKDQINALKQGKIDLGFGRLKITDPA-IRRIMLHKEQLKLAIHKHHHLN 175
Query: 180 LLN--SISLKEISNYPLITYDLSFSGRI--KLDREFSLQKLTPYIVLETINSDIIKTYVE 235
+ L +I + P++ Y +S + F+ L P + E + V
Sbjct: 176 QFAATGVHLSQIIDEPMLLYPVSQKPNFATFIQSLFTELGLVPSKLTEIREIQLALGLVA 235
Query: 236 LRMGIGII-ASIA 247
G+ I+ AS
Sbjct: 236 AGEGVCIVPASAM 248
>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional
activator, LYSR-type transcripti regulator; 1.80A
{Acinetobacter SP} PDB: 2h99_A 3k1m_A 3k1n_A 3k1p_A
2f7a_A* 2f6p_A 2f78_A 2f6g_A* 2f8d_A 2f97_A*
Length = 312
Score = 115 bits (289), Expect = 4e-30
Identities = 54/253 (21%), Positives = 101/253 (39%), Gaps = 11/253 (4%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
M L R FV AV + + T+AA L +QP +S+ I LEEEL I + R + ++
Sbjct: 1 MELRHLRYFV--AVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVK-T 57
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T G + ++ ++ + + K ++ + + I + LP+II +
Sbjct: 58 TPEGHFFYQYAIKLLSNVDQMVSMTKRIASVE-KTIRIGFVGSLLFGLLPRIIHLYRQAH 116
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
P +++ L + K TE ++ + D +S + ++ V HPL
Sbjct: 117 PNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPA-IKHSLLRNERLMVAVHASHPLN 175
Query: 180 LLN--SISLKEISNYPLITYDLSFSGRI--KLDREFSLQKLTPYIVLETINSDIIKTYVE 235
+ + L ++ + ++ Y S + FS L P + E + V
Sbjct: 176 QMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVA 235
Query: 236 LRMGIGII-ASIA 247
GI ++ AS
Sbjct: 236 AGEGISLVPASTQ 248
>2ql3_A Probable transcriptional regulator, LYSR family P; APC7314,
rhodococcus RHA1, structural genomics, PSI-2; HET: MSE;
2.05A {Rhodococcus SP}
Length = 209
Score = 93.1 bits (232), Expect = 6e-23
Identities = 25/153 (16%), Positives = 66/153 (43%), Gaps = 3/153 (1%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
G + + LP ++ FT ++P+ + + ++ + + D+AIV ++
Sbjct: 4 AGPIAVGCYPALGPTILPSMLYAFTAEYPRASVEFREDTQNRLRTQLEGGELDVAIVYDL 63
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNS-ISLKEISNYPLITYDLSFSGRIKLDRE 210
+ ++P E ++++ +HPL ++ + L +++ +P++ D S +D
Sbjct: 64 DLSPE-WQTVPLMTREPMVVLGAEHPLAGVDGPVRLADLAEHPMVLLDAPPSTNHAMD-V 121
Query: 211 FSLQKLTPYIVLETINSDIIKTYVELRMGIGII 243
P + T N + + +V +G ++
Sbjct: 122 CREAGFAPRVAYRTANFETARAFVGRGLGWTLL 154
>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped
structure, DNA binding domain, regulatory domain,
DNA-binding; 2.70A {Mycobacterium tuberculosis}
Length = 303
Score = 81.9 bits (203), Expect = 4e-18
Identities = 35/245 (14%), Positives = 75/245 (30%), Gaps = 12/245 (4%)
Query: 1 MNLHQFRFVREAVRQ-NFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
++ Q + V +F AA+ L+ + VS+ I LE+++ + +R K R
Sbjct: 6 LDGPQLAALAAVVELGSF--DAAAERLHVTPSAVSQRIKSLEQQVGQVLVVR-EKPCR-A 61
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T G +LR ++ +TIA +
Sbjct: 62 TTAGIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVL 121
Query: 120 PKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
V++ ++R A A+ TE P + Y+ +
Sbjct: 122 LDVRIEDQD----HSARLLREGVAMGAVTTERNPVPG-CRVHPLGEMRYLPVASRPFVQR 176
Query: 180 LL-NSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRM 238
L + + + P + ++ + L R+ ++ ++ +
Sbjct: 177 HLSDGFTAAAAAKAPSLAWNRDDGLQDMLVRKA-FRRAITRPTHFVPTTEGFTAAARAGL 235
Query: 239 GIGII 243
G G+
Sbjct: 236 GWGMF 240
>1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory
domain, oxidized form, transcription; 2.30A {Escherichia
coli} SCOP: c.94.1.1 PDB: 1i69_A
Length = 219
Score = 72.3 bits (178), Expect = 3e-15
Identities = 23/105 (21%), Positives = 47/105 (44%), Gaps = 1/105 (0%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
+G L I T Y LP II FPK+++ L + Q+ + + + D I+ +
Sbjct: 4 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV 63
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
S+ I +P + ++ + DHP ++ + +++ L+
Sbjct: 64 K-ESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLM 107
>3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type
transcriptional regulator, LTTR, redox, structural
genomics, OPPF; 2.39A {Neisseria meningitidis}
Length = 219
Score = 71.2 bits (175), Expect = 9e-15
Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 1/105 (0%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
G + T A Y LPK+I PK+ L L + +TE ++ D IV E
Sbjct: 3 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEP 62
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
+++ P Y + +IVP H L+++S + + ++
Sbjct: 63 F-QEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLL 106
>3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio
regulation; 1.58A {Porphyromonas gingivalis}
Length = 232
Score = 69.6 bits (171), Expect = 3e-14
Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 1/105 (0%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
TG L IA T A Y LP++ + + +++ + + + + + + D+AI+
Sbjct: 10 TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASK 69
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLIT 196
++ L Y E++ V PL + I E++ + L
Sbjct: 70 A-ETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWL 113
>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription,
PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas
aeruginosa} SCOP: a.4.5.37 c.94.1.1
Length = 310
Score = 68.4 bits (168), Expect = 2e-13
Identities = 35/165 (21%), Positives = 67/165 (40%), Gaps = 4/165 (2%)
Query: 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77
N+ AA L S S A+ L + L ++F+R G R++ T+ + + ++ ++ +
Sbjct: 26 NVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRMQ-PTQRAEHLAAAVAAALRAL 84
Query: 78 EGLKKIGKEFS-AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITE 136
+ + F A T A LP ++ P V+L L+ K E
Sbjct: 85 GEGLEEWRPFVPGQSQRTFVFAATDYTAFALLPPLMNRLQHSAPGVRLRLVNAERKLSVE 144
Query: 137 MIRNDQADIAI--VTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
+ + + D A+ E + + + + YV++ DHP L
Sbjct: 145 ALASGRIDFALGYDEEHERLPEGIQAHDWFADRYVVVARRDHPRL 189
>1uth_A LYSR-type regulatory protein; transcription regulation,
transcriptional regulator; 2.2A {Burkholderia SP} SCOP:
c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A
Length = 315
Score = 66.5 bits (163), Expect = 1e-12
Identities = 31/163 (19%), Positives = 66/163 (40%), Gaps = 3/163 (1%)
Query: 18 NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEI 77
+++ A + L +QP VS ++ L L+ D+F+R K + T + + + +
Sbjct: 30 SVSTAGEKLGLTQPAVSNSLKRLRTALNDDLFLRTSKGME-PTPYALHLAEPVIYALNTL 88
Query: 78 EGLKKIGKEFS-AYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITE 136
+ F T +A T Y +P +++ + P +++S L+ N + E
Sbjct: 89 QTALTTRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKE 148
Query: 137 MIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPLL 179
+ + D+A+ + ++ YV + DHP
Sbjct: 149 DMESGAVDLALGLLPELQTG-FFQRRLFRHRYVCMFRKDHPSA 190
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 57.0 bits (137), Expect = 3e-09
Identities = 41/235 (17%), Positives = 89/235 (37%), Gaps = 56/235 (23%)
Query: 12 AVRQNFN-LTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQ-AILRS 69
+R+N++ + + + + K E+ E + F R K + T+ Q A+
Sbjct: 1683 RIRENYSAMIF--ETIVDGKLKTEKIFKEINEHSTSYTF-RSEKGLLSATQFTQPALT-L 1738
Query: 70 IEI-IMQEI--EGLKKIGK--------EFSA--YDTGNLTIATT----HTQARY---ALP 109
+E +++ +GL E++A ++I + + A+P
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVP 1798
Query: 110 KIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCY----- 164
+ + + ++ NP ++ + +A +V + + L+ I Y
Sbjct: 1799 RD------ELGRSNYGMIAINPGRVAASF-SQEALQYVVERVGKRTGWLVEIVNYNVENQ 1851
Query: 165 QWEYVI---IVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKL 216
Q YV + LD +LN I L++I D+ I+L + SL+++
Sbjct: 1852 Q--YVAAGDLRALDTVTNVLNFIKLQKI--------DI-----IELQKSLSLEEV 1891
Score = 40.0 bits (93), Expect = 8e-04
Identities = 62/372 (16%), Positives = 102/372 (27%), Gaps = 153/372 (41%)
Query: 26 LY-TSQPGVSKAIIELEEEL--------SIDIFIRHGKRIRGL-----TKPGQAILRSIE 71
LY T V I E L + G I P + L SI
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP 235
Query: 72 IIMQEIEGL----------KKIG---KEFSAYDTGNLT----------IATTHTQARY-- 106
I I G+ K +G E +Y G IA T + +
Sbjct: 236 ISCPLI-GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFV 294
Query: 107 ALPKIIKE-FTI------QFPKVKL--SLLQ-------GNP-----------KQITEMIR 139
++ K I F I +P L S+L+ G P +Q+ + +
Sbjct: 295 SVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVN 354
Query: 140 --------NDQADIA--------IVT--------------EILSPSDKLIS-IP------ 162
Q +I+ +V+ + +PS S IP
Sbjct: 355 KTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKL 414
Query: 163 CYQWEY-VIIVPLDH-PLL------LLNSISLKEIS------NYPLITYDLSFSGRIKLD 208
+ + + P H LL + + +S P+ YD +F G D
Sbjct: 415 KFSNRFLPVASPF-HSHLLVPASDLINKDLVKNNVSFNAKDIQIPV--YD-TFDGS---D 467
Query: 209 -REFS---LQKLTPYIVLETIN-----------------------SDIIKTYVELRMGIG 241
R S +++ I+ + + + G+
Sbjct: 468 LRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGT-GVR 526
Query: 242 IIASIAFDSNRD 253
+I + D N D
Sbjct: 527 VIVAGTLDINPD 538
Score = 38.9 bits (90), Expect = 0.002
Identities = 36/218 (16%), Positives = 67/218 (30%), Gaps = 73/218 (33%)
Query: 124 LSLLQGN-------PKQI---TEMIRND-QADIAIVTEILSPSDKLISIPCYQWEYVI-- 170
L+L G+ P ++ + TE + D+ + E V
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA----ELVGKF 64
Query: 171 ---IVPLDHP--------LLLLNSISLKEI-SNYPLITYDL-SFSGRIKLDREFSLQKLT 217
+ L P +L L L E + Y L D+ + + ++ + + +L K
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNL---CLTEFENCY-LEGNDIHALAAKLLQENDTTLVK-- 118
Query: 218 PYIVLETINSDIIKTYVELRMGIGI-----IASIAFDSNRDKNLRSISASHLFGTTISRV 272
++IK Y+ R+ S F + + N + ++ +FG
Sbjct: 119 --------TKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVA---IFG------ 161
Query: 273 IIKQG---TYL----------RSYVYSFIKLLSPKLNR 297
QG Y V IK + L+
Sbjct: 162 --GQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSE 197
Score = 38.5 bits (89), Expect = 0.003
Identities = 29/175 (16%), Positives = 56/175 (32%), Gaps = 56/175 (32%)
Query: 14 RQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIF-IRHGKRIRGLTKPGQAILRSIEI 72
+N ++ ++LY G++ + + + +D I +R K
Sbjct: 374 AKNLVVSGPPQSLY----GLNLTLRKAKAPSGLDQSRIPFSER-----KL---------- 414
Query: 73 IMQEIEGLKKIGKEFSAYDTGNLTIATT-HTQARY---ALPKIIKEF---TIQFPKVKLS 125
K F L +A+ H+ A I K+ + F +
Sbjct: 415 ---------KFSNRF-------LPVASPFHSH--LLVPASDLINKDLVKNNVSFNAKDIQ 456
Query: 126 LLQGNPKQITEMIRNDQADIAIVTEILSPS--DKLISIPCYQWEYVIIVPLDHPL 178
+ P T D +D+ +++ +S D +I +P WE H L
Sbjct: 457 I----PVYDTF----DGSDLRVLSGSISERIVDCIIRLPVK-WETTTQFKATHIL 502
Score = 35.8 bits (82), Expect = 0.020
Identities = 40/210 (19%), Positives = 66/210 (31%), Gaps = 71/210 (33%)
Query: 84 GKEFSAYDTGN-----LTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQIT--- 135
G + Y T A H + Y F+I L ++ NP +T
Sbjct: 1632 GMDL--YKTSKAAQDVWNRADNHFKDTYG-------FSI------LDIVINNPVNLTIHF 1676
Query: 136 -------------EMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVP---LDH--- 176
MI D + TE + + Y + L
Sbjct: 1677 GGEKGKRIRENYSAMIFETIVDGKLKTEKIFK-EINEHSTSYTFRS----EKGLLSATQF 1731
Query: 177 --PLLLLNSIS-LKEISNYPLITYDLSF---S-GRIKLDREFS-LQKLTPYIVLETINSD 228
P L L + +++ + LI D +F S G E++ L L + +E
Sbjct: 1732 TQPALTLMEKAAFEDLKSKGLIPADATFAGHSLG------EYAALASLADVMSIE----S 1781
Query: 229 IIKTYVELRMGIGIIASIAFDSNRDKNLRS 258
+++ V R G+ +A RD+ RS
Sbjct: 1782 LVEV-VFYR---GMTMQVAVP--RDELGRS 1805
Score = 28.5 bits (63), Expect = 3.5
Identities = 18/99 (18%), Positives = 39/99 (39%), Gaps = 10/99 (10%)
Query: 128 QGNPKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYVIIVPLDHPL---LLLNSI 184
QG+ Q M + ++ + +D Y + + IV +++P+ +
Sbjct: 1624 QGS--QEQGMGMDLYKTSKAAQDVWNRADNHFK-DTYGFSILDIV-INNPVNLTIHFGGE 1679
Query: 185 SLKEI-SNYPLITYDLSFSGRIKLDREFSL--QKLTPYI 220
K I NY + ++ G++K ++ F + T Y
Sbjct: 1680 KGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT 1718
>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix,
DNA-binding, transcription factor; 2.20A {Vibrio
cholerae} PDB: 3t1b_B
Length = 291
Score = 51.4 bits (124), Expect = 8e-08
Identities = 19/127 (14%), Positives = 52/127 (40%), Gaps = 4/127 (3%)
Query: 1 MNLHQFR-FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGL 59
M L F ++ T +K +++ I LE+ L++ + RH +++ L
Sbjct: 1 MKLDDLNLFRLVVENGSY--TSTSKKTMIPVATITRRIQALEDSLNLRLLNRHARKLT-L 57
Query: 60 TKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQF 119
T+ G+ + +++ + + + + +G + I+ + + + F ++
Sbjct: 58 TEAGERFYKDCSPLLERLASMTEEITDECRGASGRIRISAPSNLTKRMMMPMFNAFMEKY 117
Query: 120 PKVKLSL 126
P + + L
Sbjct: 118 PDIHIEL 124
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 51.8 bits (123), Expect = 1e-07
Identities = 56/335 (16%), Positives = 113/335 (33%), Gaps = 85/335 (25%)
Query: 7 RFVREAVRQNFN-LTEAAKALYTSQPGVSKAIIELEEEL--SIDIFI-RHGKRIRGLTKP 62
+FV E +R N+ L K +++ IE + L +F + R++ K
Sbjct: 81 KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL 140
Query: 63 GQAI--LRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFP 120
QA+ LR + ++ I+G+ GK + + + + + +
Sbjct: 141 RQALLELRPAKNVL--IDGVLGSGK--TW-----VALDVCLS----------YKVQCKMD 181
Query: 121 -KVK-LSLLQGN---PKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQWEYV---IIV 172
K+ L+L N P+ + EM++ I S I + + + ++
Sbjct: 182 FKIFWLNL--KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239
Query: 173 PLDHP--LLLLNSISLKEI-------------SNYPLITYDLSFSGRIKLDREFSLQKLT 217
+ LL+L ++ + + + +T LS + + + LT
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT 299
Query: 218 PYIVLETINSDIIKTYVELR-------------MGIGII-ASIAFDSNRDKNLRSISASH 263
P V ++ Y++ R + II SI N + H
Sbjct: 300 PDEVKS-----LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK-----H 349
Query: 264 LFGTTISRVIIKQGTYLRSYVYSFIKLLSPKLNRK 298
+ ++ II+ S + +L P RK
Sbjct: 350 VNCDKLTT-IIE----------SSLNVLEPAEYRK 373
Score = 47.9 bits (113), Expect = 2e-06
Identities = 46/316 (14%), Positives = 90/316 (28%), Gaps = 108/316 (34%)
Query: 15 QNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH-GKRIRGLTKPGQAILRS---I 70
+ +T+ A T+ + + L + + +++ R + L P + + + +
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL--PREVLTTNPRRL 330
Query: 71 EIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGN 130
II + I + + LT II+ SL
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLT-------------TIIE----------SSLNVLE 367
Query: 131 PKQITEMIRNDQADIAIVTEILSPSDKLISIPCYQ--WEYVI------IVPLDHPLLLLN 182
P + +M +++ P I W VI +V H L+
Sbjct: 368 PAEYRKMFD----RLSVF-----PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418
Query: 183 SISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTYVELRMGIGI 242
K+ + + ++KL+ E++L + I+ Y +
Sbjct: 419 ----KQPKESTISIPSIYLELKVKLENEYALHRS------------IVDHYNIPK----- 457
Query: 243 IASIAFDSNRDKNLRSISASHLFGTTISRVIIKQGTYLRSYVYSFI------------KL 290
FDS+ + +L Y YS I
Sbjct: 458 ----TFDSD------DLIPPYLDQ----------------YFYSHIGHHLKNIEHPERMT 491
Query: 291 LSPK--LNRKFI-NKI 303
L L+ +F+ KI
Sbjct: 492 LFRMVFLDFRFLEQKI 507
>3onm_A Transcriptional regulator LRHA; LYSR, ROVM, transcription factor,
virulence factor; 2.40A {Yersinia pseudotuberculosis}
Length = 238
Score = 48.5 bits (116), Expect = 6e-07
Identities = 18/107 (16%), Positives = 38/107 (35%), Gaps = 11/107 (10%)
Query: 92 TGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEI 151
G+L I + A LP ++ +P++ + + I +M+ + + D+AI T
Sbjct: 26 EGSLIIGASDDTADTLLPFLLNRVATLYPRLAIDVRVKRSPFIADMLSSGEVDLAITTA- 84
Query: 152 LSPSDKLISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYD 198
D + + +D+ + PL+ D
Sbjct: 85 --KVDSHPHVILRTSPTLWYCSVDYQFQPGEPV--------PLVVMD 121
>3hhg_A Transcriptional regulator, LYSR family; transcription factor,
structur genomics, oxford protein production facility,
OPPF; 3.20A {Neisseria meningitidis serogroup B}
Length = 306
Score = 47.1 bits (113), Expect = 2e-06
Identities = 32/140 (22%), Positives = 65/140 (46%), Gaps = 6/140 (4%)
Query: 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67
FV+ +F + AA+ L + VS+ + LEE+L +++ R +++ LT+ G
Sbjct: 11 FVQVVESGSF--SRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRTTRQLS-LTEEGAQYF 67
Query: 68 RSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQARYALPKIIKEFTIQFPKVKLSLL 127
R + I+QE+ + G L++ + + L + +F ++P ++LSL+
Sbjct: 68 RRAQRILQEMAAAETEMLAVHEIPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLV 127
Query: 128 QGNPKQITEMIRNDQADIAI 147
+I + DIA+
Sbjct: 128 SSE--GYINLI-ERKVDIAL 144
>3mz1_A Putative transcriptional regulator; structural genomics, PSI-2,
protein structure initiative, MI center for STR uctural
genomics, MCSG; 1.88A {Sinorhizobium meliloti}
Length = 300
Score = 45.6 bits (109), Expect = 8e-06
Identities = 28/125 (22%), Positives = 52/125 (41%), Gaps = 15/125 (12%)
Query: 8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAIL 67
F+R NF T A+ +L + V+ I LE L + R +R+ +T G
Sbjct: 6 FLRVVETGNF--TRASASLNMPKATVTNLIQGLEAHLRTKLLNRTTRRVL-VTPDGALYY 62
Query: 68 -RSIEII--MQEIEGLKKIGKEFSAYDT---GNLTIATTHTQARYALPKIIKEFTIQFPK 121
R+ ++ + E++G S + G L + T A + + EF ++P
Sbjct: 63 ERAARLLSDLDELDGS------LSTAQSLPKGRLRVETASAFANLVIIPALPEFHKKYPD 116
Query: 122 VKLSL 126
+++ L
Sbjct: 117 IQIDL 121
>3oxn_A Putative transcriptional regulator, LYSR family; structural
genomics, PSI-2, protein structure initiative; 2.70A
{Vibrio parahaemolyticus}
Length = 241
Score = 43.5 bits (103), Expect = 3e-05
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 1/84 (1%)
Query: 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPS 155
TIATT + LP + + P V + L ++++ + + AD+AI
Sbjct: 22 TIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPTGPVE 81
Query: 156 DKLISIPCYQWEYVIIVPLDHPLL 179
L S + + ++ HPL
Sbjct: 82 P-LRSEILGRVGVLCLLSKQHPLA 104
>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor;
structural GE DNA-binding protein, PSI-2, PROT structure
initiative; 2.30A {Agrobacterium tumefaciens str}
Length = 135
Score = 41.9 bits (98), Expect = 4e-05
Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 4/72 (5%)
Query: 11 EAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRH--GKRIRG--LTKPGQAI 66
+ + + +++ A +A+ S + L + GK+ G LT G +
Sbjct: 33 QLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAEL 92
Query: 67 LRSIEIIMQEIE 78
L + + +
Sbjct: 93 LERYRGMEERMN 104
>2y7p_A LYSR-type regulatory protein; transcription regulator, DNA-binding,
transcription, transcr factor, transcription regulation;
HET: SAL PEU; 1.85A {Burkholderia SP} PDB: 2y7k_A*
2y84_A 2y7w_A 2y7r_A
Length = 218
Score = 42.6 bits (101), Expect = 6e-05
Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 3/85 (3%)
Query: 96 TIATTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAI-VTEILSP 154
+A T Y +P +++ + P +++S L+ N + E + + D+A+ + L
Sbjct: 11 NLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQT 70
Query: 155 SDKLISIPCYQWEYVIIVPLDHPLL 179
++ YV + DHP
Sbjct: 71 G--FFQRRLFRHRYVCMFRKDHPSA 93
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 35.5 bits (82), Expect = 0.025
Identities = 46/217 (21%), Positives = 91/217 (41%), Gaps = 24/217 (11%)
Query: 41 EEELSIDIFIRHGKRI--RGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIA 98
+ E + +++ G+RI R + + + ++ IE+ ++ I G K + K++ TG L I
Sbjct: 254 DIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAG-KVVAKDYIDESTGEL-IC 311
Query: 99 TTHTQARYALPKIIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL 158
+ + L + + + + + + I+E +R D + L
Sbjct: 312 AANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTN--------DRLSAL 363
Query: 159 ISIPCYQWEYVIIVPLDHPLLLLNSISLKEISNYPLITYDLSFSGRIKLDREFSLQKLTP 218
+ I Y ++ P + P + SL E + YDLS GR+K +R +++
Sbjct: 364 VEI------YRMMRPGE-PPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEG 416
Query: 219 YIVLETINSDI---IKTYVELRMGIGIIASIAFDSNR 252
+L DI +K +++R G G + I NR
Sbjct: 417 SGIL--SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNR 451
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.0 bits (74), Expect = 0.055
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 7/33 (21%)
Query: 10 REAVRQNFNLTEAAKALYT--SQPGVS-KAIIE 39
++A+++ L + K LY S P ++ KA +E
Sbjct: 19 KQALKK---LQASLK-LYADDSAPALAIKATME 47
Score = 27.2 bits (59), Expect = 4.6
Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 15/40 (37%)
Query: 35 KAIIELEEELSI---DIFIRHGKRIRGLTKPGQAILRSIE 71
+A+ +L+ L + D + P AI ++E
Sbjct: 20 QALKKLQASLKLYADD------------SAPALAIKATME 47
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein
structure initiative; 2.20A {Thermoplasma acidophilum
dsm 1728} SCOP: a.4.5.28 b.43.5.2
Length = 230
Score = 32.0 bits (72), Expect = 0.16
Identities = 17/74 (22%), Positives = 31/74 (41%)
Query: 20 TEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKRIRGLTKPGQAILRSIEIIMQEIEG 79
++ A L SQ S+ II+LE+ I + +I +T+ G +L + + I
Sbjct: 31 SKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTEFADLSRILA 90
Query: 80 LKKIGKEFSAYDTG 93
+K +G
Sbjct: 91 IKNNVVITGTVTSG 104
>3zqp_A Terminase small subunit; DNA-binding protein, DNA packaging; 3.00A
{Bacillus phage SF6} PDB: 3zqq_A
Length = 164
Score = 31.7 bits (71), Expect = 0.17
Identities = 20/100 (20%), Positives = 36/100 (36%), Gaps = 13/100 (13%)
Query: 5 QFRFVREAVRQNFNLTEAAKALYTSQ-------------PGVSKAIIELEEELSIDIFIR 51
Q RF+ E + N T+AA A S+ P + I +E++ ++
Sbjct: 29 QERFIEEYFINDMNATKAAIAAGYSKNSASAIGAENLQKPAIRARIDARLKEINEKKILQ 88
Query: 52 HGKRIRGLTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYD 91
+ + LT+ + ++ K E SA D
Sbjct: 89 ANEVLEHLTRIALGQEKEQVLMGIGKGAETKTHVEVSAKD 128
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase,
structural genomics, structural GEN consortium, SGC,
transferase; HET: RIS; 1.80A {Homo sapiens} PDB:
4dem_F* 1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A*
2vf6_A* 1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F*
2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ...
Length = 374
Score = 31.3 bits (71), Expect = 0.38
Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 7/65 (10%)
Query: 1 MNLHQFRFVREAVRQNF-----NLTEAAKALYTSQPGVSKAIIELEEELSIDIFIRHGKR 55
MN Q V +Q+F + P + AI L+E ++ GK
Sbjct: 22 MNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKE--VLEYNAIGGKY 79
Query: 56 IRGLT 60
RGLT
Sbjct: 80 NRGLT 84
>2fxu_A Alpha-actin-1, actin, alpha skeletal muscle; actin complexed to
bistramide A, structural protein; HET: HIC ATP BID;
1.35A {Oryctolagus cuniculus} SCOP: c.55.1.1 c.55.1.1
PDB: 1h1v_A* 1kxp_A* 1lot_B* 1m8q_7* 1ma9_B* 1mvw_1*
1nwk_A* 1o18_1* 1o19_1* 1o1a_1* 1o1b_0* 1o1c_0* 1o1d_0*
1o1e_1* 1o1f_0* 1o1g_1* 1j6z_A* 1qz6_A* 1rdw_X* 1rfq_A*
...
Length = 375
Score = 30.4 bits (69), Expect = 0.78
Identities = 19/93 (20%), Positives = 30/93 (32%), Gaps = 22/93 (23%)
Query: 118 QFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKL-ISIPCYQ----------- 165
P+ + G P+ M+ Q D + E S L + P
Sbjct: 25 DAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEK 84
Query: 166 -WEYVI-----IVPLDHPLLL----LNSISLKE 188
W + + P +HP LL LN + +E
Sbjct: 85 IWHHTFYNELRVAPEEHPTLLTEAPLNPKANRE 117
>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR
genomics, PSI, protein structure initiative; 1.80A
{Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2
Length = 200
Score = 28.8 bits (64), Expect = 1.8
Identities = 23/110 (20%), Positives = 42/110 (38%), Gaps = 8/110 (7%)
Query: 59 LTKPGQAILRSIEIIMQEIEGLKKIGKEFSAYDTGNLTIATTHTQ--------ARYALPK 110
LT G+ I + + E G+ G A N + A+ A+
Sbjct: 69 LTLKGKEIRDKLLSMFSEPIGVSVDGYPGIAIVVKNPPEFKSIELRDEAIKFDAKGAMIL 128
Query: 111 IIKEFTIQFPKVKLSLLQGNPKQITEMIRNDQADIAIVTEILSPSDKLIS 160
+K+ I FP+ L + P+ +++ + D I+T +P+ L S
Sbjct: 129 TVKDNEIVFPEDFRPLKEMYPEVAKKIVDYEDGDAVIITWAETPAKALKS 178
>2cmp_A G1P, terminase small subunit; DNA packaging, DNA binding DO;
1.58A {Bacteriophage SF6}
Length = 63
Score = 25.9 bits (57), Expect = 3.9
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 1 MNLHQFRFVREAVRQNFNLTEAA-KALY 27
++ Q RF+ E + N T+AA A Y
Sbjct: 9 LSPKQERFIEEYFINDMNATKAAIAAGY 36
>1meo_A Phosophoribosylglycinamide formyltransferase; purine biosynthesis;
1.72A {Homo sapiens} SCOP: c.65.1.1 PDB: 1njs_A* 1rbm_A*
1rbq_A* 1rby_A* 1rbz_A* 1rc0_A* 1rc1_A* 1zly_A* 1zlx_A*
1mej_B 1men_A*
Length = 209
Score = 26.7 bits (60), Expect = 7.3
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 287 FIKLLSPKLNRKFINKILN 305
F+++LS +K+ K+LN
Sbjct: 88 FMRILSGPFVQKWNGKMLN 106
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 27.3 bits (61), Expect = 7.6
Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 197 YDLSFSGRIK----LDREFSLQKLTPYIVLETINSDI---IKTYVELRMGIGIIASIAFD 249
YDL +GR K L S + L + E + ++ L G+ D
Sbjct: 267 YDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDID 326
Query: 250 SNRDKNLRSI 259
++ +R++
Sbjct: 327 HLGNRRIRTV 336
>3lti_A DNA-directed RNA polymerase subunit beta; BBM2,
nucleotidyltransferase, transcription, transferase; HET:
MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A
Length = 296
Score = 27.1 bits (61), Expect = 7.7
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 197 YDLSFSGRIKLDREFSLQKLTPYIVLETINSDIIKTY---VELRMGIGII 243
YDLS GR+ +R +++ +L DII +++R G G +
Sbjct: 248 YDLSAVGRMXFNRSLLREEIEGSGILS--XDDIIDVMXXLIDIRNGXGEV 295
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.138 0.383
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,671,790
Number of extensions: 292841
Number of successful extensions: 693
Number of sequences better than 10.0: 1
Number of HSP's gapped: 657
Number of HSP's successfully gapped: 59
Length of query: 306
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 213
Effective length of database: 4,105,140
Effective search space: 874394820
Effective search space used: 874394820
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: 57 (25.8 bits)