RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8476
(421 letters)
>3bjc_A CGMP-specific 3',5'-cyclic phosphodiesterase; PDE5, erectIle
dysfunction, inhibitor design, allosteric enzyme,
alternative splicing, CGMP binding; HET: WAN; 2.00A
{Homo sapiens} SCOP: a.211.1.2 PDB: 3mf0_A 3lfv_A 2xss_A
2k31_A*
Length = 878
Score = 164 bits (415), Expect = 2e-44
Identities = 102/445 (22%), Positives = 148/445 (33%), Gaps = 117/445 (26%)
Query: 24 QNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKS 83
E ++ LL+L + I ++ L KI L+ +R ++FL+
Sbjct: 137 MPLTPPRFDHDEGDQCSRLLELVKDISSH-LDVTALCHKIFLHIHGLISADRYSLFLVCE 195
Query: 84 ETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPG 143
++S L L D+ + + E
Sbjct: 196 DSSNDKFLISRLF-----------------------DVAEGSTLEEVSNNCIRLEWN--- 229
Query: 144 GEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDE-DEESDFTTR 202
I +VA+ G+ LNI D + N E D+ + + T+
Sbjct: 230 -------------------KGIVGHVAALGEPLNIKDA---YEDPRFNAEVDQITGYKTQ 267
Query: 203 CILCMPIFNGQKTVIGVAQLINKISERKP------------------------------- 231
ILCMPI N ++ V+GVAQ INK S
Sbjct: 268 SILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSL 327
Query: 232 -LCRRE-----------SNNVDIEDILAHTPEDPSIAF----STVFEL------------ 263
+R +E IL T+F +
Sbjct: 328 LENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVF 387
Query: 264 -GGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMR-EEVCNDEDEES 321
+ + A+YV +T + LNI DV R + +
Sbjct: 388 HMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVN 447
Query: 322 DFTTRCILCMPIFNGQK-TVIGVAQLINKV-----TRQPFTDCDVSIFEAFAIFCGLGIH 375
R +LC PI NG+K VIGV QL+NK+ +PF D EAF IFCGLGI
Sbjct: 448 QQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQ 507
Query: 376 NTQMYENACKLMAKQKVFQRYLTFC 400
NTQMYE + MAKQ V L++
Sbjct: 508 NTQMYEAVERAMAKQMVTLEVLSYH 532
Score = 133 bits (336), Expect = 5e-34
Identities = 66/221 (29%), Positives = 98/221 (44%), Gaps = 47/221 (21%)
Query: 10 QVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARD 69
+ F YL FCGI + NAQL+E S+LE +RNQ+LL LA IFEEQ +LE ++ KI
Sbjct: 304 KDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIIS 363
Query: 70 LLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDP 129
++ ++C +F++ + S+
Sbjct: 364 FMQVQKCTIFIVDEDCSD------------------------------------------ 381
Query: 130 SIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMR-EE 188
+FS+VF + E + + A+YV +T + LNI DV R
Sbjct: 382 --SFSSVFHMECEELEKS-SDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPW 438
Query: 189 VCNDEDEESDFTTRCILCMPIFNGQK-TVIGVAQLINKISE 228
+ + R +LC PI NG+K VIGV QL+NK+ E
Sbjct: 439 TTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEE 479
>1mc0_A 3',5'-cyclic nucleotide phosphodiesterase 2A; GAF domain, 3',5'
guanosine monophosphate, hydrolase; HET: PCG; 2.86A {Mus
musculus} SCOP: d.110.2.1 d.110.2.1
Length = 368
Score = 135 bits (341), Expect = 3e-36
Identities = 69/397 (17%), Positives = 142/397 (35%), Gaps = 76/397 (19%)
Query: 37 ERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSE-------AS 89
+ ++ +L+L +F+ + L K++ + + C + L+ + +
Sbjct: 11 DHDRKILQLCGELFDL--DATSLQLKVLQYLQQETQATHCCLLLVSEDNLQLSCKVIGDK 68
Query: 90 HLERILERP------GRVISERKPLCRRESNNVDIEDILAHT--PEDPSIAFSTVFELGG 141
L + P G+V+ +++ + ++D+ + + L
Sbjct: 69 VLGEEVSFPLTMGRLGQVVEDKQCIQ--------LKDLTSDDVQQLQNMLGCELQAMLCV 120
Query: 142 PGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTT 201
P ++ + V +A N + +E DE
Sbjct: 121 P----VISRATDQV------VALA--------CAFNKLG-GDFFTDE---DEHVIQHCFH 158
Query: 202 RCILCMPIFNGQKTVIGVAQLINKISERKPLCRRESNNVD--IEDILAHTPE-------- 251
+ + + + + ++V +++I+
Sbjct: 159 YTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICS 218
Query: 252 ----DPSIAFSTVFELGGPGGEAL-VKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVP 306
D + + VF+ G E+ ++ P + IA +VA+TGQILNI D
Sbjct: 219 VFLLDQNELVAKVFDGGVVDDESYEIRIPADQ---------GIAGHVATTGQILNIPDAY 269
Query: 307 SWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAF 366
+ D+ + F TR ILC PI N + VIGVA+L+NK+ F+ D + AF
Sbjct: 270 AHPLFY--RGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAF 327
Query: 367 AIFCGLGIHNTQMYENACKLMAKQKVFQ---RYLTFC 400
+I+CG+ I ++ +Y+ + + + YL
Sbjct: 328 SIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYLEHH 364
Score = 89.7 bits (222), Expect = 6e-20
Identities = 19/129 (14%), Positives = 44/129 (34%), Gaps = 5/129 (3%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIF-NGQKTVIGVAQLI 347
V Q + + D+ + + +LC+P+ V+ +A
Sbjct: 82 RLGQVVEDKQCIQLKDL----TSDDVQQLQNMLGCELQAMLCVPVISRATDQVVALACAF 137
Query: 348 NKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMAKQKVFQRYLTFCGIGIQNA 407
NK+ FTD D + + + G + +T ++ KL + + + + +
Sbjct: 138 NKLGGDFFTDEDEHVIQHCFHYTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDV 197
Query: 408 QLFEMSILE 416
+ I+
Sbjct: 198 SVLLQEIIT 206
Score = 55.8 bits (134), Expect = 1e-08
Identities = 22/72 (30%), Positives = 38/72 (52%)
Query: 10 QVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARD 69
V Q + G + + F+ Q LL++A+++F ++ L+ +I+TEAR+
Sbjct: 151 HVIQHCFHYTGTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARN 210
Query: 70 LLKCERCAVFLL 81
L E C+VFLL
Sbjct: 211 LSNAEICSVFLL 222
Score = 32.7 bits (74), Expect = 0.23
Identities = 6/46 (13%), Positives = 19/46 (41%)
Query: 10 QVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSN 55
+ + +CGI I ++ L++ R+ + ++ + +
Sbjct: 322 DLATAFSIYCGISIAHSLLYKKVNEAQYRSHLANEMMMYLEHHHHH 367
>3ibj_A CGMP-dependent 3',5'-cyclic phosphodiesterase; PDE2A, GAF-domains,
allosteric regulation hydrolase, membrane; 3.02A {Homo
sapiens}
Length = 691
Score = 133 bits (335), Expect = 6e-34
Identities = 57/218 (26%), Positives = 86/218 (39%), Gaps = 56/218 (25%)
Query: 10 QVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARD 69
V Q + + + F+ Q LL++A+++F ++ L+ +I+TEAR+
Sbjct: 151 HVIQHCFHYTSTVLTSTLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARN 210
Query: 70 LLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDP 129
L E C+VFLL D
Sbjct: 211 LSNAEICSVFLL----------------------------------------------DQ 224
Query: 130 SIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEV 189
+ + VF+ G E+ IA +VA+TGQILNI D +
Sbjct: 225 NELVAKVFDGGVVDDESYEIRI--------PADQGIAGHVATTGQILNIPDAYAHPLFY- 275
Query: 190 CNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKIS 227
D+ + F TR ILC PI N + VIGVA+L+NKI+
Sbjct: 276 -RGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKIN 312
Score = 129 bits (325), Expect = 1e-32
Identities = 60/326 (18%), Positives = 113/326 (34%), Gaps = 74/326 (22%)
Query: 135 TVFELGGPGGEALVKSPGNTVCNTHSR--LATIAKYVASTGQILNIGDVPSWMREEVCND 192
+ + + K G+ V L V + + + D+ S +++
Sbjct: 50 CLLLVSEDNLQLSCKVIGDKVLGEEVSFPLTGCLGQVVEDKKSIQLKDLTSEDVQQL--- 106
Query: 193 EDEESDFTTRCILCMPIFN-GQKTVIGV-------------------------------- 219
+ +LC+P+ + V+ +
Sbjct: 107 -QSMLGCELQAMLCVPVISRATDQVVALACAFNKLEGDLFTDEDEHVIQHCFHYTSTVLT 165
Query: 220 -AQLINKISERKPLCR----------RESNNVD--IEDILAHTPE------------DPS 254
K + K C+ ++V +++I+ D +
Sbjct: 166 STLAFQKEQKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQN 225
Query: 255 IAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVC 314
+ VF+ G E+ IA +VA+TGQILNI D +
Sbjct: 226 ELVAKVFDGGVVDDESYEIRI--------PADQGIAGHVATTGQILNIPDAYAHPLFY-- 275
Query: 315 NDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGI 374
D+ + F TR ILC PI N + VIGVA+L+NK+ F+ D + AF+I+CG+ I
Sbjct: 276 RGVDDSTGFRTRNILCFPIKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISI 335
Query: 375 HNTQMYENACKLMAKQKVFQRYLTFC 400
++ +Y+ + + + + +
Sbjct: 336 AHSLLYKKVNEAQYRSHLANEMMMYH 361
>1ykd_A Adenylate cyclase; GAF domain, bound cyclic AMP ligand, lyase; HET:
CMP; 1.90A {Anabaena SP}
Length = 398
Score = 125 bits (314), Expect = 3e-32
Identities = 70/403 (17%), Positives = 135/403 (33%), Gaps = 60/403 (14%)
Query: 35 EFERNQILLKLARSIFEEQS---NLECLVTKIMTEARDLLKCERCAVFLLKSETSE---- 87
E E+ ++ S+ + L+ ++ I + +LL +R +FLL E E
Sbjct: 3 EVEQKLQIVHQTLSMLDSHGFENILQEMLQSITLKTGELLGADRTTIFLLDEEKQELWSI 62
Query: 88 --ASHLERILERP--------GRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVF 137
A +R LE G V + ++ + I DP F+
Sbjct: 63 VAAGEGDRSLEIRIPADKGIAGEVATFKQVVN-----------IPFDFYHDPRSIFAQKQ 111
Query: 138 -ELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEE 196
++ G ++ P + + RL + + + + + + +E
Sbjct: 112 EKITGYRTYTMLALP---LLSEQGRLVAVVQLLNKLKPYSPPDALLAERIDNQGFTSADE 168
Query: 197 SDFTTRCILCMPIFNGQKTVIGVAQLINKISE-----RKPLCRRESNNVDIEDILAHTPE 251
F I ++ Q + + ++ ++ E
Sbjct: 169 QLFQEFAPSIRLILESSRSFYIATQKQRAAAAMMKAVKSLSQSSLDLEDTLKRVMDEAKE 228
Query: 252 DPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRL---ATIAKYVASTGQILNIGDVPSW 308
+ ST++ + E K + R+ A VA++GQ LNI
Sbjct: 229 LMNADRSTLWLIDRDRHELWTKITQDNGSTKELRVPIGKGFAGIVAASGQKLNIPFDLYD 288
Query: 309 MREEVCNDE-DEESDFTTRCILCMPIFNGQKTVIGVAQLINK------------------ 349
+ + D+++ + T +LCMP+FNG + +IGV QL+NK
Sbjct: 289 HPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIAP 348
Query: 350 -VTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMAKQK 391
+ F D EAF I G+ + N Q++ + +
Sbjct: 349 ECFQASFDRNDEEFMEAFNIQAGVALQNAQLFATVKQQEQGSR 391
Score = 40.6 bits (94), Expect = 6e-04
Identities = 15/81 (18%), Positives = 43/81 (53%)
Query: 7 ERNQVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTE 66
Q+FQ + + +++++ F ++ + ++K +S+ + +LE + ++M E
Sbjct: 166 ADEQLFQEFAPSIRLILESSRSFYIATQKQRAAAAMMKAVKSLSQSSLDLEDTLKRVMDE 225
Query: 67 ARDLLKCERCAVFLLKSETSE 87
A++L+ +R ++L+ + E
Sbjct: 226 AKELMNADRSTLWLIDRDRHE 246
Score = 32.5 bits (73), Expect = 0.25
Identities = 7/36 (19%), Positives = 16/36 (44%)
Query: 10 QVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKL 45
+ + + G+ +QNAQLF + + ++
Sbjct: 361 EFMEAFNIQAGVALQNAQLFATVKQQEQGSRSHHHH 396
>2e4s_A CAMP and CAMP-inhibited CGMP 3',5'-cyclic phosphodiesterase 10A;
GAF domain, structural genomics, NPPSFA; HET: MSE CMP;
2.10A {Homo sapiens} PDB: 2zmf_A*
Length = 189
Score = 104 bits (261), Expect = 1e-26
Identities = 40/97 (41%), Positives = 56/97 (57%), Gaps = 9/97 (9%)
Query: 289 IAKYVASTGQILNIGDV---PSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQ 345
IA VA TG++LNI D P + R + D + +TTR ILCMPI + VIGV Q
Sbjct: 92 IAGQVARTGEVLNIPDAYADPRFNR-----EVDLYTGYTTRNILCMPIVSRGS-VIGVVQ 145
Query: 346 LINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYEN 382
++NK++ F+ D + F+ FA+FC L +H MY
Sbjct: 146 MVNKISGSAFSKTDENNFKMFAVFCALALHCANMYHR 182
Score = 99.4 bits (248), Expect = 9e-25
Identities = 49/198 (24%), Positives = 80/198 (40%), Gaps = 55/198 (27%)
Query: 35 EFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERI 94
+ E N LL ++++ F+ ++ L+ IM A++L+ +RCA+F + + E
Sbjct: 8 QTELNDFLLDVSKTYFDNIVAIDSLLEHIMIYAKNLVNADRCALFQVDHKNKE------- 60
Query: 95 LERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNT 154
L + + ++ + I F +
Sbjct: 61 -------------LYSDLFDIGEEKEGKPVFKKTKEIRF--------SIEK--------- 90
Query: 155 VCNTHSRLATIAKYVASTGQILNIGDV---PSWMREEVCNDEDEESDFTTRCILCMPIFN 211
IA VA TG++LNI D P + R + D + +TTR ILCMPI +
Sbjct: 91 ---------GIAGQVARTGEVLNIPDAYADPRFNR-----EVDLYTGYTTRNILCMPIVS 136
Query: 212 GQKTVIGVAQLINKISER 229
VIGV Q++NKIS
Sbjct: 137 RGS-VIGVVQMVNKISGS 153
Score = 30.4 bits (69), Expect = 0.77
Identities = 4/24 (16%), Positives = 10/24 (41%)
Query: 7 ERNQVFQRYLTFCGIGIQNAQLFE 30
F+ + FC + + A ++
Sbjct: 158 TDENNFKMFAVFCALALHCANMYH 181
>3dba_A CONE CGMP-specific 3',5'-cyclic phosphodiesterase alpha'; 3', GAF
domain, cyclic nucleotide phosphodiesterase hydrolase,
lipoprotein, membrane; HET: 35G; 2.57A {Gallus gallus}
Length = 180
Score = 102 bits (255), Expect = 7e-26
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 3/93 (3%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348
IA +VA T + NI DV + D+++ +TT ++ +PI G++ V+ V +N
Sbjct: 89 IAGWVAHTKKFFNIPDV--KKNNHFSDYLDKKTGYTTVNMMAIPITQGKE-VLAVVMALN 145
Query: 349 KVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381
K+ F+ D +F+ + F L + +
Sbjct: 146 KLNASEFSKEDEEVFKKYLNFISLVLRLEHHHH 178
Score = 94.9 bits (236), Expect = 4e-23
Identities = 39/196 (19%), Positives = 74/196 (37%), Gaps = 46/196 (23%)
Query: 34 LEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLER 93
+ E IL +L I +E ++E +V K + LL +RC++F+ +S R
Sbjct: 1 MRLEECNILFELLTEIQDEAGSMEKIVHKTLQRLSQLLAADRCSMFICRSRNGIPEVATR 60
Query: 94 ILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGN 153
+L ++ ++ FE + P +
Sbjct: 61 LL----------------------------------NVTPTSKFEDNLVNPDKETVFPLD 86
Query: 154 TVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQ 213
IA +VA T + NI DV + D+++ +TT ++ +PI G+
Sbjct: 87 I---------GIAGWVAHTKKFFNIPDV--KKNNHFSDYLDKKTGYTTVNMMAIPITQGK 135
Query: 214 KTVIGVAQLINKISER 229
+ V+ V +NK++
Sbjct: 136 E-VLAVVMALNKLNAS 150
Score = 30.2 bits (68), Expect = 0.85
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 10 QVFQRYLTFCGIGIQNAQLFEM 31
+VF++YL F + ++
Sbjct: 158 EVFKKYLNFISLVLRLEHHHHH 179
>3oov_A Methyl-accepting chemotaxis protein, putative; structural genomics,
PSI-2, protein structure initiative; 2.20A {Geobacter
sulfurreducens}
Length = 169
Score = 90.1 bits (224), Expect = 2e-21
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 2/95 (2%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCN-DEDEESDFTTRCILCMPIFNGQKTVIGVAQLI 347
+ + Q+ I DV ++ + D ++ + PI + IGV +
Sbjct: 75 VITKCFTDRQVYMIDDVSAYPTDFRLQSPYDAIRALRSKSFVICPIVVKGE-AIGVFAVD 133
Query: 348 NKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYEN 382
N+ +R+ D DV + FA I + +
Sbjct: 134 NRSSRRSLNDTDVDTIKLFADQASSAIVRINLLKA 168
Score = 67.3 bits (165), Expect = 2e-13
Identities = 24/191 (12%), Positives = 51/191 (26%), Gaps = 54/191 (28%)
Query: 40 QILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPG 99
+++ I + +++ ++ D+L ER + + + + L
Sbjct: 2 NAFHQISSRIQKSI-DVDEVLRLCAEGLHDVLGYERVNILMADTARTS-------LS--- 50
Query: 100 RVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTH 159
+A V L GG
Sbjct: 51 ---------------------FVAAVGTADFNPAGVVLPLDQRGG--------------- 74
Query: 160 SRLATIAKYVASTGQILNIGDVPSWMREEVCN-DEDEESDFTTRCILCMPIFNGQKTVIG 218
+ + Q+ I DV ++ + D ++ + PI + IG
Sbjct: 75 -----VITKCFTDRQVYMIDDVSAYPTDFRLQSPYDAIRALRSKSFVICPIVVKGE-AIG 128
Query: 219 VAQLINKISER 229
V + N+ S R
Sbjct: 129 VFAVDNRSSRR 139
>2w3g_A DOSS, two component sensor histidine kinase DEVS (GAF family
protein); redox sensor, heme, hypoxia, GAF domain,
transferase; HET: HEM; 1.40A {Mycobacterium
tuberculosis} PDB: 2w3d_A* 2w3f_A* 2w3e_A* 2w3h_A*
2y79_A* 2y8h_A* 2vzw_A*
Length = 153
Score = 81.5 bits (202), Expect = 1e-18
Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 5/95 (5%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348
+ + + L + DV + R L +P+ + G L +
Sbjct: 63 VIGLLIEDPKPLRLDDVSAHPAS----IGFPPYHPPMRTFLGVPVRVRDE-SFGTLYLTD 117
Query: 349 KVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENA 383
K QPF+D D + +A A G+ + N ++Y+ A
Sbjct: 118 KTNGQPFSDDDEVLVQALAAAAGIAVANARLYQQA 152
Score = 49.6 bits (119), Expect = 2e-07
Identities = 9/65 (13%), Positives = 20/65 (30%), Gaps = 5/65 (7%)
Query: 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 224
+ + + L + DV + R L +P+ + G L +
Sbjct: 63 VIGLLIEDPKPLRLDDVSAHPAS----IGFPPYHPPMRTFLGVPVRVRDE-SFGTLYLTD 117
Query: 225 KISER 229
K + +
Sbjct: 118 KTNGQ 122
Score = 39.9 bits (94), Expect = 3e-04
Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 23/85 (27%)
Query: 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASH---------LERILERP------G 99
+LE + I+ A L+ A+ + + + RI P G
Sbjct: 6 DLEATLRAIVHSATSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPKGLGVIG 65
Query: 100 RVISERKPLCRRESNNVDIEDILAH 124
+I + KPL ++D+ AH
Sbjct: 66 LLIEDPKPLR--------LDDVSAH 82
>3ci6_A Phosphoenolpyruvate-protein phosphotransferase;
PEP-phosphotransferase, GAF domain, structura genomics,
PSI-2, protein structure initiative; HET: MSE P4G; 1.55A
{Acinetobacter SP}
Length = 171
Score = 69.7 bits (171), Expect = 2e-14
Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 5/94 (5%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348
+ V +I+N+ + R E + L +P+ +K V+GV + N
Sbjct: 81 LVGLVGQREEIVNLENASKHER---FAYLPETGEEIYNSFLGVPVMYRRK-VMGVLVVQN 136
Query: 349 KVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYEN 382
K + F++ S I + N
Sbjct: 137 KQPQ-DFSEAAESFLVTLCAQLSGVIAHAHAVGN 169
Score = 45.0 bits (107), Expect = 7e-06
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 224
+ V +I+N+ + R E + L +P+ +K V+GV + N
Sbjct: 81 LVGLVGQREEIVNLENASKHER---FAYLPETGEEIYNSFLGVPVMYRRK-VMGVLVVQN 136
Query: 225 K 225
K
Sbjct: 137 K 137
Score = 36.1 bits (84), Expect = 0.007
Identities = 14/119 (11%), Positives = 36/119 (30%), Gaps = 30/119 (25%)
Query: 40 QILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSE----------AS 89
L ++ + I +L + ++ + D +K + C+++LL
Sbjct: 10 DTLRRIVQEI-NSSVSLHDSLDIMVNQVADAMKVDVCSIYLLDERNQRYLLMASKGLNPE 68
Query: 90 HLERILERP-----GRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPG 143
+ + + G V + + L + + F+ + E G
Sbjct: 69 SVGHVSLQLSEGLVGLVGQREEIV------------NLENASKHER--FAYLPETGEEI 113
>3trc_A Phosphoenolpyruvate-protein phosphotransferase; signal
transduction; HET: MSE; 1.65A {Coxiella burnetii}
Length = 171
Score = 65.4 bits (160), Expect = 7e-13
Identities = 15/98 (15%), Positives = 32/98 (32%), Gaps = 5/98 (5%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348
+ V + +N+ D P E + L +PI + ++G+ +
Sbjct: 79 LIGLVGEREEPINLADAPLHPA---YKHRPELGEEDYHGFLGIPIIEQGE-LLGILVIQQ 134
Query: 349 KVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKL 386
+ F + + + AI I + + KL
Sbjct: 135 LESH-HFAEEEEAFCVTLAIHLAAEIAHARAKGALEKL 171
Score = 40.4 bits (95), Expect = 3e-04
Identities = 9/61 (14%), Positives = 20/61 (32%), Gaps = 4/61 (6%)
Query: 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 224
+ V + +N+ D P E + L +PI + ++G+ +
Sbjct: 79 LIGLVGEREEPINLADAPLHPA---YKHRPELGEEDYHGFLGIPIIEQGE-LLGILVIQQ 134
Query: 225 K 225
Sbjct: 135 L 135
Score = 37.7 bits (88), Expect = 0.002
Identities = 21/124 (16%), Positives = 43/124 (34%), Gaps = 30/124 (24%)
Query: 40 QILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSE----ASH----- 90
+IL ++ + + NLE + ++ + L + C++F+ E A+
Sbjct: 8 KILRQITQEVNAA-PNLEQALKLVVVRLCEALPADACSLFICDDVHGEYVLMATQGLNSK 66
Query: 91 -LERILERP-----GRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGG 144
+ ++ + G V +P+ LA P P A+ ELG
Sbjct: 67 QVGKLRLKFGEGLIGLVGEREEPI------------NLADAPLHP--AYKHRPELGEEDY 112
Query: 145 EALV 148
+
Sbjct: 113 HGFL 116
>3o5y_A Sensor protein; GAF domain, histidine, kinase, PSI, MCSG,
structural genomics, midwest center for structural
genomics, protein S initiative; 2.45A {Bacillus
halodurans}
Length = 165
Score = 58.9 bits (143), Expect = 1e-10
Identities = 14/94 (14%), Positives = 34/94 (36%), Gaps = 5/94 (5%)
Query: 288 TIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLI 347
++ Q + + ++ + + IL +PI++ K +GV +
Sbjct: 60 SLYWSALDQRQTIFRSLTDTQDNFY---EKQYLAILDLKSILVIPIYSKNK-RVGVLSIG 115
Query: 348 NKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381
K ++ D++ E + I N ++Y
Sbjct: 116 RKQQID-WSLDDLAFLEQLTDHLAVSIENVELYG 148
Score = 40.8 bits (96), Expect = 2e-04
Identities = 17/171 (9%), Positives = 46/171 (26%), Gaps = 58/171 (33%)
Query: 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESN 114
+L+ ++ ++ + + L+ +R + LL +ET +
Sbjct: 5 SLDDIINNMIDKLKLLVHFDRISFLLLANETLKL-------------------------- 38
Query: 115 NVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQ 174
+ S+ + ++ Q
Sbjct: 39 ------SHVYPKGSHSLDIGSTIPKEQ----------------------SLYWSALDQRQ 70
Query: 175 ILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINK 225
+ + ++ + + IL +PI++ K +GV + K
Sbjct: 71 TIFRSLTDTQDNFY---EKQYLAILDLKSILVIPIYSKNK-RVGVLSIGRK 117
>3eea_A GAF domain/HD domain protein; structural genomics, PSI, MCSG,
protein structure initiative, midwest center for
structural genomics; HET: PG6; 1.80A {Geobacter
sulfurreducens}
Length = 162
Score = 58.6 bits (142), Expect = 2e-10
Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 5/95 (5%)
Query: 287 ATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQL 346
+ K + Q L + D S C+L +P+ + VIG +
Sbjct: 72 IPLLKSMLRKRQHLMLTDPGSSDLL----TPKLRKLLRNLCVLAVPMVV-RTQVIGAVFM 126
Query: 347 INKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381
PF+D + +I L + + Q+++
Sbjct: 127 ARTRDNPPFSDAETAIIRDLVSHAALVVSHMQLFD 161
Score = 40.1 bits (94), Expect = 3e-04
Identities = 21/188 (11%), Positives = 47/188 (25%), Gaps = 55/188 (29%)
Query: 42 LLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRV 101
L++ + + ++++ ++ + R L+K AV+ E +
Sbjct: 1 LIEGSERLSGL-TDVDEVIKDLSRLLRKLVKTRWIAVYFFDRERRDF------------- 46
Query: 102 ISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSR 161
A + P+ E+ +
Sbjct: 47 -------------------APARSTGLPASFLPVFREMPLAPDKI--------------- 72
Query: 162 LATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQ 221
+ K + Q L + D S C+L +P+ + VIG
Sbjct: 73 --PLLKSMLRKRQHLMLTDPGSSDLL----TPKLRKLLRNLCVLAVPMVV-RTQVIGAVF 125
Query: 222 LINKISER 229
+
Sbjct: 126 MARTRDNP 133
>3e0y_A Conserved domain protein; APC87688.2, geobacter sulfurreducens PCA,
structural genomics, PSI-2, midwest center for
structural G MCSG; 3.10A {Geobacter sulfurreducens}
Length = 181
Score = 57.7 bits (140), Expect = 4e-10
Identities = 18/95 (18%), Positives = 32/95 (33%), Gaps = 5/95 (5%)
Query: 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348
I VA GQ +++ + E + +L PI + ++ V GV L
Sbjct: 84 ITGSVARDGQYISLSRASQ---DPRYRYFPELQEEKYNSMLSFPIGDKKE-VYGVINLNT 139
Query: 349 KVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENA 383
R F + ++ A I Q ++
Sbjct: 140 TSIR-SFHEDEIYFVSIIANLILTAIKLRQQVASS 173
Score = 37.3 bits (87), Expect = 0.004
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 224
I VA GQ +++ + E + +L PI + ++ V GV L
Sbjct: 84 ITGSVARDGQYISLSRASQ---DPRYRYFPELQEEKYNSMLSFPIGDKKE-VYGVINLNT 139
Query: 225 K 225
Sbjct: 140 T 140
Score = 35.7 bits (83), Expect = 0.011
Identities = 14/119 (11%), Positives = 36/119 (30%), Gaps = 30/119 (25%)
Query: 26 AQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSET 85
+ + + E L +++ + +L ++ + + LK C ++L + +
Sbjct: 1 SNAMQRANREHLEIISLEEISMLV-SSDFDLPEVLQHVTAKVATQLKVSVCNIYLREGDE 59
Query: 86 ----------SEASHLERILERP-----GRVISERKPLCRRESNNVDIEDILAHTPEDP 129
RI + G V + + + L+ +DP
Sbjct: 60 VVLAATHGFDPAFIGKIRI--KIGDGITGSVARDGQYI------------SLSRASQDP 104
>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 = 58.5 bits (141), Expect = 3e-09
Identities = 76/510 (14%), Positives = 149/510 (29%), Gaps = 183/510 (35%)
Query: 2 SILEFERNQVFQRYLTFCGIGIQNA------QLFEMSILEFERNQILLKLARSIFEEQSN 55
+ E ++L + ++ + Q+ + + EFE + E ++
Sbjct: 56 TPAEL-----VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENC----------YLEGND 100
Query: 56 LECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNN 115
+ L K++ E L + L+K+ A R++++R + S
Sbjct: 101 IHALAAKLLQENDTTLVKTK---ELIKNYI-TA-----------RIMAKRPFDKKSNS-- 143
Query: 116 VDIEDILAHTPEDPSIAFSTVFELGGPG---------------GEALVKSPGNTVCNTHS 160
L + + +F GG G LV + +
Sbjct: 144 -----ALFRAVGEGNAQLVAIF--GGQGNTDDYFEELRDLYQTYHVLVGD---LIKFSAE 193
Query: 161 RLATIAKYVASTGQILNIG-DVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGV 219
L+ + + ++ G ++ W+ + D+ + P+ IGV
Sbjct: 194 TLSELIRTTLDAEKVFTQGLNILEWLENP---SNTPDKDYLLSIPISCPL-------IGV 243
Query: 220 AQLINKISERKPLCRRESNNVDI--------EDIL-----AHTPEDPSI------AFSTV 260
QL + + K L + ++ A T S A + +
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL 303
Query: 261 FELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWM-------REEV 313
F +G EA P NT + + + + N G VPS M +E+V
Sbjct: 304 FFIGVRCYEAY---P-----NTSLPPSILEDSLEN-----NEG-VPSPMLSISNLTQEQV 349
Query: 314 ------CNDE-DEESDFTTRCILCMPIFNGQKTVI---------GVAQLINKV------- 350
N + + + NG K ++ G+ + K
Sbjct: 350 QDYVNKTNSHLPAGKQ------VEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD 403
Query: 351 -TRQPFTDCDVSIFEAF----AIFCGLGIHNTQMYENACKLM--AKQKVFQR-------- 395
+R PF++ + F + F H L+ A + +
Sbjct: 404 QSRIPFSERKLKFSNRFLPVASPF-----H--------SHLLVPASDLINKDLVKNNVSF 450
Query: 396 ---------YLTFCGIGIQNAQLFEMSILE 416
Y TF G + ++ SI E
Sbjct: 451 NAKDIQIPVYDTFDG---SDLRVLSGSISE 477
Score = 50.8 bits (121), Expect = 7e-07
Identities = 50/383 (13%), Positives = 96/383 (25%), Gaps = 148/383 (38%)
Query: 51 EEQSNLECLVTKIMTEARDLLKCERCAVFLL----KSETSEASHLERILERPGRVIS--E 104
E + E LV K FL E S+ +++L ++ E
Sbjct: 53 EPTTPAE-LVGK----------------FLGYVSSLVEPSKVGQFDQVLNL---CLTEFE 92
Query: 105 RKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLAT 164
L N DI + A ++ EL
Sbjct: 93 NCYL----EGN-DIHALAAKLLQENDTTLVKTKEL------------------------- 122
Query: 165 IAKYVAS---TGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQ 221
I Y+ + + + + R + + + IF GQ G
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFR----AVGEGNAQL-------VAIFGGQ----G--- 164
Query: 222 LINKISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCN 281
+ +D E +++ L+K
Sbjct: 165 -------------------NTDDYF---EE-----LRDLYQTYHVLVGDLIKF------- 190
Query: 282 THSRLATIAKYVASTGQILNIG-DVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTV 340
+ L+ + + ++ G ++ W+ + D+ + P+
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENP---SNTPDKDYLLSIPISCPL------- 240
Query: 341 IGVAQLIN-KVTRQPFTDCDVSIFEAFAIFCGLGIHNT---------------QMYENAC 384
IGV QL + VT + + E + G H+ + +
Sbjct: 241 IGVIQLAHYVVTAK---LLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVR 297
Query: 385 KLMAKQKVFQRYLTFCGIGIQNA 407
K + L F G+ A
Sbjct: 298 KAI-------TVLFFIGVRCYEA 313
Score = 48.5 bits (115), Expect = 4e-06
Identities = 42/281 (14%), Positives = 85/281 (30%), Gaps = 110/281 (39%)
Query: 111 RESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVA 170
+++ I DI+ + P + +I F GG G+ + R Y A
Sbjct: 1654 KDTYGFSILDIVINNPVNLTIHF------GGEKGKRI-------------R----ENYSA 1690
Query: 171 STGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQK-------------TVI 217
+ + G + + E++ + +E +T F +K T++
Sbjct: 1691 MIFETIVDGKLKT---EKIFKEINEH---STSY-----TFRSEKGLLSATQFTQPALTLM 1739
Query: 218 GVAQLINKISERKPLCRRESNNVDIEDILA-HTPEDPSI-------AFSTVFELGGPGGE 269
A + L + + + A H S+ + + V + E
Sbjct: 1740 EKAAF-------EDL--KSKGLIPADATFAGH-----SLGEYAALASLADVMSI-----E 1780
Query: 270 A---LVKSPGNTVCNT-------HSRLATIAKYVASTGQILNIGDVPSWMREE----VCN 315
+ +V G T+ S IA +N G V + +E V
Sbjct: 1781 SLVEVVFYRGMTMQVAVPRDELGRSNYGMIA---------INPGRVAASFSQEALQYVVE 1831
Query: 316 DEDEESDFTTRCILCMPI-FN--GQKTVIG-----VAQLIN 348
+ + + L + +N Q+ V + + N
Sbjct: 1832 RVGKRTGW-----LVEIVNYNVENQQYVAAGDLRALDTVTN 1867
Score = 48.5 bits (115), Expect = 4e-06
Identities = 73/460 (15%), Positives = 132/460 (28%), Gaps = 170/460 (36%)
Query: 7 ERNQVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLAR--SIFEEQSNLE-CLVTKI 63
+ ++ + Y+T + + S L F A+ +IF Q N +
Sbjct: 118 KTKELIKNYITARIMAKRPFDKKSNSAL-FRAVGE--GNAQLVAIFGGQGNTDDYF---- 170
Query: 64 MTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILA 123
E RDL + V L + A L ++ + + + + ++I + L
Sbjct: 171 -EELRDLYQTYHVLVGDLIKFS--AETLSELIRTT----LDAEKVFTQ---GLNILEWLE 220
Query: 124 H---TPEDP---SIAFS--------------TVFELGGPGGEALVKSPGNTVCNTHSRLA 163
+ TP+ SI S T LG GE G T + L
Sbjct: 221 NPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHS--QGLV 278
Query: 164 TIAKYVASTG----------QILN----IG----------DV-PSWMREEVCNDEDEESD 198
T A +A T + + IG + PS + + + N+E S
Sbjct: 279 T-AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS- 336
Query: 199 FTTRCILCMPIFNGQKTVIGV--AQLINKISERKPLCRRESNNVDIEDILAHTPEDPSIA 256
P+ + + + Q+ + + ++N +H P +
Sbjct: 337 ---------PMLS----ISNLTQEQVQDYV--------NKTN--------SHLPAGKQVE 367
Query: 257 FSTV-----FELGGPGGEAL---------VKSPGNT------------VCNT-------- 282
S V + GP ++L K+P +
Sbjct: 368 ISLVNGAKNLVVSGPP-QSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASP 426
Query: 283 -HSRL-----ATIAKYVASTGQILNIGD--VPSW-------MREEVCNDEDEESDFTTRC 327
HS L I K + N D +P + +R S+ C
Sbjct: 427 FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVL----SGSISERIVDC 482
Query: 328 ILCMPI---------------FNGQKTVIGVAQLINKVTR 352
I+ +P+ F G G+ L ++
Sbjct: 483 IIRLPVKWETTTQFKATHILDF-GPGGASGLGVLTHRNKD 521
>2qyb_A Membrane protein, putative; GAF domain, domain of putative membrane
protein, PSI-2, MCSG structural genomics; 2.40A
{Geobacter sulfurreducens pca}
Length = 181
Score = 52.7 bits (127), Expect = 2e-08
Identities = 9/96 (9%), Positives = 28/96 (29%), Gaps = 3/96 (3%)
Query: 288 TIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLI 347
T + ++ + D + + + +PI + G+ +
Sbjct: 73 TYIGEAFLSNRLQFVNDTQYMTKPL---TRELMQKEGIKSFAHIPISRKGEPPFGILSVF 129
Query: 348 NKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENA 383
++ F + +++ E+ A + E
Sbjct: 130 SRTIVGLFNEPFLNLLESLAGQLAQAVKIVTEMEAK 165
Score = 34.6 bits (80), Expect = 0.030
Identities = 7/85 (8%), Positives = 24/85 (28%), Gaps = 16/85 (18%)
Query: 39 NQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSE---------TSEAS 89
N + L+ + + +L+ ++ ++ K + + L+ + +
Sbjct: 2 NAVRLRASEIMNRTL-DLQIIMDDLLNLLLKEFKLDLAVIRLVDEKGVLRVRSYSGKGIA 60
Query: 90 HLERILERP------GRVISERKPL 108
+ P G +
Sbjct: 61 GIAGKDWEPEIETYIGEAFLSNRLQ 85
Score = 30.4 bits (69), Expect = 0.69
Identities = 5/62 (8%), Positives = 18/62 (29%), Gaps = 3/62 (4%)
Query: 164 TIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLI 223
T + ++ + D + + + +PI + G+ +
Sbjct: 73 TYIGEAFLSNRLQFVNDTQYMTKPL---TRELMQKEGIKSFAHIPISRKGEPPFGILSVF 129
Query: 224 NK 225
++
Sbjct: 130 SR 131
>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 = 4e-07
Identities = 50/369 (13%), Positives = 107/369 (28%), Gaps = 138/369 (37%)
Query: 29 FEMSILEFERNQILLKLARSIFEEQ--SNLECLVTKIMTEARDLLKCERCAVFLLKSETS 86
FE +++ IL S+FE+ N +C + +D+ K ++ +
Sbjct: 9 FETGEHQYQYKDIL-----SVFEDAFVDNFDC------KDVQDMPK----SIL-----SK 48
Query: 87 EASHLERILERPGRVISERK---PLCRRESNNVD--IEDILAHTPEDPSIAFSTVFELGG 141
E ++ I+ V + L ++ V +E++L + F
Sbjct: 49 E--EIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL-----RINYKF-------- 93
Query: 142 PGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFT- 200
+ SP T S + Y+ R+ + ND + +
Sbjct: 94 ------LMSPIKTEQRQPSMMTR--MYIEQ--------------RDRLYNDNQVFAKYNV 131
Query: 201 TRCILCMPIFNGQKTVIGVAQLINKISERKPLCR-RESNNVDIEDILAHTPEDPSIAFST 259
+R Q K+ R+ L R + NV
Sbjct: 132 SR-----------------LQPYLKL--RQALLELRPAKNV------------------L 154
Query: 260 VFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDE 319
+ + G G + VC ++ + +I W+ + CN +
Sbjct: 155 IDGVLGSGKTWVALD----VCLSYKVQCKMD------FKIF-------WLNLKNCNSPET 197
Query: 320 ESD------FTTRCILCMPIFNGQKTVIGVAQLINKVTR----QPFTDC-----DV---S 361
+ + + + + + ++ R +P+ +C +V
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 362 IFEAFAIFC 370
+ AF + C
Sbjct: 258 AWNAFNLSC 266
>2vjw_A GAF-B, GAF family protein; histidine kinase, hypoxia sensing,
hydrolase; HET: MSE; 2.0A {Mycobacterium smegmatis} PDB:
2vks_A
Length = 149
Score = 47.9 bits (114), Expect = 6e-07
Identities = 11/72 (15%), Positives = 20/72 (27%), Gaps = 1/72 (1%)
Query: 312 EVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCG 371
+ + L +P+ TV GV + +PFT + + FA
Sbjct: 71 APRRLDVLDGPGLGGPALVLPLRATD-TVAGVLVAVQGSGARPFTAEQLEMMTGFADQAA 129
Query: 372 LGIHNTQMYENA 383
+
Sbjct: 130 VAWQLASSQRRM 141
>3p01_A Two-component response regulator; PSI-2, midwest center for
structural genomics, protein struc initiative, MCSG,
signali protein; 2.65A {Nostoc SP}
Length = 184
Score = 45.3 bits (108), Expect = 7e-06
Identities = 11/89 (12%), Positives = 32/89 (35%), Gaps = 5/89 (5%)
Query: 288 TIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLI 347
+ +TGQI ++ + + D + + +PI + ++GV L
Sbjct: 96 PLTNEAIATGQIQVAANIAK---DPKLASISQYQDNGIQSHVVIPITYRNE-MLGVLSLQ 151
Query: 348 NKVTRQPFTDCDVSIFEAFAIFCGLGIHN 376
+ + ++++ A + + +
Sbjct: 152 WQQPIS-LREDELTLIHLSAQLVAIALTS 179
Score = 37.6 bits (88), Expect = 0.002
Identities = 16/102 (15%), Positives = 38/102 (37%), Gaps = 15/102 (14%)
Query: 37 ERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSET--------SEA 88
+ +L L + + ++LE ++T I T + C + +L+ +T S+
Sbjct: 27 AQMSLLTVLVQVT-QASNSLEAILTPIATAFAESFAVNACILQMLEGQTLSTIQGFYSQQ 85
Query: 89 SHLERILER---PGRVISERKPLCRRESNNVDIEDILAHTPE 127
+ L + I+ + + N+ + LA +
Sbjct: 86 GTVNNWLNQDPLTNEAIATGQIQV---AANIAKDPKLASISQ 124
Score = 31.8 bits (73), Expect = 0.20
Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 164 TIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGV 219
+ +TGQI ++ + + D + + +PI + ++GV
Sbjct: 96 PLTNEAIATGQIQVAANIAK---DPKLASISQYQDNGIQSHVVIPITYRNE-MLGV 147
>3k2n_A Sigma-54-dependent transcriptional regulator; PSI-2, protein
structure initiative, structural genomics; 2.50A
{Chlorobium tepidum tls}
Length = 177
Score = 44.4 bits (105), Expect = 2e-05
Identities = 16/95 (16%), Positives = 37/95 (38%), Gaps = 5/95 (5%)
Query: 289 IAKYVASTGQIL--NIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQL 346
+ ++ + D+PS+ + + R I+ P+ +G + VIG
Sbjct: 80 LEGHLDDRTVTVASIARDIPSFGADGAPLLWTLH-ELGMRQIVLSPLRSGGR-VIGFLSF 137
Query: 347 INKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381
++ + ++D D S+ + + + N YE
Sbjct: 138 VSAEEK-LWSDGDKSLLSGVSSSIAIAVSNALAYE 171
Score = 32.0 bits (73), Expect = 0.18
Identities = 8/53 (15%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 37 ERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEAS 89
+++ + +I + + + L + + R L + + + E EAS
Sbjct: 3 AALKLMQYIGDAIGTIR-DPQELFRTVTDKLRLLFAFDSAVIITIDRERREAS 54
>3hcy_A Putative two-component sensor histidine kinase PR; two-component
sensor histidine kinase protein, structural GE PSI,
MCSG; 2.80A {Sinorhizobium meliloti}
Length = 151
Score = 38.4 bits (90), Expect = 0.001
Identities = 10/89 (11%), Positives = 24/89 (26%), Gaps = 4/89 (4%)
Query: 293 VASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTR 352
A+ + + + +V + + P+ + +IG
Sbjct: 60 GANEPEPIFVENVDDAEFSRELKESIVGEGI--AALGFFPLVTEGR-LIGKFMTYYDRPH 116
Query: 353 QPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381
F D ++ + A G I +
Sbjct: 117 -RFADSEIGMALTIARQLGFSIQRMRAEY 144
>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 = 29.9 bits (66), Expect = 0.90
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 9/37 (24%)
Query: 104 ERKPLCRRESNNVDIEDILA-HTPED-PSIAFSTVFE 138
E++ L + +++ L + + P++A E
Sbjct: 18 EKQALKKLQAS-------LKLYADDSAPALAIKATME 47
Score = 29.9 bits (66), Expect = 0.90
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 9/37 (24%)
Query: 228 ERKPLCRRESNNVDIEDILA-HTPED-PSIAFSTVFE 262
E++ L + +++ L + + P++A E
Sbjct: 18 EKQALKKLQAS-------LKLYADDSAPALAIKATME 47
>1f5m_A GAF; CGMP binding, signaling protein; 1.90A {Saccharomyces
cerevisiae} SCOP: d.110.2.1 PDB: 3ko6_A*
Length = 180
Score = 29.9 bits (67), Expect = 0.95
Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 14/78 (17%)
Query: 293 VASTGQILNIGDVPSWMREEVCNDEDE---ESDFTTRCILCMPIFNGQKTVIGVAQLINK 349
AST + + DV ++ D T+ + +PI + +GV I+
Sbjct: 104 AASTKETQIVPDV----------NKYPGHIACDGETKSEIVVPIISNDGKTLGVID-IDC 152
Query: 350 VTRQPFTDCDVSIFEAFA 367
+ + F D E A
Sbjct: 153 LDYEGFDHVDKEFLEKLA 170
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 265
Score = 29.3 bits (65), Expect = 1.9
Identities = 19/117 (16%), Positives = 29/117 (24%), Gaps = 10/117 (8%)
Query: 104 ERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSP---GNTVCNTHS 160
++ ++ D DP I + ++ + + GN V T
Sbjct: 127 RSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGG 186
Query: 161 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVI 217
R G I N D F TR I G K +
Sbjct: 187 R------NTGRVGVIKNREKHKGSFETIHVEDALGH-QFATRLGNVFTIGKGNKPWV 236
Score = 29.3 bits (65), Expect = 1.9
Identities = 19/117 (16%), Positives = 29/117 (24%), Gaps = 10/117 (8%)
Query: 228 ERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSP---GNTVCNTHS 284
++ ++ D DP I + ++ + + GN V T
Sbjct: 127 RSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGG 186
Query: 285 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVI 341
R G I N D F TR I G K +
Sbjct: 187 R------NTGRVGVIKNREKHKGSFETIHVEDALGH-QFATRLGNVFTIGKGNKPWV 236
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena
thermophila} PDB: 2xzn_W
Length = 260
Score = 28.5 bits (63), Expect = 3.6
Identities = 16/117 (13%), Positives = 26/117 (22%), Gaps = 10/117 (8%)
Query: 104 ERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGG---EALVKSPGNTVCNTHS 160
K + + + D +P I + GN
Sbjct: 129 TAKAIGPNQIPYIVTHDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQG 188
Query: 161 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVI 217
+ G I +I D F TR + G+K+ I
Sbjct: 189 N------NIGRVGIIQHIEKHQGSFDICHVKDAKGN-AFATRLGNIFVLGQGKKSWI 238
Score = 28.5 bits (63), Expect = 3.6
Identities = 16/117 (13%), Positives = 26/117 (22%), Gaps = 10/117 (8%)
Query: 228 ERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGG---EALVKSPGNTVCNTHS 284
K + + + D +P I + GN
Sbjct: 129 TAKAIGPNQIPYIVTHDSRTIRFPNPEIKIGDTLKYDLVNNKIENFAHLESGNVCYIQQG 188
Query: 285 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVI 341
+ G I +I D F TR + G+K+ I
Sbjct: 189 N------NIGRVGIIQHIEKHQGSFDICHVKDAKGN-AFATRLGNIFVLGQGKKSWI 238
>1wsc_A Hypothetical protein ST0229; structural genomics, function
unknown protein, unknown function; 2.45A {Sulfolobus
tokodaii} SCOP: d.309.1.1
Length = 230
Score = 28.5 bits (63), Expect = 3.6
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 24 QNAQLFEMSILEFERNQILLKLAR-SIFEEQSNLECLVTKIMTEARDLLKCERCAVF 79
QL ++ L ++L+K+AR SI + L+ + ++ D + ++ F
Sbjct: 2 SQEQLVAVNELNENLGKVLIKIARDSIANKLGILKINLEDYLSSLNDPILNKKGLAF 58
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 28.7 bits (65), Expect = 3.8
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 47 RSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILER 97
R + EEQ V ++ E R++L ER A LL+ ET A +R++E
Sbjct: 423 RRLIEEQYQR---VKALLLEKREVL--ERVAETLLERETLTAEEFQRVVEG 468
>2di4_A Zinc protease, cell division protein FTSH homolog;
metalloproteinase, hexamer-ring, hydrolase; 2.79A
{Aquifex aeolicus} SCOP: a.269.1.1
Length = 238
Score = 27.9 bits (63), Expect = 5.3
Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 4/76 (5%)
Query: 61 TKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIED 120
I+ E ++ L + LL+ ET + + I + + E + D +
Sbjct: 167 KAIVEEYKEPL--KAVVKKLLEKETITCEEFVEVFK--LYGIELKDKCKKEELFDKDRKS 222
Query: 121 ILAHTPEDPSIAFSTV 136
+ + V
Sbjct: 223 EENKELKSEEVKEEVV 238
>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A
{Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB:
2cea_A* 3kds_E*
Length = 476
Score = 28.3 bits (64), Expect = 6.1
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 62 KIMTEARDLLKCERCAVFLLKSETSEASHLERILER 97
+I+ + R L + LL+ ET E L RIL
Sbjct: 425 EIIRKYRKQL--DNIVEILLEKETIEGDELRRILSE 458
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_D 3u5g_E
Length = 261
Score = 27.7 bits (61), Expect = 6.7
Identities = 9/51 (17%), Positives = 14/51 (27%), Gaps = 1/51 (1%)
Query: 167 KYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVI 217
+ + G I++ D + F TR I K I
Sbjct: 187 RNLGRIGTIVHKERHDGGFDLVHIKDSLDN-TFVTRLNNVFVIGEQGKPYI 236
Score = 27.7 bits (61), Expect = 6.7
Identities = 9/51 (17%), Positives = 14/51 (27%), Gaps = 1/51 (1%)
Query: 291 KYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVI 341
+ + G I++ D + F TR I K I
Sbjct: 187 RNLGRIGTIVHKERHDGGFDLVHIKDSLDN-TFVTRLNNVFVIGEQGKPYI 236
>1lxi_A Bone morphogenetic protein 7; cystine-knot growth factor,
hormone-growth factor complex; HET: NAG; 2.00A {Homo
sapiens} SCOP: g.17.1.2 PDB: 1lx5_A* 1bmp_A* 1m4u_L*
2qcw_A 2r53_A
Length = 139
Score = 26.9 bits (59), Expect = 7.2
Identities = 7/40 (17%), Positives = 17/40 (42%)
Query: 82 KSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDI 121
+S+T + R+ S+++ C++ V D+
Sbjct: 11 RSKTPKNQEALRMANVAENSSSDQRQACKKHELYVSFRDL 50
>1vqq_A Saupbp2A, penicillin-binding protein MECA, low-affinity;
beta-lactam, D- transpeptidase, D-carboxypeptidase,
biosynthetic protein; 1.80A {Staphylococcus aureus}
SCOP: d.17.4.5 d.175.1.1 e.3.1.1 PDB: 1mwu_A* 1mwr_A
1mws_A* 1mwt_A*
Length = 646
Score = 27.7 bits (62), Expect = 8.4
Identities = 3/26 (11%), Positives = 10/26 (38%)
Query: 126 PEDPSIAFSTVFELGGPGGEALVKSP 151
++P++ + + G A +
Sbjct: 600 KDNPNMMMAINVKDVQDKGMASYNAK 625
Score = 27.7 bits (62), Expect = 8.4
Identities = 3/26 (11%), Positives = 10/26 (38%)
Query: 250 PEDPSIAFSTVFELGGPGGEALVKSP 275
++P++ + + G A +
Sbjct: 600 KDNPNMMMAINVKDVQDKGMASYNAK 625
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
0.321 0.136 0.403
Gapped
Lambda K H
0.267 0.0531 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,320,502
Number of extensions: 380549
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 92
Length of query: 421
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 325
Effective length of database: 4,021,377
Effective search space: 1306947525
Effective search space used: 1306947525
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: 59 (27.0 bits)