RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781079|ref|YP_003065492.1| diguanylate cyclase
[Candidatus Liberibacter asiaticus str. psy62]
(266 letters)
>1w25_A Stalked-cell differentiation controlling protein; two-component
system, response regulator, diguanylate cyclase, ggdef
domain; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP:
c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A*
Length = 459
Score = 147 bits (371), Expect = 3e-36
Identities = 51/170 (30%), Positives = 84/170 (49%), Gaps = 9/170 (5%)
Query: 96 SYNRISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGH 148
+ + +L+ D L+GL N L S + +S + DID+FK+IND FGH
Sbjct: 280 NLDHSLELAVTDQLTGLHNRRYMTGQLDSLVKRATLGGDPVSALLIDIDFFKKINDTFGH 339
Query: 149 PVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQI 208
+GD+V+ + +L R GGEEF ++ +A +A +R + S
Sbjct: 340 DIGDEVLREFALRLASNVRAIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPF 399
Query: 209 NISSG-PSIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVV 256
++ G +++TIS G++ + ++ RAD+ +Y AK SGRN VV
Sbjct: 400 TVAHGREMLNVTISIGVSATAGEGDTPEALLKRADEGVYQAKASGRNAVV 449
>3ezu_A Ggdef domain protein; multidomain protein of unknown function with
ggdef-domain, structural genomics; 1.95A {Geobacter
sulfurreducens}
Length = 342
Score = 137 bits (346), Expect = 2e-33
Identities = 50/195 (25%), Positives = 89/195 (45%), Gaps = 16/195 (8%)
Query: 73 IISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGS-------Y 125
I S ++ + G L L+ +++ S D L+G++ + F ++GS
Sbjct: 151 IGSCGLATAETELLGEALFRLWNEARQLAAQSHFDALTGVMTRAGFFKTVGSLAYAAQRS 210
Query: 126 NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAAL 185
+ I+ D+DYFK + DN+GH GD+++ +++ + VGR G+EF
Sbjct: 211 GSNVGIMLIDLDYFKLVGDNYGHQTGDRILQLVAETITSHLRRSDVVGRYDGDEFVVYLS 270
Query: 186 GSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC----HKEPISTIIYRAD 241
+A +LR+ IE S + +T S G+A+ I ++ AD
Sbjct: 271 PVEPASLRTVAENLRRSIEE-----ESARMVPVTASIGVAQGILGTDVDGGIEELVRLAD 325
Query: 242 QALYVAKKSGRNRVV 256
+ L AK +G+N+VV
Sbjct: 326 ECLMQAKYTGKNKVV 340
>3bre_A Probable two-component response regulator; protein-nucleotide
complex, signaling protein; HET: C2E; 2.40A {Pseudomonas
aeruginosa PAO1} PDB: 3i5a_A*
Length = 358
Score = 137 bits (346), Expect = 3e-33
Identities = 56/173 (32%), Positives = 83/173 (47%), Gaps = 12/173 (6%)
Query: 99 RISQLSRIDCLSGLLNHSAFISSLG-------SYNEKLSIVFFDIDYFKQINDNFGHPVG 151
+ +L D L+GL N F L +LS++ D+DYFK ND FGH G
Sbjct: 166 VLQRLMNSDGLTGLSNRRHFDEYLEMEWRRSLREQSQLSLLMIDVDYFKSYNDTFGHVAG 225
Query: 152 DKVIAFLSDQLVVVFGTPM-FVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINI 210
D+ + ++ + R GGEEFA G+S A +LA +R+ +E+ QI+
Sbjct: 226 DEALRQVAGAIREGCSRSSDLAARYGGEEFAMVLPGTSPGGARLLAEKVRRTVESLQISH 285
Query: 211 S-SGPSIHITISAGIAERC---HKEPISTIIYRADQALYVAKKSGRNRVVCFS 259
P H+T+S G++ + +I ADQALY AK +GRN+V
Sbjct: 286 DQPRPGSHLTVSIGVSTLVPGGGGQTFRVLIEMADQALYQAKNNGRNQVGLME 338
>3ign_A Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A,
structural genomics, PSI-2, protein structure
initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8}
Length = 177
Score = 121 bits (305), Expect = 1e-28
Identities = 60/170 (35%), Positives = 90/170 (52%), Gaps = 9/170 (5%)
Query: 99 RISQLSRIDCLSGLLNHSAF-------ISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVG 151
++++LS D L+GLLN + Y + S+V FDID+FK +ND +GH G
Sbjct: 3 QLAKLSMTDRLTGLLNRGTWENLVDAEYERFRRYGQATSLVMFDIDHFKPVNDTYGHLAG 62
Query: 152 DKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS 211
D+VI +D GR GGEEF + + A ++ +R+ IE S ++ S
Sbjct: 63 DEVIRHTADVTRNNIRQSDSAGRYGGEEFGIILPETDAESARVICERIREAIEKSTVSTS 122
Query: 212 SGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKKSGRNRVVCFSD 260
+G I T+S GIA+ E + +AD+ALY AK+SGRN+VV +
Sbjct: 123 AGD-IQYTVSMGIAQLTETPENYMQWMQKADEALYKAKESGRNKVVVSLE 171
>3mtk_A Diguanylate cyclase/phosphodiesterase; structural genomics, PSI-2,
protein structure initiative; 2.24A
{Caldicellulosiruptor saccharolyticus}
Length = 178
Score = 121 bits (304), Expect = 2e-28
Identities = 36/168 (21%), Positives = 75/168 (44%), Gaps = 11/168 (6%)
Query: 99 RISQLSRIDCLSGLLNHSAFISSLG-----SYNEKLSIVFFDIDYFKQINDNFGHPVGDK 153
++ L+ D L+GL N ++ I L ++F ++ +++N +G+ + D+
Sbjct: 2 KLEFLAFYDELTGLPNKNSLIRWLNLKVSQMDCIDTYLIFLEVRDLEKLNVTYGYDLVDE 61
Query: 154 VIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSG 213
+I +S ++ + G ++G + F A + SE + + L +++ +N
Sbjct: 62 LIIHISKRIKDIAGEGNKAFKIGFDRF--AIICKSENISDFIERMLSQLLLPYNVNG--- 116
Query: 214 PSIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVVCFSD 260
I + + G A+ E + ++ R D AL AK+ G N V F
Sbjct: 117 NLIRVNFNIGAAQIENSNEAAANLMRRCDLALIKAKEEGLNEYVIFKP 164
>3icl_A EAL/ggdef domain protein; structural genomics, PSI-2, protein
structure initiative, northeast structural genomics,
consortium, NESG; HET: MSE; 2.00A {Methylococcus
capsulatus}
Length = 171
Score = 112 bits (280), Expect = 1e-25
Identities = 43/163 (26%), Positives = 74/163 (45%), Gaps = 9/163 (5%)
Query: 106 IDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFL 158
+D ++GL N F L + ++F D+D FK IND+ GH VGD+++
Sbjct: 1 MDTVTGLPNRQLFCDRLLQALAAHERDGNPVVLLFLDVDNFKSINDSLGHLVGDRLLRAT 60
Query: 159 SDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHI 218
++++ V R+GG++F G+ + + + +Q + I I
Sbjct: 61 AERIRTAVRDGDTVARIGGDKFTILLNGAKDTLNGA-LVAQKILDGLAQPFVFGAQQIVI 119
Query: 219 TISAGIAERC-HKEPISTIIYRADQALYVAKKSGRNRVVCFSD 260
++S GIA E + ++ AD A+Y AK G+N FS
Sbjct: 120 SVSIGIAVSPADGETMEQLLRNADTAMYHAKSRGKNNYQFFSP 162
>3hvw_A Diguanylate-cyclase (DGC); alpha-beta protein., structural
genomics, PSI-2, protein structure initiative; 1.70A
{Pseudomonas aeruginosa}
Length = 176
Score = 107 bits (268), Expect = 2e-24
Identities = 19/165 (11%), Positives = 47/165 (28%), Gaps = 11/165 (6%)
Query: 106 IDCLSGLLNHSAFISSLGSYNEK------LSIVFFDIDYFKQINDNFGHPVGDKVIAFLS 159
ID +GL N + ++ ++ + I G+P + ++
Sbjct: 2 IDEPTGLYNRLRLQEDVSLRLQRDGALTVIAADLLPLALLNTIIRTLGYPFSNDLMLEAR 61
Query: 160 DQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHIT 219
D++ + ++ F ++E + L + E + G I
Sbjct: 62 DRIRAEL-PDFTLYKISPTRFGLLLPRQQQEETESVCLRLLRAFE--SPVVCRGIPIKAN 118
Query: 220 ISAGIAE--RCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIE 262
+ G+ + + A A+ G ++
Sbjct: 119 VGLGVLPLADDTLDGDQDWLRLVVSAADDARDRGVGWARYNPPLD 163
>3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase;
2.99A {Pseudomonas aeruginosa PAO1}
Length = 437
Score = 83.7 bits (205), Expect = 3e-17
Identities = 28/175 (16%), Positives = 67/175 (38%), Gaps = 7/175 (4%)
Query: 99 RISQLSRIDCLSGLLNHSAFISSLG-------SYNEKLSIVFFDIDYFKQINDNFGHPVG 151
++ ++S D ++GL N S F+ + + + ++ + ++ + + + G
Sbjct: 8 KLREVSSQDPVTGLYNRSHFLDLMDAAVQQAVTARKPSTLAYIHLNGYPSLQADHGLSGI 67
Query: 152 DKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS 211
D ++ L+ + FG + R G FAA G + ++A L K +EN ++
Sbjct: 68 DLLLGQLAGLMREQFGEEADLARFGDSIFAALFKGKTPEQAQAALQRLLKKVENHLFELN 127
Query: 212 SGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENNTC 266
+ ++ RA + A + G +++ ++ E
Sbjct: 128 GRSAQATLSIGVAGLDEKTAKAQDVMNRAHRCADDAARKGGSQIKQYNPAEELAA 182
>3i5c_A Fusion of general control protein GCN4 and WSPR response regulator
protein; C-DI-GMP, ggdef, leucine zipper, signaling
protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1}
PDB: 3i5b_A*
Length = 206
Score = 76.7 bits (187), Expect = 4e-15
Identities = 57/181 (31%), Positives = 81/181 (44%), Gaps = 12/181 (6%)
Query: 91 KELFISYNRISQLSRIDCLSGLLNHSAFIS-------SLGSYNEKLSIVFFDIDYFKQIN 143
L R+ +L D L+GL N F +LS++ D+DYFK N
Sbjct: 17 YHLENEVARLKKLVNSDGLTGLSNRRHFDEYLEMEWRRSLREQSQLSLLMIDVDYFKSYN 76
Query: 144 DNFGHPVGD-KVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKI 202
D FGH GD + + R GGEEFA G+S A +LA +R+
Sbjct: 77 DTFGHVAGDEALRQVAGAIREGCSRSSDLAARYGGEEFAMVLPGTSPGGARLLAEKVRRT 136
Query: 203 IENSQINIS-SGPSIHITISAGIAERC---HKEPISTIIYRADQALYVAKKSGRNRVVCF 258
+E+ QI+ P H+T+S G++ + +I ADQALY AK +GRN+V
Sbjct: 137 VESLQISHDQPRPGSHLTVSIGVSTLVPGGGGQTFRVLIEMADQALYQAKNNGRNQVGLM 196
Query: 259 S 259
Sbjct: 197 E 197
>3hva_A Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP,
transferase; 2.04A {Pseudomonas aeruginosa PAO1}
Length = 177
Score = 69.8 bits (169), Expect = 6e-13
Identities = 33/169 (19%), Positives = 73/169 (43%), Gaps = 9/169 (5%)
Query: 99 RISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVG 151
++ ++S D ++GL N S F+ + + + ++ + ++ + + + G
Sbjct: 8 KLREVSSQDPVTGLYNRSHFLDLMDAAVQQAVTARKPSTLAYIHLNGYPSLQADHGLSGI 67
Query: 152 DKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS 211
D ++ L+ + FG + R G FAA G + ++A L K +EN ++
Sbjct: 68 DLLLGQLAGLMREQFGEEADLARFGDSIFAALFKGKTPEQAQAALQRLLKKVENHLFELN 127
Query: 212 SGPSIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVVCFS 259
G S T+S G+A ++ RA + A + G +++ ++
Sbjct: 128 -GRSAQATLSIGVAGLDEKTAKAQDVMNRAHRCADDAARKGGSQIKQYN 175
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 42.6 bits (100), Expect = 9e-05
Identities = 61/338 (18%), Positives = 98/338 (28%), Gaps = 131/338 (38%)
Query: 13 LCHE----KNLESFSPHTFMIYFS--------IFFSIFIATVI----FIANI-----FLF 51
L H K L F+P Y + ++ IA F ++ LF
Sbjct: 246 LAHYVVTAKLLG-FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF 304
Query: 52 YIGL-----TPFYGLE-YIL---VEN--------LSLVIISITISLLLGYI--SGSIL-- 90
+IG+ P L IL +EN LS I ++T + Y+ + S L
Sbjct: 305 FIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS--ISNLTQEQVQDYVNKTNSHLPA 362
Query: 91 -KELFIS-----------------YNRISQLSRIDCLSGLLNHSAFISSLGSYNEKLSIV 132
K++ IS Y L + SG L+ S S KL
Sbjct: 363 GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG-LDQSRIPFS----ERKLKFS 417
Query: 133 --FFDI------DYFKQINDNFGHPVGDKVIAFLSDQLVV-VFGTPMFVGRLGGEEFAAA 183
F + +D + ++F + + + V+ T F G
Sbjct: 418 NRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT--FDGS--------- 466
Query: 184 ALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKE-----PISTIIY 238
DLR + + I+ I + I E + I+
Sbjct: 467 --------------DLRVLSGS--IS----ERI---VDCIIRLPVKWETTTQFKATHIL- 502
Query: 239 RAD---------QALYVAK-KSGRN-RVVCFSDIENNT 265
D L + K G RV+ ++ N
Sbjct: 503 --DFGPGGASGLGVL-THRNKDGTGVRVIVAGTLDINP 537
Score = 39.5 bits (92), Expect = 9e-04
Identities = 35/272 (12%), Positives = 69/272 (25%), Gaps = 94/272 (34%)
Query: 18 NLESFSPHTFMIYFSIFFSIFIATVIFIA-----NIFLFYIGLTPFYGLEYILVENLSLV 72
+ + + S+ + + T F F + P + + +
Sbjct: 5 STRPLTLS----HGSLEHVLLVPTASFFIASQLQEQFNKIL---PEPTEGFAADDEPTTP 57
Query: 73 IISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLN------------HSAFIS 120
L+ ++ G + + S L+ L H+ +
Sbjct: 58 -----AELVGKFL-GYVSSLVEPS----KVGQFDQVLNLCLTEFENCYLEGNDIHA-LAA 106
Query: 121 SLGSYNEKLSIVFFDI--DYFK---QINDNFGHPVGDKVIAFLSD------QLVVVFG-- 167
L N+ + ++ +Y F A QLV +FG
Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS---ALFRAVGEGNAQLVAIFGGQ 163
Query: 168 -----------------TPMFVGRLGGEEFAAAA-----LGSSEQEAAILAN---DLRKI 202
VG L +A L + +A + ++ +
Sbjct: 164 GNTDDYFEELRDLYQTYHV-LVGDL----IKFSAETLSELIRTTLDAEKVFTQGLNILEW 218
Query: 203 IENSQINISSGPSIHITISAGIAERCHKEPIS 234
+EN S+ P +S PIS
Sbjct: 219 LENP----SNTPDKDYLLSI---------PIS 237
>3mkt_A Multi antimicrobial extrusion protein (Na(+)/drug antiporter)
MATE-like MDR efflux...; multidrug transporter,
cation-bound, transport protein; 3.65A {Vibrio cholerae}
PDB: 3mku_A
Length = 460
Score = 28.2 bits (62), Expect = 2.1
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 154 VIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSS 188
+IA ++ + T + G + + AA ++ +S
Sbjct: 22 LIASVAQTGMGFVDT-IMAGGVSAIDMAAVSIAAS 55
>3ixz_A Potassium-transporting ATPase alpha; ION pump, H+, K+-ATPase,
P-type ATPase, membrane protein, hydrolase, aluminium
fluoride, ATP-binding; 6.50A {Sus scrofa} PDB: 1iwc_A
1iwf_A
Length = 1034
Score = 27.8 bits (61), Expect = 2.6
Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 7/57 (12%)
Query: 28 MIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGY 84
I +++ +I T I + L IL L I S+ L Y
Sbjct: 785 SIAYTLTKNIPELTPYLIYITVSVPLPLGCI----TILFIEL---CTDIFPSVSLAY 834
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 2ziy_A*
Length = 448
Score = 27.3 bits (59), Expect = 4.2
Identities = 15/93 (16%), Positives = 28/93 (30%), Gaps = 15/93 (16%)
Query: 1 MTRSLKDFLSIW-----LCHEKNLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGL 55
M R L+D + W + H E + Y F + N + Y+
Sbjct: 1 MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT 60
Query: 56 ------TPFYGLEYILVENLSLVIISITISLLL 82
TP + + NL+ + ++
Sbjct: 61 KTKSLQTPA----NMFIINLAFSDFTFSLVNGF 89
>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A
resolution, N-formylmethionine, alpha subunit; HET: FME;
2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1
c.10.2.2 PDB: 1ltx_A*
Length = 567
Score = 27.0 bits (59), Expect = 4.8
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 90 LKELFISYNRISQLSRIDCLSGLLN 114
L+EL + NR+ Q + I L
Sbjct: 510 LQELLLCNNRLQQSAAIQPLVSCPR 534
>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine
disulfide, MARR-family transcriptional regulator,
DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB:
3hse_A 3hrm_A
Length = 140
Score = 26.0 bits (57), Expect = 9.9
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 183 AALGSSEQEAAILANDLRKIIEN 205
SE+EA+ + N+LR +
Sbjct: 116 NEFNISEREASDIINNLRNFVSK 138
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.326 0.142 0.409
Gapped
Lambda K H
0.267 0.0497 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,271,212
Number of extensions: 105896
Number of successful extensions: 511
Number of sequences better than 10.0: 1
Number of HSP's gapped: 477
Number of HSP's successfully gapped: 57
Length of query: 266
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 175
Effective length of database: 3,487,026
Effective search space: 610229550
Effective search space used: 610229550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.9 bits)