RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5056
(182 letters)
>3idb_B CAMP-dependent protein kinase type II-beta regulatory subunit,
CAMP-dependent protein kinase catalytic subunit alpha;
PKA, SPR, affinity; HET: TPO SEP ANP; 1.62A {Rattus
norvegicus} PDB: 3idc_B*
Length = 161
Score = 96.3 bits (240), Expect = 7e-26
Identities = 44/98 (44%), Positives = 62/98 (63%), Gaps = 18/98 (18%)
Query: 36 TRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------DQMNDVIDA 83
TRR SV AE+YNP+++E+D ++I+PK+D+QR L E+ +QM+ V+DA
Sbjct: 1 TRRASVCAEAYNPDEEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDA 60
Query: 84 MFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
MFEK V+ G+ VI QGDDGD FYVI+ G +
Sbjct: 61 MFEKLVKEGEHVIDQGDDGDNFYVIDR------GTFDI 92
>3pna_A CAMP-dependent protein kinase type I-alpha regula subunit;
beta-barrel, CAMP-binding, catalytic subunit,
transferase; HET: CMP; 1.50A {Bos taurus} PDB: 3fhi_B*
3iia_A 3plq_A* 1u7e_B* 3pvb_B*
Length = 154
Score = 88.6 bits (220), Expect = 5e-23
Identities = 31/97 (31%), Positives = 49/97 (50%), Gaps = 20/97 (20%)
Query: 37 RRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------DQMNDVIDAM 84
RR ++ AE Y ED + + PK + +LA++ ++ +D+ DAM
Sbjct: 4 RRGAISAEVYTEEDAASYV--RKVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAM 61
Query: 85 FEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
F AG+ VI+QGD+GD FYVI+ G++ V
Sbjct: 62 FPVSFIAGETVIQQGDEGDNFYVIDQ------GEMDV 92
>3tnp_B CAMP-dependent protein kinase type II-beta regula subunit; PKA RIIB
tetrameric holoenzyme, transferase; HET: SEP TPO; 2.30A
{Mus musculus} PDB: 3tnq_A* 1cx4_A* 2qvs_B*
Length = 416
Score = 85.6 bits (211), Expect = 4e-20
Identities = 45/94 (47%), Positives = 62/94 (65%), Gaps = 12/94 (12%)
Query: 28 EPPVARFNTRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------D 75
PV TRR SV AE+YNP+++E+D ++I+PK+D+QR L E+ +
Sbjct: 100 NAPVINRFTRRASVCAEAYNPDEEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPE 159
Query: 76 QMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIE 109
QM+ V+DAMFEK V+ G+ VI QGDDGD FYVI+
Sbjct: 160 QMSQVLDAMFEKLVKEGEHVIDQGDDGDNFYVID 193
Score = 52.1 bits (124), Expect = 2e-08
Identities = 14/62 (22%), Positives = 26/62 (41%)
Query: 119 VSVPDELRDILLEFTISYLLEQPSDVIEYGVDFFTKLKLNRRTTPEEPTTPEDDIDDGPN 178
+ +P L ++L FT+ L QP+D++E+ + FT+L+ E
Sbjct: 3 IEIPAGLTELLQGFTVEVLRHQPADLLEFALQHFTRLQQENERKGAARFGHEGRTWGDAG 62
Query: 179 ER 180
Sbjct: 63 AA 64
Score = 41.7 bits (97), Expect = 6e-05
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
E + V+D + K G+ +I QGD D F+++ES G+V +
Sbjct: 279 EVSERLKVVDVIGTKVYNDGEQIIAQGDLADSFFIVES------GEVKI 321
>2qcs_B CAMP-dependent protein kinase type I-alpha regula subunit,
CAMP-dependent protein kinase, alpha-catalytic SU;
cyclic adenosine monophosphate; HET: SEP TPO ANP TAM;
2.20A {Bos taurus} PDB: 1rl3_A* 1rgs_A* 1ne6_A* 1ne4_A*
Length = 291
Score = 77.4 bits (190), Expect = 1e-17
Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 14/86 (16%)
Query: 37 RRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------DQMNDVIDAM 84
RR ++ AE Y ED + + PK + +LA++ ++ +D+ DAM
Sbjct: 5 RRGAISAEVYTEEDAASY--VRKVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAM 62
Query: 85 FEKPVEAGDIVIRQGDDGDFFYVIES 110
F AG+ VI+QGD+GD FYVI+
Sbjct: 63 FPVSFIAGETVIQQGDEGDNFYVIDQ 88
Score = 43.1 bits (101), Expect = 1e-05
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIES 110
+ + V DA+ E G ++ QG+ GD F++I
Sbjct: 169 DKWERLTVADALEPVQFEDGQKIVVQGEPGDEFFIILE 206
>4din_B CAMP-dependent protein kinase type I-beta regulat subunit,
CAMP-dependent protein kinase catalytic subunit A;
isoform diversity; HET: TPO SEP ATP; 3.70A {Homo
sapiens}
Length = 381
Score = 75.5 bits (185), Expect = 1e-16
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 14/95 (14%)
Query: 27 QEPPVARFNTRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------ 74
PV + RR V AE Y ED + + PK + +LA++
Sbjct: 86 PPNPVVKARRRRGGVSAEVYTEEDAVSY--VRKVIPKDYKTMTALAKAISKNVLFAHLDD 143
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIE 109
++ +D+ DAMF AG+ VI+QG++GD FYV++
Sbjct: 144 NERSDIFDAMFPVTHIAGETVIQQGNEGDNFYVVD 178
Score = 43.6 bits (102), Expect = 1e-05
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDILLEF 132
E + V DA+ E G+ ++ QG+ GD FY+I G SV
Sbjct: 260 EKWERLTVADALEPVQFEDGEKIVVQGEPGDDFYIITE------GTASVLQRRSPNEEYV 313
Query: 133 TISYL 137
+ L
Sbjct: 314 EVGRL 318
Score = 34.7 bits (79), Expect = 0.011
Identities = 7/56 (12%), Positives = 19/56 (33%)
Query: 124 ELRDILLEFTISYLLEQPSDVIEYGVDFFTKLKLNRRTTPEEPTTPEDDIDDGPNE 179
++ +L + + + +P +++ + F KL+ D E
Sbjct: 26 GIQQVLKDCIVHLCISKPERPMKFLREHFEKLEKEENRQILARQKSNSQSDSHDEE 81
>3ocp_A PRKG1 protein; serine/threonine kinase, TF2I and IRAG, transferase;
HET: CMP; 2.49A {Homo sapiens} PDB: 3od0_A* 3ogj_A*
Length = 139
Score = 64.6 bits (158), Expect = 5e-14
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 18/77 (23%)
Query: 57 PKVIYPKSDEQRRSLAES------------DQMNDVIDAMFEKPVEAGDIVIRQGDDGDF 104
YPKS + + + E+ Q+ +++D M+ +I++GD G
Sbjct: 7 TLPFYPKSPQSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSL 66
Query: 105 FYVIESMNRAQLGKVSV 121
YV+E GKV V
Sbjct: 67 VYVMED------GKVEV 77
>3shr_A CGMP-dependent protein kinase 1; cyclic nucleotide binding domains,
cyclic nucleotide protein transferase, PKG; HET: CMP;
2.50A {Bos taurus}
Length = 299
Score = 64.6 bits (157), Expect = 5e-13
Identities = 18/102 (17%), Positives = 34/102 (33%), Gaps = 24/102 (23%)
Query: 32 ARFNTRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------DQMND 79
+ + E + KS+ + + E+ Q+ +
Sbjct: 4 SHHHHHHGMASIEGRGSMQ------AFRKFTKSERSKDLIKEAILDNDFMKNLELSQIQE 57
Query: 80 VIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
++D M+ +I++GD G YV+E GKV V
Sbjct: 58 IVDCMYPVEYGKDSCIIKEGDVGSLVYVMED------GKVEV 93
Score = 45.7 bits (108), Expect = 2e-06
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDILLEF 132
+ ++ + D + E E G+ +IRQG GD F++I GKV+V E
Sbjct: 169 PEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISK------GKVNVTREDSPNEDPV 222
Query: 133 TISYL 137
+ L
Sbjct: 223 FLRTL 227
>1o7f_A CAMP-dependent RAP1 guanine-nucleotide exchange factor; EPAC2,
CAMP-GEF2, campb binding doamin, regulation; 2.5A {Mus
musculus} SCOP: a.4.5.31 b.82.3.2 b.82.3.2
Length = 469
Score = 62.6 bits (151), Expect = 4e-12
Identities = 17/105 (16%), Positives = 32/105 (30%), Gaps = 25/105 (23%)
Query: 29 PPVARFNTRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAES------------DQ 76
P+ + AE D K +S E + +
Sbjct: 5 IPMVAAHAAHSQSSAEWIACLD-------KRPLERSSEDVDIIFTRLKGVKAFEKFHPNL 57
Query: 77 MNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ + + + +E G + RQGD G +Y + + G + V
Sbjct: 58 LRQICLCGYYENLEKGITLFRQGDIGTNWYAVLA------GSLDV 96
Score = 47.6 bits (112), Expect = 6e-07
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 75 DQMNDVIDAM-FEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDIL 129
++ + FE + G ++ QG++G +Y+I G V+V + ++
Sbjct: 351 TVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILK------GSVNVVIYGKGVV 400
>2izy_A CAMP-dependent protein kinase regulatory subunit II; D/D, RII, PKA,
acetylation, transferase, CAMP- binding,
phosphorylation, nucleotide-binding; 2.2A {Mus musculus}
SCOP: a.31.1.1 PDB: 1l6e_A 1r2a_A 2drn_A 2h9r_A
Length = 54
Score = 55.7 bits (134), Expect = 2e-11
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 116 LGKVSVPDELRDILLEFTISYLLEQPSDVIEYGVDFFTKLKLNRRTTPE 164
+G + +P L ++L +T+ L +QP D++++ V++FT+L+ RR
Sbjct: 1 MGHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARRGLEH 49
>2kyg_A CAMP-dependent protein kinase type II-alpha regul subunit;
protein/protein, homodimer bound to monomer, protein
binding; NMR {Homo sapiens}
Length = 50
Score = 53.7 bits (129), Expect = 9e-11
Identities = 14/42 (33%), Positives = 28/42 (66%)
Query: 118 KVSVPDELRDILLEFTISYLLEQPSDVIEYGVDFFTKLKLNR 159
+ +P L ++L +T+ L +QP D++E+ V++FT+L+ R
Sbjct: 8 HIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 49
>2izx_A CAMP-dependent protein kinase type II-alpha regulatory subunit;
CAMP-binding, phosphorylation, nucleotide-binding, PKA,
CAMP, anchor, kinase, acetylation; 1.3A {Homo sapiens}
PDB: 2hwn_A
Length = 41
Score = 52.1 bits (125), Expect = 3e-10
Identities = 14/41 (34%), Positives = 28/41 (68%)
Query: 119 VSVPDELRDILLEFTISYLLEQPSDVIEYGVDFFTKLKLNR 159
+ +P L ++L +T+ L +QP D++E+ V++FT+L+ R
Sbjct: 1 IQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 41
>3of1_A CAMP-dependent protein kinase regulatory subunit; cyclic nucleotide
binding domain, evolution, PKA signaling, transfer; HET:
CMP; 2.21A {Saccharomyces cerevisiae}
Length = 246
Score = 56.0 bits (135), Expect = 4e-10
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+SD VI+ + EK V G +I+QGD GD+FYV+E G V
Sbjct: 19 DSDSKRLVINCLEEKSVPKGATIIKQGDQGDYFYVVEK------GTVDF 61
Score = 45.6 bits (108), Expect = 2e-06
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ + DA+ K + G+ +IR+GD G+ FY+IE G V V
Sbjct: 137 TTYDRAKLADALDTKIYQPGETIIREGDQGENFYLIEY------GAVDV 179
>1vp6_A CNBD, cyclic-nucleotide binding domain of mesorhizobium LOTI CNG
potassium channel; dimer helical bundle beta barrel core
with cyclic AMP bound; HET: CMP; 1.70A {Mesorhizobium
loti} SCOP: b.82.3.2 PDB: 3cl1_A* 2k0g_A* 2kxl_A 3clp_A*
1u12_A 3co2_A
Length = 138
Score = 44.2 bits (105), Expect = 2e-06
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 72 AESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ +++ A+ + V AG ++ R G+ GD + + G VSV
Sbjct: 22 LGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVE------GSVSV 65
>2d93_A RAP guanine nucleotide exchange factor 6; CNMP_binding domain, PDZ
domain containing guanine nucleotide exchange factor 2,
PDZ-GEF2, RA-GEF-2; NMR {Homo sapiens}
Length = 134
Score = 43.9 bits (104), Expect = 2e-06
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 75 DQMNDVIDAM-FEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
++ M FE +AG I++ G + D +YVI + G V +
Sbjct: 30 SVRRELCSVMIFEVVEQAGAIILEDGQELDSWYVILN------GTVEI 71
>3mdp_A Cyclic nucleotide-binding domain (CNMP-BD) protei; structural
genomics, joint center for structural genomics; HET:
MSE; 1.90A {Geobacter metallireducens}
Length = 142
Score = 43.8 bits (104), Expect = 3e-06
Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 17/76 (22%)
Query: 64 SDEQRRSLAESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV-- 121
+DEQ + +A EK G ++ ++ D ++ G V +
Sbjct: 18 TDEQLKDIAL---------ISEEKSFPTGSVIFKENSKADNLMLLLE------GGVELFY 62
Query: 122 PDELRDILLEFTISYL 137
+ T+ +
Sbjct: 63 SNGGAGSAANSTVCSV 78
>4ava_A Lysine acetyltransferase; allosteric regulation, domain coupling;
HET: ACO; 1.70A {Mycobacterium tuberculosis} PDB:
4avb_A* 4avc_A*
Length = 333
Score = 43.9 bits (103), Expect = 9e-06
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRD 127
++ + + ++ AG +++RQG+ F +I S G V D
Sbjct: 25 PAEGLVSLAASVQPLRAAAGQVLLRQGEPAVSFLLISS------GSAEVSHVGDD 73
>3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; nucleotide
binding protein, structural genomics; HET: MSE CMP;
1.79A {Methylobacillus flagellatus KT}
Length = 187
Score = 43.2 bits (102), Expect = 9e-06
Identities = 9/47 (19%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+++ + M ++ +GD GD+ +I + G+V+V
Sbjct: 53 EEVRYLCSYMQCYAAPRDCQLLTEGDPGDYLLLILT------GEVNV 93
>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 = 41.6 bits (97), Expect = 7e-05
Identities = 32/191 (16%), Positives = 56/191 (29%), Gaps = 89/191 (46%)
Query: 8 HSAEVSELPLHLS---------LRSTYFQEPPVARFNTRRKSVYAESYNPEDDEEDEGPK 58
H+ ++L +++ Y AR +R P
Sbjct: 102 HAL-AAKLLQENDTTLVKTKELIKN-YIT----ARIMAKR------------------PF 137
Query: 59 VIYPKSDEQRRSLAESDQMNDV-IDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLG 117
S +L + + + A+F G QG+ D+F
Sbjct: 138 DKKSNS-----ALFRAVGEGNAQLVAIF-----GG-----QGNTDDYF------------ 170
Query: 118 KVSVPDELRDI----------LLEF---TISYLLEQPSDVIEY---GVDFFTKLKLNRRT 161
+ELRD+ L++F T+S L+ D + G++ L
Sbjct: 171 -----EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL-----E 220
Query: 162 TPEEPTTPEDD 172
P TP+ D
Sbjct: 221 NPS--NTPDKD 229
Score = 30.4 bits (68), Expect = 0.36
Identities = 19/95 (20%), Positives = 30/95 (31%), Gaps = 22/95 (23%)
Query: 7 QHSAEVSELPLHLSLRSTYFQEPPV-ARFNTRRKSVYAESYNPEDDEEDEGPKVIYPKSD 65
Q SE L S R F PV + F+ S + +++ V + D
Sbjct: 404 QSRIPFSERKLKFSNR---FL--PVASPFH----SHLLVPASDLINKDLVKNNVSFNAKD 454
Query: 66 -----------EQRRSLAESDQMNDVIDAMFEKPV 89
R L+ S ++D + PV
Sbjct: 455 IQIPVYDTFDGSDLRVLSGSI-SERIVDCIIRLPV 488
>2pqq_A Putative transcriptional regulator; APC7345, streptomyces
coelicolor structural genomics, PSI-2, protein structure
initiative; 2.00A {Streptomyces coelicolor A3}
Length = 149
Score = 39.2 bits (92), Expect = 1e-04
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+Q ++ +M E + GD + +GD GD YV+ GKV +
Sbjct: 19 EQSAELRASMSEVTLARGDTLFHEGDPGDRLYVVTE------GKVKL 59
>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 = 40.2 bits (93), Expect = 2e-04
Identities = 31/203 (15%), Positives = 55/203 (27%), Gaps = 39/203 (19%)
Query: 4 RQIQHSAEVSEL---PLHLSLRSTYF--------QEPPVARF-NTRRKSVY---AESYNP 48
+ I E+ + +S T QE V +F + Y
Sbjct: 43 KSILSKEEIDHIIMSKDAVS--GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIK- 99
Query: 49 EDDEEDEGPKVIYPKSDEQRRSLAESDQMNDVIDAMF---EKPVEAGDIVIRQGDDGDFF 105
E P ++ EQR L N V +P + +
Sbjct: 100 ---TEQRQPSMMTRMYIEQRDRLYND---NQVFAKYNVSRLQPYLKLRQALLELRPAKNV 153
Query: 106 YVIESMNRAQLGK-VSVPDELRDILLE----FTISYL----LEQPSDVIEYGVDFFTKLK 156
+I+ + GK D ++ F I +L P V+E ++
Sbjct: 154 -LIDGV--LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID 210
Query: 157 LNRRTTPEEPTTPEDDIDDGPNE 179
N + + + + I E
Sbjct: 211 PNWTSRSDHSSNIKLRIHSIQAE 233
Score = 31.7 bits (71), Expect = 0.14
Identities = 19/136 (13%), Positives = 36/136 (26%), Gaps = 38/136 (27%)
Query: 36 TRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAESDQMN---DVIDAMFEK-PVEA 91
TR K V + + + D +L + + +D + P E
Sbjct: 272 TRFKQV-TDFLSAA--------TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV 322
Query: 92 GDI----------VIRQGDDG-DFF--YVIESMNRAQLGKVSV----PDELRDILLEFTI 134
IR G D + + + + S+ P E R + ++
Sbjct: 323 LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII--ESSLNVLEPAEYRKMFDRLSV 380
Query: 135 SYLLEQPSDV-IEYGV 149
P I +
Sbjct: 381 F-----PPSAHIPTIL 391
Score = 26.7 bits (58), Expect = 6.4
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 121 VPDELRDILLEFTISYLLEQPSDVIEYGVDF-FTKLKLNRRTTPEE 165
V D + IL + I +++ G F L + ++
Sbjct: 38 VQDMPKSILSKEEIDHIIMSKDA--VSGTLRLFWTLLSKQEEMVQK 81
>2z69_A DNR protein; beta barrel, dimerization helix, transcription
regulator; 2.10A {Pseudomonas aeruginosa}
Length = 154
Score = 38.4 bits (90), Expect = 3e-04
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
Q+ +++ + ++ G V RQG+ FY + S G V +
Sbjct: 26 VQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLIS------GCVKI 66
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix,
transcription factor, CAMP-B proteins, CAMP receptor
protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.4 b.82.3.2
Length = 207
Score = 38.0 bits (89), Expect = 7e-04
Identities = 7/49 (14%), Positives = 18/49 (36%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ ++ ++ + A +I GD + + I G V++
Sbjct: 2 KLKHLDKLLAHCHRRRYTAKSTIIYAGDRCETLFFIIK------GSVTI 44
>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity,
CRP, CLP, C-DI-GMP receptor, quorum SENS binding,
transcription; 2.30A {Xanthomonas campestris PV}
Length = 230
Score = 37.3 bits (87), Expect = 0.001
Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
++ + + + V R GD Y + S G VS+
Sbjct: 23 DAGTIERFLAHSHRRRYPTRTDVFRPGDPAGTLYYVIS------GSVSI 65
>4ev0_A Transcription regulator, CRP family; CAMP binding, winged
helix-turn-helix motif, DNA binding, transcription
activator; HET: CMP; 2.40A {Thermus thermophilus}
Length = 216
Score = 37.2 bits (87), Expect = 0.001
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
++++ + + G + QGD G Y++ S GKV +
Sbjct: 13 EEVDLALSYFQRRLYPQGKPIFYQGDLGQALYLVAS------GKVRL 53
>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP
regulatory protein, structural genomi 2, protein
structure initiative; 2.20A {Ruegeria pomeroyi} PDB:
3h3z_A*
Length = 237
Score = 37.3 bits (87), Expect = 0.001
Identities = 3/36 (8%), Positives = 14/36 (38%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIES 110
++ ++ + + G+ + Q + +V+
Sbjct: 25 QHVDALLSQAVWRSYDRGETLFLQEEKAQAIHVVID 60
>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP),
dimer, inactive(APO, unliganded allostery, DNA binding,
cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB:
3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*
Length = 227
Score = 37.2 bits (87), Expect = 0.001
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ + + G V +G+ GD Y+I S GKV +
Sbjct: 20 SAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIIS------GKVKI 60
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration;
HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP:
a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A*
3e5q_A 2h6b_A* 2h6c_A
Length = 250
Score = 36.9 bits (86), Expect = 0.002
Identities = 6/49 (12%), Positives = 16/49 (32%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+++ + + G VI G++ + GK+ +
Sbjct: 21 PIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVE------GKIKL 63
>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA
transcription regulator, DNA binding protein; HET: HEM;
2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*
Length = 220
Score = 36.9 bits (86), Expect = 0.002
Identities = 9/62 (14%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLG--KVSVPDELRDILL 130
S++ + V+ E+ I+ + + ++++S G +V + E ++ L
Sbjct: 16 NSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKS------GRVRVYLAYEDKEFTL 69
Query: 131 EF 132
Sbjct: 70 AI 71
>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery,
DNA binding cyclic A transcription regulator; HET: CMP;
1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A*
3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A*
1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A*
3rdi_A* 3rou_A* 3rpq_A* ...
Length = 210
Score = 36.4 bits (85), Expect = 0.002
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ + + +I QG+ + Y I G V+V
Sbjct: 10 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVK------GSVAV 50
>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}
Length = 231
Score = 36.1 bits (84), Expect = 0.003
Identities = 9/47 (19%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
D M + + + E+ + ++V+ Q +G+ +++ + G V V
Sbjct: 20 DAMREALKVVTERNFQPDELVVEQDAEGEALHLVTT------GVVRV 60
>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding,
DNA-binding nucleotide-binding, transcription,
transcription regulation; HET: CMP; 1.66A {Escherichia
coli}
Length = 260
Score = 35.8 bits (83), Expect = 0.004
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ + + +I QG+ + Y I G V+V
Sbjct: 60 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVK------GSVAV 100
>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic
nucleotide-binding domain, structural genomics, joint
for structural genomics; 2.55A {Eubacterium rectale atcc
33656}
Length = 220
Score = 35.7 bits (83), Expect = 0.004
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIES 110
+ Q + D + + V+ G I+ D +++S
Sbjct: 15 NTAQKKLISDNLITQHVKKGTIIHNGNMDCTGLLLVKS 52
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix,
homodimer, transcription regulator; 3.60A {Pseudomonas
aeruginosa}
Length = 227
Score = 35.7 bits (83), Expect = 0.004
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
Q+ +++ + ++ G V RQG+ FY + S G V +
Sbjct: 23 VQLQELLASSDLVNLDKGAYVFRQGEPAHAFYYLIS------GCVKI 63
>1ft9_A Carbon monoxide oxidation system transcription regulator; heme
sensor, catabolite gene activator protein; HET: HEM;
2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1
Length = 222
Score = 35.7 bits (83), Expect = 0.004
Identities = 8/49 (16%), Positives = 14/49 (28%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
S K G +V D + +V+ G++ V
Sbjct: 12 LSPDGETFFRGFRSKIHAKGSLVCTGEGDENGVFVVVD------GRLRV 54
>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics,
porphyromona gingivalis, PSI, protein structure
initiative; 1.90A {Porphyromonas gingivalis} SCOP:
a.4.5.4 b.82.3.2
Length = 232
Score = 35.7 bits (83), Expect = 0.004
Identities = 6/47 (12%), Positives = 17/47 (36%), Gaps = 6/47 (12%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
++ + + P + V +GD + + + GK+ +
Sbjct: 24 EERELLDKEIQPFPCKKASTVFSEGDIPNNLFYLYE------GKIKI 64
>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG,
PSI, protein structure initiative, joint center for S
genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2
Length = 213
Score = 34.9 bits (81), Expect = 0.007
Identities = 6/49 (12%), Positives = 14/49 (28%), Gaps = 6/49 (12%)
Query: 73 ESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
+ ++ G+IV Q D + ++ G +
Sbjct: 11 HHMDLKKLLPCGKVIVFRKGEIVKHQDDPIEDVLILLE------GTLKT 53
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription,
transcription regulation; HET: BOG; 1.90A {Anabaena}
PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*
Length = 243
Score = 35.0 bits (81), Expect = 0.007
Identities = 11/59 (18%), Positives = 18/59 (30%), Gaps = 7/59 (11%)
Query: 64 SDEQRRSLAES-DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
Q ++LA QM + E + GD + Y + G V +
Sbjct: 22 IVTQDKALANVFRQMATGAFPPVVETFERNKTIFFPGDPAERVYFLLK------GAVKL 74
>1wgp_A Probable cyclic nucleotide-gated ION channel 6; cyclic nucleotide
monophosphate, CNMP, CNMP-binding, structural genomics;
NMR {Arabidopsis thaliana} SCOP: b.82.3.2
Length = 137
Score = 32.9 bits (75), Expect = 0.022
Identities = 7/66 (10%), Positives = 20/66 (30%), Gaps = 6/66 (9%)
Query: 72 AESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDILLE 131
+ ++ + + + ++R+GD + I G++
Sbjct: 17 MDERLLDAICERLKPCLFTEKSYLVREGDPVNEMLFIIR------GRLESVTTDGGRSGF 70
Query: 132 FTISYL 137
+ S L
Sbjct: 71 YNRSLL 76
>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat
transcription; HET: PR3; 2.3A {Listeria monocytogenes}
SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A
Length = 238
Score = 33.5 bits (77), Expect = 0.026
Identities = 5/52 (9%), Positives = 19/52 (36%), Gaps = 8/52 (15%)
Query: 72 AESDQMNDVIDA--MFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
A++++ ++ + K +++ Q D ++ + G +
Sbjct: 4 AQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYD------GITKL 49
>3b02_A Transcriptional regulator, CRP family; structural genomics, riken
structural genomics/proteomics in RSGI; 1.92A {Thermus
thermophilus} PDB: 2zdb_A
Length = 195
Score = 32.2 bits (74), Expect = 0.055
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 6/35 (17%)
Query: 87 KPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
K + + +G++ Y +E G V V
Sbjct: 2 KRFARKETIYLRGEEARTLYRLEE------GLVRV 30
>3beh_A MLL3241 protein; transmembrane protein, membrane protein; HET: LDA;
3.10A {Mesorhizobium loti} PDB: 2zd9_A*
Length = 355
Score = 32.1 bits (73), Expect = 0.077
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 11/82 (13%)
Query: 40 SVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAESDQMNDVIDAMFEKPVEAGDIVIRQG 99
+ + + D + P + + + +++ A+ + V AG ++ R G
Sbjct: 212 TGFYQEVRRGDFVRNWQLVAAVPLFQKLGPA-----VLVEIVRALRARTVPAGAVICRIG 266
Query: 100 DDGDFFYVIESMNRAQLGKVSV 121
+ GD + + G VSV
Sbjct: 267 EPGDRMFFVVE------GSVSV 282
>2byv_E RAP guanine nucleotide exchange factor 4; EPAC2, CAMP-GEF2, CAMP,
cyclic nucleotide, regulation, auto-inhibition, CDC25
homology domain; 2.7A {Mus musculus}
Length = 999
Score = 32.5 bits (73), Expect = 0.077
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 9/45 (20%)
Query: 64 SDEQRRSLAESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVI 108
R + + + +E G + RQGD G +Y +
Sbjct: 54 HPNLLRQICL---------CGYYENLEKGITLFRQGDIGTNWYAV 89
Score = 29.0 bits (64), Expect = 0.87
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 84 MFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPD 123
+FE + G ++ QG++G +Y+I G V+V
Sbjct: 361 IFESHAKGGTVLFNQGEEGTSWYIILK------GSVNVVI 394
>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural
genomics, joint center for structura genomics, JCSG;
2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4
b.82.3.2
Length = 232
Score = 30.7 bits (70), Expect = 0.17
Identities = 8/58 (13%), Positives = 22/58 (37%), Gaps = 13/58 (22%)
Query: 64 SDEQRRSLAESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
E S+ + +++ +AG+ +I+ G+ + G++S+
Sbjct: 30 CHEDFTSILDKVKLH-------FIKHKAGETIIKSGNPCTQLCFLLK------GEISI 74
>3jux_A Protein translocase subunit SECA; protein translocation, ATPase,
conformational change, peptide binding, ATP-binding,
cell inner membrane; HET: ADP; 3.10A {Thermotoga
maritima} PDB: 3din_A*
Length = 822
Score = 30.7 bits (70), Expect = 0.29
Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 11/81 (13%)
Query: 58 KVIYPKSDEQRRSLAESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLG 117
+ +Y R + ++ + +FE V G + D + S++ G
Sbjct: 653 RAVY----SLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKNSLSFFPAG 708
Query: 118 KVSV-------PDELRDILLE 131
+ +EL D L
Sbjct: 709 LFDLDEKQFSSSEELHDYLFN 729
>3cf6_E RAP guanine nucleotide exchange factor (GEF) 4; EPAC, rapgef4,
CAMP, SP-camps, GEF, gunanine nucleotide exchange
factor, G-protein, GTP-binding, nucleotide-binding; HET:
SP1; 2.20A {Mus musculus}
Length = 694
Score = 30.2 bits (67), Expect = 0.46
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 84 MFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDIL 129
+FE + G ++ QG++G +Y+I G V+V + ++
Sbjct: 56 IFESHAKGGTVLFNQGEEGTSWYIILK------GSVNVVIYGKGVV 95
>4f8a_A Potassium voltage-gated channel subfamily H membe; probable
regulatory domain of potassium channel, membrane PR
transport protein; 2.20A {Mus musculus}
Length = 160
Score = 28.8 bits (65), Expect = 0.64
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 6/30 (20%)
Query: 92 GDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
GD++ G+ D + S G + V
Sbjct: 58 GDLIYHAGESVDSLCFVVS------GSLEV 81
>3dww_A Prostaglandin E synthase; membrane protein, four helix bundle,
isomerase, membrane, transmembrane; HET: GSH; 3.50A
{Homo sapiens}
Length = 158
Score = 28.1 bits (62), Expect = 1.1
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 34 FNTRRKSVYAESYNPEDDEEDEGPKVIYPKSDEQRRSLAESDQMNDV 80
RK +A NPED GP+ D +R A ND+
Sbjct: 42 QVRLRKKAFA---NPEDALRHGGPQYCRSDPDVERCLRA---HRNDM 82
>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase,
protein translocation, protein transport; 2.00A
{Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A
3bxz_A*
Length = 853
Score = 28.7 bits (65), Expect = 1.3
Identities = 8/34 (23%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 58 KVIYPKSDEQRRSLAESDQMNDVIDAMFEKPVEA 91
+ IY QR L + +++ I+++ E +A
Sbjct: 649 RAIY----SQRNELLDVSDVSETINSIREDVFKA 678
>3dn7_A Cyclic nucleotide binding regulatory protein; structural genomics,
APC88869, cyclic nucleotide binding REG protein, PSI-2;
1.80A {Cytophaga hutchinsonii}
Length = 194
Score = 27.8 bits (62), Expect = 1.7
Identities = 4/36 (11%), Positives = 12/36 (33%)
Query: 75 DQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIES 110
+ + K V + +++ G+ Y +
Sbjct: 21 EDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVK 56
>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase,
translocation, secretion, protein transport; 2.18A
{Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19
c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A
3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A
Length = 844
Score = 27.6 bits (62), Expect = 2.6
Identities = 8/33 (24%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 58 KVIYPKSDEQRRSLAESDQMNDVIDAMFEKPVE 90
+VIY +QR + +S+ + ++++ M + +E
Sbjct: 611 EVIY----KQRFEVIDSENLREIVENMIKSSLE 639
>2ptm_A Hyperpolarization-activated (IH) channel; ION channel, cyclic
nucleotide binding domain, C-linker, CAM SPHCN1, HCN;
HET: CMP; 1.93A {Strongylocentrotus purpuratus}
Length = 198
Score = 27.2 bits (61), Expect = 2.6
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 92 GDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
D VI++G GD + I+ G V +
Sbjct: 102 ADYVIQEGTFGDRMFFIQQ------GIVDI 125
>3ugj_A Phosphoribosylformylglycinamidine synthase; amidotransferase,
glutaminase, thioester intermediate, ligas; HET: ADP;
1.78A {Salmonella enterica subsp} PDB: 1t3t_A* 3ujn_A*
3umm_A*
Length = 1303
Score = 27.7 bits (61), Expect = 2.8
Identities = 23/109 (21%), Positives = 39/109 (35%), Gaps = 13/109 (11%)
Query: 74 SDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDILLEFT 133
++Q V + ++ +E + D F + A + V + E R L++
Sbjct: 129 AEQWRQVAAELHDRMMET--VFSSLTDAEKLFIHHQ---PAPVSSVDLLGEGRQALIDAN 183
Query: 134 ISYLLEQPSDVIEYGVDFFTKLKLNRRTTPEEPTTPE-DDIDDGPNERC 181
+ L D I+Y + FTKL N P E +E C
Sbjct: 184 LRLGLALAEDEIDYLQEAFTKLGRN-------PNDIELYMFAQANSEHC 225
>3bpz_A Potassium/sodium hyperpolarization-activated cyclic
nucleotide-gated channel 2; CNBD, C-linker, pacemaker,
HCN, HCN2, CAP, PKA, CAMP, ION channel; HET: CMP; 1.65A
{Mus musculus} PDB: 3ffq_A 1q3e_A* 1q43_A* 1q5o_A*
3u10_A* 2q0a_A* 3etq_A* 3u11_A* 3otf_A* 3u0z_A*
Length = 202
Score = 26.9 bits (60), Expect = 3.0
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 92 GDIVIRQGDDGDFFYVIESMNRAQLGKVSV 121
GD +IR+G G Y I+ G VSV
Sbjct: 103 GDYIIREGTIGKKMYFIQH------GVVSV 126
>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary
phase, DNA-binding, transcription regulation; 1.50A
{Thermus thermophilus}
Length = 202
Score = 26.4 bits (59), Expect = 4.5
Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 8/42 (19%)
Query: 82 DAMFEKPVEAGDIVIRQGDDG--DFFYVIESMNRAQLGKVSV 121
+AGD+++ G G D Y + G V +
Sbjct: 3 QVRETVSFKAGDVILYPGVPGPRDRAYRVLE------GLVRL 38
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 26.6 bits (58), Expect = 5.7
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 18/64 (28%)
Query: 56 GPKVIYP------KSDEQRRSLAESDQMNDVIDAMFEKPVEAGDIVIRQGDDGDFFYVIE 109
GP +P + R L S + D ++ G V R D D V+
Sbjct: 395 GPNE-HPGAKYVIRDSGDRIDLRYSKRAGD-------IQLQYGWKVERHIMDND--PVL- 443
Query: 110 SMNR 113
NR
Sbjct: 444 -FNR 446
>2re3_A Uncharacterized protein; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: MSE; 2.50A {Silicibacter pomeroyi dss-3}
Length = 194
Score = 25.8 bits (56), Expect = 7.1
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 5/64 (7%)
Query: 87 KPVEAGDIVIRQGDDGDFFYVIESMNRAQLGKVSVPDELRDILLEFTISYLLEQPSDVIE 146
P GDI +R DG +FY +NR + ++ IL + L P + +
Sbjct: 34 NPPFNGDIDMRIARDGTWFYQGTPINRPAMVRL-----FSSILKREEDRFYLVTPVEKVG 88
Query: 147 YGVD 150
VD
Sbjct: 89 IRVD 92
>1wl8_A GMP synthase [glutamine-hydrolyzing] subunit A; transferase,
gatases, riken structural genomics/proteomics
initiative, RSGI; 1.45A {Pyrococcus horikoshii} SCOP:
c.23.16.1 PDB: 2d7j_A
Length = 189
Score = 25.3 bits (56), Expect = 9.3
Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 6 IQHSAEVSELPLHLSLRSTYFQEPPVARFNTRRKSVYAESYNPEDDEEDEGPKVI 60
H EV ELP + + + P+ +Y ++PE ++G +++
Sbjct: 126 ESHMDEVKELPPKFKILARS-ETCPIEAMKHEELPIYGVQFHPEVAHTEKGEEIL 179
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
0.314 0.135 0.381
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,893,077
Number of extensions: 174326
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 443
Number of HSP's successfully gapped: 79
Length of query: 182
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 94
Effective length of database: 4,244,745
Effective search space: 399006030
Effective search space used: 399006030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (24.6 bits)