RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9602
(239 letters)
>2nuw_A 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho aldolase; TIM
barrel, lyase; 1.80A {Sulfolobus acidocaldarius dsm 639}
PDB: 2nux_A 2nuy_A
Length = 288
Score = 59.1 bits (144), Expect = 1e-10
Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 5/106 (4%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
VNGTTG G +++ E++ NL A ++ Q+G +V+EL K + +++
Sbjct: 39 VNGTTGLGPALSKDEKRQNLNALYDVTHK----LIFQVGSLNLNDVMELVKFSNEMDILG 94
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
V +F + L Y ++ + L+ Y+ P T +
Sbjct: 95 VSSHSPYYFPRLPEKFLAKYYEEIARISS-HSLYIYNYPAATGYDI 139
>1w3i_A EDA, 2-keto-3-deoxy gluconate aldolase; archaeal metabolism,
pyruvate; 1.7A {Sulfolobus solfataricus} SCOP: c.1.10.1
PDB: 1w37_A 1w3n_A* 1w3t_A* 2yda_A*
Length = 293
Score = 54.9 bits (133), Expect = 3e-09
Identities = 28/106 (26%), Positives = 52/106 (49%), Gaps = 5/106 (4%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
VNGTTG G S++ E+ NL+A ++ Q+GG + + LAK ++ ++
Sbjct: 39 VNGTTGLGPSLSPEEKLENLKAVYDVTNK----IIFQVGGLNLDDAIRLAKLSKDFDIVG 94
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
+ ++ S + LV Y + + E +P P++ Y+ P T +
Sbjct: 95 IASYAPYYYPRMSEKHLVKYFKTLCEVSP-HPVYLYNYPTATGKDI 139
>3b4u_A Dihydrodipicolinate synthase; structural genomics, PSI-2, MC
protein structure initiative, midwest center for
structural genomics; 1.20A {Agrobacterium tumefaciens
str}
Length = 294
Score = 52.7 bits (127), Expect = 2e-08
Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 3/106 (2%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVL 194
GTTGEG S+ + ER+ L +++ ++ + ++ + + A + +L
Sbjct: 45 GTTGEGCSVGSRERQAILSSFIAAGI-APSRIVTGVLVDSIEDAADQSAEALNAGARNIL 103
Query: 195 CLPELFFTPASVEDLVDYLRDVGEA--APATPLFYYHIPMFTRVTL 238
P +F S + L + V A + Y+IP T VTL
Sbjct: 104 LAPPSYFKNVSDDGLFAWFSAVFSKIGKDARDILVYNIPSVTMVTL 149
>3qfe_A Putative dihydrodipicolinate synthase family PROT; seattle
structural genomics center for infectious disease, S
coccidioides, valley fever; 2.35A {Coccidioides immitis}
Length = 318
Score = 50.7 bits (122), Expect = 9e-08
Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 3/100 (3%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
+ GT E +T ER + F +M +G ++V+E A +
Sbjct: 51 ILGTNAEAFLLTREERAQLIATARKAVGPD-FPIMAGVGAHSTRQVLEHINDASVAGANY 109
Query: 193 VLCLPELFFTPASVEDLV-DYLRDVGEAAPATPLFYYHIP 231
VL LP +F A+ ++ + DV +P P+ Y+ P
Sbjct: 110 VLVLPPAYFGKATTPPVIKSFFDDVSCQSP-LPVVIYNFP 148
>3dz1_A Dihydrodipicolinate synthase; lysine biosynthesis, pyruvate, TIM
barrel, NYSGXRC, PSI2, structural genomics; 1.87A
{Rhodopseudomonas palustris}
Length = 313
Score = 49.5 bits (119), Expect = 2e-07
Identities = 23/107 (21%), Positives = 38/107 (35%), Gaps = 5/107 (4%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V G GE + AE + ++ AK V+V + F + LA+ +
Sbjct: 48 VLGILGEAPKLDAAEAEAVATRFIKRAK--SMQVIVGVSAPGFAAMRRLARLSMDAGAAG 105
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPAT-PLFYYHIPMFTRVTL 238
V+ P + + E + Y R EA P P+ V +
Sbjct: 106 VMIAP--PPSLRTDEQITTYFRQATEAIGDDVPWVLQDYPLTLSVVM 150
>3eb2_A Putative dihydrodipicolinate synthetase; lysine biosynthesis,
pyruvate, TIM barrel, NYSGXRC, PSI2., structural
genomics; HET: PGE; 2.04A {Rhodopseudomonas palustris}
Length = 300
Score = 49.1 bits (118), Expect = 3e-07
Identities = 28/106 (26%), Positives = 45/106 (42%), Gaps = 3/106 (2%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
G+TGE + TA+R+ + A + A+ V+ + T + V AK E L
Sbjct: 44 PLGSTGEFAYLGTAQREAVVRATIEAAQ-RRVPVVAGVASTSVADAVAQAKLYEKLGADG 102
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
+L + E +F + Y R + +A P+ Y P F R L
Sbjct: 103 ILAILEAYFPL-KDAQIESYFRAIADAVE-IPVVIYTNPQFQRSDL 146
>2r91_A 2-keto-3-deoxy-(6-phospho-)gluconate aldolase; TIM barrel,
thermophilic, lyase; 2.00A {Thermoproteus tenax} PDB:
2r94_A
Length = 286
Score = 48.3 bits (116), Expect = 6e-07
Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 15/104 (14%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GTTG G +++ E+ +A + A+ V+VQ+ E + LAK+AES A
Sbjct: 38 VAGTTGLGPALSLQEKMELTDAATSAARR----VIVQVASLNADEAIALAKYAESRGAEA 93
Query: 193 VLCLPELFFTP-----ASVEDLVDYLRDVGEAAPATPLFYYHIP 231
V L P S + Y RD+ A P+F Y+ P
Sbjct: 94 VASL-----PPYYFPRLSERQIAKYFRDLCSAVS-IPVFLYNYP 131
>1f6k_A N-acetylneuraminate lyase; beta barrel; 1.60A {Haemophilus
influenzae} SCOP: c.1.10.1 PDB: 1f5z_A 1f6p_A 1f73_A*
1f74_A* 1f7b_A*
Length = 293
Score = 47.9 bits (115), Expect = 7e-07
Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 11/103 (10%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V G+TGE ++T E+K EAK ++ Q+G +E VEL K+A L
Sbjct: 44 VGGSTGENFMLSTEEKKEIFRIAKDEAK-DQIALIAQVGSVNLKEAVELGKYATELGYDC 102
Query: 193 VLCLPELFFTP----ASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+ + TP S ++ Y + + + Y IP
Sbjct: 103 LSAV-----TPFYYKFSFPEIKHYYDTIIAETG-SNMIVYSIP 139
>3fkr_A L-2-keto-3-deoxyarabonate dehydratase; DHDPS/NAL family, complex,
pyruvate, lyase; HET: KPI; 1.80A {Azospirillum
brasilense} PDB: 3fkk_A
Length = 309
Score = 47.8 bits (114), Expect = 1e-06
Identities = 15/101 (14%), Positives = 30/101 (29%), Gaps = 4/101 (3%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
+ E ++T ER + + V+V Q + A+ L
Sbjct: 48 ILANFSEQFAITDDERDVLTRTILEHVA-GRVPVIVTTSHYSTQVCAARSLRAQQLGAAM 106
Query: 193 VLCLPELF--FTPASVEDLVDYLRDVGEAAPATPLFYYHIP 231
V+ +P + ++ V +A P+ P
Sbjct: 107 VMAMPPYHGATFRVPEAQIFEFYARVSDAIA-IPIMVQDAP 146
>2wkj_A N-acetylneuraminate lyase; directed evolution, sialic acid
mimetics, aldolase, S base, carbohydrate metabolism,
N-acetylneuraminic acid LYAS; HET: KPI PYR; 1.45A
{Escherichia coli} PDB: 2wnq_A 2xfw_A* 2wpb_A* 2wnz_A*
2ygy_A* 2wo5_A* 2wnn_A* 3lbm_A 3lbc_A 3lcf_A 3lcl_A
3lcg_A 3lch_A 3lci_A 1hl2_A 1fdy_A 1fdz_A 1nal_1 3lcx_A
3lcw_A
Length = 303
Score = 43.5 bits (103), Expect = 2e-05
Identities = 29/101 (28%), Positives = 46/101 (45%), Gaps = 10/101 (9%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVL 194
G+TGE + +ER+ LE EAK ++ +G E +LA A+ AV
Sbjct: 53 GSTGEAFVQSLSEREQVLEIVAEEAK-GKIKLIAHVGCVSTAESQQLAASAKRYGFDAVS 111
Query: 195 CLPELFFTP----ASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+ TP S E+ D+ R + ++A P+ Y+IP
Sbjct: 112 AV-----TPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIP 147
>2hmc_A AGR_L_411P, dihydrodipicolinate synthase; alpha-beta barrel (TIM
barrel), structural genomics, PSI-2, structure
initiative; HET: MSE; 1.90A {Agrobacterium tumefaciens
str}
Length = 344
Score = 42.7 bits (101), Expect = 5e-05
Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 4/104 (3%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVL 194
G+ G+ +T +R +E G V+V G V A HA+ + ++
Sbjct: 68 GSMGDWPLLTDEQRMEGVE----RLVKAGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLM 123
Query: 195 CLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
+P + + + + + + AAP P Y+ P + T
Sbjct: 124 VIPRVLSRGSVIAAQKAHFKAILSAAPEIPAVIYNSPYYGFATR 167
>3na8_A Putative dihydrodipicolinate synthetase; lyase; HET: MSE; 1.85A
{Pseudomonas aeruginosa}
Length = 315
Score = 41.4 bits (98), Expect = 1e-04
Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 11/103 (10%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
G+TGEG ++ E ++ + H +V + + V A+ AESL A
Sbjct: 64 PLGSTGEGAYLSDPEWDEVVDFTLKTVA-HRVPTIVSVSDLTTAKTVRRAQFAESLGAEA 122
Query: 193 VLCLPELFFTP----ASVEDLVDYLRDVGEAAPATPLFYYHIP 231
V+ L + ++ + R VGEA P+ Y+ P
Sbjct: 123 VMVL-----PISYWKLNEAEVFQHYRAVGEAIG-VPVMLYNNP 159
>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 = 41.4 bits (96), Expect = 2e-04
Identities = 28/227 (12%), Positives = 64/227 (28%), Gaps = 59/227 (25%)
Query: 8 VTTITTGGGSGRQNSAEEEAEKAAQTIAQRARRGGHDRS---KRFTQTRKVDNHHNSRPA 64
T+ + Q EE + + + S + + + R D +N
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR--DRLYNDNQV 125
Query: 65 ASQ--IRRKKKRKRRRKRLRNAHGEVVMIDPSDLPKRAKWTIIITAGLLLLTCML----- 117
++ + R + + R+ L + AK ++ G +L
Sbjct: 126 FAKYNVSRLQPYLKLRQALLEL-------------RPAKN--VLIDG------VLGSGKT 164
Query: 118 -LVGITLRMAPIIDQMVNGTTGEGVSMTTAERKLNLEAWMTEAKTH-GFTVMVQIGGTCF 175
+ + +M W+ + TV+ + +
Sbjct: 165 WVALDVCLSYKVQCKMDFKI-----------------FWLNLKNCNSPETVLEMLQKLLY 207
Query: 176 Q---EVVELAKHAES--LNVHAV-LCLPELFFTPASVEDLVDYLRDV 216
Q + H+ + L +H++ L L + L+ L +V
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV-LLNV 253
Score = 41.4 bits (96), Expect = 2e-04
Identities = 40/244 (16%), Positives = 73/244 (29%), Gaps = 61/244 (25%)
Query: 18 GRQNSAEEEAEKAAQTIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRR 77
NS E E Q + + RS D+ N + I+ + +R +
Sbjct: 190 KNCNSPETVLEML-QKLLYQIDPNWTSRS---------DHSSNIKLRIHSIQAELRRLLK 239
Query: 78 RKRLRNAHGEVVMIDPSDLPKRAKWTIIITAGLLLLTCMLLVGITLRMAPIIDQMVNGTT 137
K N +V+++ + A L+C +L+ T R + D + TT
Sbjct: 240 SKPYENCL--LVLLNVQN-----AK--AWNA--FNLSCKILL--TTRFKQVTDFLSAATT 286
Query: 138 GE------GVSMTTAERKLNLEAWMT--------EAKTHGFTVMVQIGGTCFQEVVELAK 183
+++T E K L ++ E T + I ++ +
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII-AESIRDGLATWD 345
Query: 184 HAESLNVHAV-----LCLPELFFTPASVEDLVDYL----RDVGEAAPATPLFYYHIPMFT 234
+ + +N + L L PA + D L HIP
Sbjct: 346 NWKHVNCDKLTTIIESSLNVL--EPAEYRKMFDRLSVFPPSA------------HIPTIL 391
Query: 235 RVTL 238
+
Sbjct: 392 LSLI 395
>3s5o_A 4-hydroxy-2-oxoglutarate aldolase, mitochondrial; beta barrel,
schiff base, hydroxyproline metabolis; HET: KPI; 1.97A
{Homo sapiens} PDB: 3s5n_A
Length = 307
Score = 40.8 bits (96), Expect = 2e-04
Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 3/100 (3%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V G+ GE +T++ER + ++ G Q VE+ + A
Sbjct: 54 VQGSNGEFPFLTSSERLEVVSRVRQAMP-KNRLLLAGSGCESTQATVEMTVSMAQVGADA 112
Query: 193 VLCL-PELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+ + P + S L+ + V + +P P+ Y +P
Sbjct: 113 AMVVTPCYYRGRMSSAALIHHYTKVADLSP-IPVVLYSVP 151
>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 = 41.2 bits (96), Expect = 2e-04
Identities = 22/106 (20%), Positives = 33/106 (31%), Gaps = 36/106 (33%)
Query: 152 LEAWMTEAKTHGFT---VMVQIGG--TCFQEVV-----ELAKHAESLNVHAVLCLPELFF 201
L ++ AK GFT + + G Q +V ES V + LFF
Sbjct: 246 LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF 305
Query: 202 --------------TPASVEDLVDYLRDVGEAAPATPLFYYHIPMF 233
P+ +ED + + E P+ PM
Sbjct: 306 IGVRCYEAYPNTSLPPSILEDSL----ENNEGVPS--------PML 339
Score = 38.1 bits (88), Expect = 0.002
Identities = 50/283 (17%), Positives = 78/283 (27%), Gaps = 118/283 (41%)
Query: 15 GGSGRQNSAE--EE---------------AEKAAQTIAQRARRGGHDRSKRFTQTRKVD- 56
GG G N+ + EE + +A+T+++ R D K FTQ +
Sbjct: 161 GGQG--NTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIR-TTLDAEKVFTQGLNILE 217
Query: 57 --NHHNSRP--------AAS-------QIRRKKKRKRRRKRLRNAHGEVVM----IDPSD 95
+ ++ P S Q+ AH V P +
Sbjct: 218 WLENPSNTPDKDYLLSIPISCPLIGVIQL---------------AHYVVTAKLLGFTPGE 262
Query: 96 LPKRAKWTIIITAGLLLLTCMLLVGITLRMAPIIDQMVNGTTGE---------------- 139
L K + GL+ A I + + E
Sbjct: 263 LRSYLKGATGHSQGLV-------------TAVAIAE---TDSWESFFVSVRKAITVLFFI 306
Query: 140 GVSMTTAERKLNLEAWMT-EAKTHGFTV---MVQIGGTCFQEVVELAKHAESLNVHAVLC 195
GV A +L + ++ + V M+ I QE V+ + N H
Sbjct: 307 GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN-LTQEQVQ--DYVNKTNSH---- 359
Query: 196 LPE-------LF-----F----TPASVEDLVDYLRDVGEAAPA 222
LP L P S+ L LR AP+
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKA--KAPS 400
>2pcq_A Putative dihydrodipicolinate synthase; lyase, lysine biosynthesis,
dihydrodipicoliante, S genomics, NPPSFA; 2.10A {Thermus
thermophilus}
Length = 283
Score = 39.8 bits (94), Expect = 4e-04
Identities = 25/104 (24%), Positives = 36/104 (34%), Gaps = 18/104 (17%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V G+ GEGV +T ER L A +V + + A++ A
Sbjct: 37 VYGSNGEGVHLTPEERARGLRALRPRKP-----FLVGLMEETLPQAEGALLEAKAAGAMA 91
Query: 193 VLCLPELFFTPA-----SVEDLVDYLRDVGEAAPATPLFYYHIP 231
+L P L+ Y + A PLF YH+P
Sbjct: 92 LLAT-----PPRYYHGSLGAGLLRYYEAL---AEKMPLFLYHVP 127
>3m5v_A DHDPS, dihydrodipicolinate synthase; TIM barrel, csgid, amino-acid
biosynthesis, diaminopimelate biosynthesis, lyase,
lysine biosynthesis; HET: MSE; 1.80A {Campylobacter
jejuni} PDB: 3ler_A*
Length = 301
Score = 39.0 bits (92), Expect = 6e-04
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++T E + +E + K G V V + G E V LAK A+
Sbjct: 49 GTTGESATLTHEEHRTCIEIAVETCK--GTKVKV-LAGAGSNATHEAVGLAKFAKEHGAD 105
Query: 192 AVLC 195
+L
Sbjct: 106 GILS 109
>2v9d_A YAGE; dihydrodipicolinic acid synthase, N-acetyl neuraminate lyase,
NAL, lyase, DHDPS, prophage; 2.15A {Escherichia coli}
PDB: 2v8z_A 3nev_A* 3n2x_A*
Length = 343
Score = 37.6 bits (88), Expect = 0.002
Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 11/101 (10%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVL 194
G+ GE + ERK + V++ GGT +E +EL++HA+ ++
Sbjct: 73 GSGGEFSQLGAEERKAIARFAIDHVD-RRVPVLIGTGGTNARETIELSQHAQQAGADGIV 131
Query: 195 CLPELFFTP----ASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+ P S +L+ Y V ++ P+ Y+ P
Sbjct: 132 VI-----NPYYWKVSEANLIRYFEQVADSVT-LPVMLYNFP 166
>3l21_A DHDPS, dihydrodipicolinate synthase; DAPA, dimer, RV2753C, lysine
biosynthesis, amino-acid biosynthesis, diaminopimelate
biosynthesis; HET: KPI CME; 2.10A {Mycobacterium
tuberculosis} PDB: 1xxx_A
Length = 304
Score = 37.0 bits (86), Expect = 0.003
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V+GTTGE + T E K+ L + EA V+ G + LAK + H
Sbjct: 55 VSGTTGESPTTTDGE-KIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHG 113
Query: 193 VL 194
+L
Sbjct: 114 LL 115
>3cpr_A Dihydrodipicolinate synthetase; (beta/alpha)8-barrel fold with A
C-terminal alpha-helical segment, amino-acid
biosynthesis, cytoplasm; HET: MCL; 2.20A
{Corynebacterium glutamicum}
Length = 304
Score = 37.0 bits (86), Expect = 0.003
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
+ GTTGE + T AE KL L + E ++ +G + VELA+ A S
Sbjct: 56 LAGTTGESPTTTAAE-KLELLKAVREEVGDRAKLIAGVGTNNTRTSVELAEAAASAGADG 114
Query: 193 VL 194
+L
Sbjct: 115 LL 116
>3si9_A DHDPS, dihydrodipicolinate synthase; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, TIM barrel; 2.10A {Bartonella henselae}
Length = 315
Score = 35.6 bits (83), Expect = 0.009
Identities = 24/64 (37%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++T E K +E + + V V + G E VELAKHAE
Sbjct: 64 GTTGESPTLTHEEHKRIIELCVEQVAKR---VPV-VAGAGSNSTSEAVELAKHAEKAGAD 119
Query: 192 AVLC 195
AVL
Sbjct: 120 AVLV 123
>2vc6_A MOSA, dihydrodipicolinate synthase; DHDPS, TIM barrel, schiff base,
lyase; HET: MCL; 1.95A {Sinorhizobium meliloti}
Length = 292
Score = 35.3 bits (82), Expect = 0.011
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE +++ +E + +E + A V V I G E + +HA++
Sbjct: 42 GTTGESPTLSKSEHEQVVEITIKTANGR---VPV-IAGAGSNSTAEAIAFVRHAQNAGAD 97
Query: 192 AVLC 195
VL
Sbjct: 98 GVLI 101
>1xky_A Dihydrodipicolinate synthase; TIM barrel, , lysine
biosynthesis;spine, lyase; 1.94A {Bacillus anthracis}
SCOP: c.1.10.1 PDB: 1xl9_A 3hij_A*
Length = 301
Score = 35.2 bits (82), Expect = 0.012
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GTTGE ++T+ E K+ L + V+ G ++L K A + V A
Sbjct: 52 VGGTTGESPTLTSEE-KVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDA 110
Query: 193 VL 194
V+
Sbjct: 111 VM 112
>2r8w_A AGR_C_1641P; APC7498, dihydrodipicolinate synthase, agrobacterium
tumefac C58, structural genomics, PSI-2; HET: MSE; 1.80A
{Agrobacterium tumefaciens str}
Length = 332
Score = 35.3 bits (82), Expect = 0.012
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVL 194
G+TG + +T ER+ +EA T + T+M IG E V LAK AE+ A+L
Sbjct: 76 GSTGIYMYLTREERRRAIEAAATILR-GRRTLMAGIGALRTDEAVALAKDAEAAGADALL 134
>1o5k_A DHDPS, dihydrodipicolinate synthase; TM1521, structural genomics, J
protein structure initiative, joint center for
structural G lyase; HET: MCL; 1.80A {Thermotoga
maritima} SCOP: c.1.10.1 PDB: 3pb2_A 3pb0_A
Length = 306
Score = 35.0 bits (81), Expect = 0.013
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++ ER+ + + + V I G ++ ++L K AE L +
Sbjct: 54 GTTGESPTVNEDEREKLVSRTLEIVDGK---IPV-IVGAGTNSTEKTLKLVKQAEKLGAN 109
Query: 192 AVL 194
VL
Sbjct: 110 GVL 112
>4dpp_A DHDPS 2, dihydrodipicolinate synthase 2, chloroplastic; amino-acid
biosynthesis, (S)-lysine biosynthesis VIA DAP PAT
(beta/alpha)8-barrel; 2.00A {Arabidopsis thaliana} PDB:
4dpq_A*
Length = 360
Score = 35.0 bits (81), Expect = 0.014
Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 19/104 (18%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGEG M+ E + + + + V IG T +E + + ++ +H
Sbjct: 101 GTTGEGQLMSWDEHIMLIGHTVNCFGGS---IKV-IGNTGSNSTREAIHATEQGFAVGMH 156
Query: 192 AVLCLPELFFTP----ASVEDLVDYLRDVGEAAPATPLFYYHIP 231
A L + P S+E L+ + + V P Y++P
Sbjct: 157 AALHI-----NPYYGKTSIEGLIAHFQSV---LHMGPTIIYNVP 192
>2ehh_A DHDPS, dihydrodipicolinate synthase; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; 1.90A {Aquifex aeolicus}
Length = 294
Score = 35.2 bits (82), Expect = 0.014
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++T E + +E + A + V I GT E V L HA+ +
Sbjct: 42 GTTGESPTLTFEEHEKVIEFAVKRAAGR---IKV-IAGTGGNATHEAVHLTAHAKEVGAD 97
Query: 192 AVL 194
L
Sbjct: 98 GAL 100
>2rfg_A Dihydrodipicolinate synthase; beta barrel, amino-acid biosynthesis,
diaminopimelate biosyn lyase, lysine biosynthesis,
schiff base; 1.50A {Hahella chejuensis}
Length = 297
Score = 34.8 bits (81), Expect = 0.017
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++T E K + +A+ V V I G E V A+HA+
Sbjct: 42 GTTGESPTLTEEEHKRVVALVAEQAQGR---VPV-IAGAGSNNPVEAVRYAQHAQQAGAD 97
Query: 192 AVL 194
AVL
Sbjct: 98 AVL 100
>3tak_A DHDPS, dihydrodipicolinate synthase; TIM barrel, lysine
biosynthesis, pyruvate, lyase; 1.42A {Acinetobacter
baumannii} PDB: 3pud_A* 3pue_A* 3pul_A 3rk8_A 3tce_A*
3tdf_A 3u8g_A 3uqn_A 4dxv_A
Length = 291
Score = 34.4 bits (80), Expect = 0.020
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE +++ E ++ + A + + I GT +E +EL K A+ L
Sbjct: 43 GTTGEASTLSMEEHTQVIKEIIRVANKR---IPI-IAGTGANSTREAIELTKAAKDLGAD 98
Query: 192 AVL 194
A L
Sbjct: 99 AAL 101
>3flu_A DHDPS, dihydrodipicolinate synthase; TIM barrel, beta-alpha-barrel,
amino-acid biosynthesis, diaminopimelate biosynthesis;
2.00A {Neisseria meningitidis serogroup B}
Length = 297
Score = 34.4 bits (80), Expect = 0.021
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE +++ E +EA + V V I GT E + L++ AE
Sbjct: 49 GTTGESATLSVEEHTAVIEAVVKHVAKR---VPV-IAGTGANNTVEAIALSQAAEKAGAD 104
Query: 192 AVL 194
L
Sbjct: 105 YTL 107
>2yxg_A DHDPS, dihydrodipicolinate synthase; MJ0244, TIM beta/alpha-barrel
fold, structural genomics, NPPSFA; 2.20A
{Methanocaldococcus jannaschii DSM2661}
Length = 289
Score = 34.4 bits (80), Expect = 0.025
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE +++ E K +E + V V I G C +E +EL+ AE +
Sbjct: 42 GTTGESPTLSHEEHKKVIEKVVDVVNGR---VQV-IAGAGSNCTEEAIELSVFAEDVGAD 97
Query: 192 AVLC 195
AVL
Sbjct: 98 AVLS 101
>3qze_A DHDPS, dihydrodipicolinate synthase; alpha beta barrel,
cytoplasmic; 1.59A {Pseudomonas aeruginosa} PDB: 3puo_A*
3noe_A 3ps7_A* 3s8h_A
Length = 314
Score = 34.5 bits (80), Expect = 0.025
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++ E + + + K + V I GT +E V L + A+S
Sbjct: 65 GTTGESATLDVEEHIQVIRRVVDQVKGR---IPV-IAGTGANSTREAVALTEAAKSGGAD 120
Query: 192 AVL 194
A L
Sbjct: 121 ACL 123
>3a5f_A Dihydrodipicolinate synthase; TIM barrel, enzyme, amino-acid
biosynthesis, cytoplasm, diaminopimelate biosynthesis,
lyase; HET: KPI; 1.19A {Clostridium botulinum A} PDB:
3bi8_A* 3ird_A*
Length = 291
Score = 33.8 bits (78), Expect = 0.039
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE +MT ERK ++ + + + V I GT + ++K AES+ V
Sbjct: 43 GTTGEATTMTETERKETIKFVIDKVNKR---IPV-IAGTGSNNTAASIAMSKWAESIGVD 98
Query: 192 AVL 194
+L
Sbjct: 99 GLL 101
>2ojp_A DHDPS, dihydrodipicolinate synthase; dimer, lysine biosynthe lyase;
HET: KGC GOL; 1.70A {Escherichia coli} PDB: 1yxc_A
1dhp_A 1yxd_A* 2ats_A* 3du0_A* 3c0j_A* 3ubs_A* 4eou_A*
3i7q_A* 3i7r_A* 3i7s_A* 2pur_A* 1s5v_A 1s5w_A 1s5t_A
3den_A* 2a6l_A 2a6n_A 3g0s_A
Length = 292
Score = 33.4 bits (77), Expect = 0.053
Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 7/63 (11%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLNVH 191
GTTGE ++ E + + A + V I GT E + L + +
Sbjct: 43 GTTGESATLNHDEHADVVMMTLDLADGR---IPV-IAGTGANATAEAISLTQRFNDSGIV 98
Query: 192 AVL 194
L
Sbjct: 99 GCL 101
>3daq_A DHDPS, dihydrodipicolinate synthase; lysine biosynthesis, amino-ACI
biosynthesis, diaminopimelate biosynthesis, lyase,
schiff B; 1.45A {Staphylococcus aureus} PDB: 3di1_A
3di0_A
Length = 292
Score = 33.2 bits (77), Expect = 0.057
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLN 189
VNGTT E ++TT E++L L+ + V V I GT ++ ++ + A++L
Sbjct: 42 VNGTTAESPTLTTDEKELILKTVIDLVDKR---VPV-IAGTGTNDTEKSIQASIQAKALG 97
Query: 190 VHAVL 194
A++
Sbjct: 98 ADAIM 102
>3e96_A Dihydrodipicolinate synthase; structural genomics, nysgrc, target
9375C, operon, PSI-2; 1.80A {Bacillus clausii ksm-k16}
Length = 316
Score = 32.2 bits (74), Expect = 0.13
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT--CFQEVVELAKHAESLNV 190
G T E +++ E K + + +V + G +EL A++
Sbjct: 52 PCGNTSEFYALSLEEAKEEVRRTVEYVHGR---ALV-VAGIGYATSTAIELGNAAKAAGA 107
Query: 191 HAVL 194
AV+
Sbjct: 108 DAVM 111
>3d0c_A Dihydrodipicolinate synthase; lysine biosynthesis, pyruvate, TIM
barrel, NYSGXRC, PSI-2, structural genomics; 1.90A
{Oceanobacillus iheyensis HTE831}
Length = 314
Score = 31.8 bits (73), Expect = 0.16
Identities = 15/64 (23%), Positives = 20/64 (31%), Gaps = 6/64 (9%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT--CFQEVVELAKHAESLNV 190
NG TGE ++T E K V + G +EL K A
Sbjct: 52 PNGNTGEFYALTIEEAKQVATRVTELVNGR---ATV-VAGIGYSVDTAIELGKSAIDSGA 107
Query: 191 HAVL 194
V+
Sbjct: 108 DCVM 111
>3sdb_A Glutamine-dependent NAD(+) synthetase; glutamine-amidotransferase,
glutaminase, glutamine-dependent synthetase, ligase;
2.00A {Mycobacterium tuberculosis} PDB: 3seq_A* 3sez_A*
3szg_A* 3dla_A* 3syt_A*
Length = 680
Score = 31.3 bits (71), Expect = 0.29
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 176 QEVVELAKHAESLNVHAVLCLPELFFTPASVEDLV---DYLRDVGEA 219
V+++A+ + PEL + S+ED++ L V +A
Sbjct: 32 ASVLDMARACHDDGAA-LAVFPELTLSGYSIEDVLLQDSLLDAVEDA 77
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.7 bits (66), Expect = 0.63
Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 3/56 (5%)
Query: 19 RQNSAEEEAEKAAQTIAQRARRGGHDRSKRF-TQTRKVDNHHNSRPAASQIRRKKK 73
R + ++ Q ++A++ + ++R Q K N N+R A ++
Sbjct: 97 RLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEK--NKINNRIADKAFYQQPD 150
Score = 26.3 bits (57), Expect = 8.8
Identities = 7/71 (9%), Positives = 26/71 (36%), Gaps = 14/71 (19%)
Query: 20 QNSAEEEA-----EKAAQTIAQRARRGGHDRSKRFTQTRK-VDNHHNSRPAASQIRRKKK 73
+ + E E+ E+ + + + + + +K ++ + R+ ++
Sbjct: 79 RLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQ--------RQSEQ 130
Query: 74 RKRRRKRLRNA 84
++ + R A
Sbjct: 131 VEKNKINNRIA 141
>3h5d_A DHDPS, dihydrodipicolinate synthase; lysine biosynthesis, amino-ACI
biosynthesis, schiff base, cytoplasm, diaminopimelate
biosy lyase; HET: MES; 1.99A {Streptococcus pneumoniae}
Length = 311
Score = 29.1 bits (66), Expect = 1.3
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKH-AESLNVH 191
+ GTT E ++T E +L L A + + ++ +G ++ +E K AE
Sbjct: 47 LAGTTAESPTLTHDE-ELELFAAVQKVVNGRVPLIAGVGTNDTRDSIEFVKEVAEFGGFA 105
Query: 192 AVL 194
A L
Sbjct: 106 AGL 108
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 29.1 bits (65), Expect = 1.4
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 19 RQNSAEEEAEKAAQTIAQRAR-RGGHDRSKRFTQTRKVDNHHNS-RPAASQIRRKKKRKR 76
++ E A AQ QR R R + ++ + D+ ++ R + K KR
Sbjct: 401 KKEEEERRARMEAQLKEQRERERKMRKAKENSEESGEFDDLVSALRSGEVFDKDLSKLKR 460
Query: 77 RRKRLRNAHGE 87
RKR+ N +
Sbjct: 461 NRKRITNQMTD 471
>3ilv_A Glutamine-dependent NAD(+) synthetase; protein structure initiative
II(PSI II), NYSGXRC, structural genomics; 1.79A
{Cytophaga hutchinsonii atcc 33406}
Length = 634
Score = 29.1 bits (66), Expect = 1.5
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 176 QEVVELAKHAESLNVHAVLCLPELFFTPASVEDLV---DYLRDVGEA 219
+ +++ + A++ NV +LCLPEL T EDL E
Sbjct: 25 KNILDAIEEAKNANVE-ILCLPELCITGYGCEDLFLTDWVAETAIEY 70
>3obv_E Protein diaphanous homolog 1; autoinhibition, actin, nucleation,
cytoskeleton, structural; HET: SUC; 2.75A {Mus musculus}
PDB: 3o4x_E 2bap_D
Length = 457
Score = 28.7 bits (64), Expect = 1.8
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 19 RQNSAEEEAEKAAQTIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRR 78
R A+E+AEK Q+ R D + +T +D+ + + + RRK+ ++
Sbjct: 395 RAKLAKEKAEKERLE-KQQKREQLIDMNAEGDETGVMDSLLEALQSGAAFRRKRGPRQVN 453
Query: 79 KR 80
++
Sbjct: 454 RK 455
Score = 26.8 bits (59), Expect = 7.9
Identities = 10/70 (14%), Positives = 24/70 (34%), Gaps = 8/70 (11%)
Query: 19 RQNSAEEEAEKAAQTIAQRARRGGHDRSKRFTQTRKVDNHHNS--------RPAASQIRR 70
R+ + K A+ A++ R + ++ + + A+ R+
Sbjct: 387 RETEEKMRRAKLAKEKAEKERLEKQQKREQLIDMNAEGDETGVMDSLLEALQSGAAFRRK 446
Query: 71 KKKRKRRRKR 80
+ R+ RK
Sbjct: 447 RGPRQVNRKA 456
>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM,
protein engineering, structural protein; HET: ADP; 2.80A
{Dictyostelium discoideum} SCOP: k.1.1.1
Length = 1010
Score = 28.1 bits (63), Expect = 2.9
Identities = 5/59 (8%), Positives = 19/59 (32%), Gaps = 1/59 (1%)
Query: 25 EEAEKAAQTIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRLRN 83
E+ + QT + +R ++ + + + + ++ + K+
Sbjct: 759 EQRLGSEQTKSDYLKRA-NELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKTEK 816
>1v54_A Cytochrome C oxidase polypeptide I; oxidoreductase; HET: FME TPO
HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: f.24.1.1 PDB: 1oco_A* 1occ_A* 1ocz_A* 1ocr_A*
1v55_A* 2dyr_A* 2dys_A* 2eij_A* 2eik_A* 2eil_A* 2eim_A*
2ein_A* 2occ_A* 2y69_A* 2ybb_L* 2zxw_A* 3abk_A* 3abl_A*
3abm_A* 3ag1_A* ...
Length = 514
Score = 26.8 bits (60), Expect = 7.1
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 102 WTIIITAGLLLLTCMLLVG-IT 122
W+++ITA LLLL+ +L IT
Sbjct: 186 WSVMITAVLLLLSLPVLAAGIT 207
>1nov_A Nodamura virus coat proteins; insect virus, icosahedral VIRU;
3.50A {Nodamura virus} SCOP: b.121.4.4
Length = 355
Score = 26.8 bits (58), Expect = 7.5
Identities = 11/49 (22%), Positives = 23/49 (46%)
Query: 45 RSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRLRNAHGEVVMIDP 93
+R R+ ++R + RR+ +R RR++R+ + + M P
Sbjct: 6 ARRRRAAPRQQQRQQSNRASNQPRRRRARRTRRQQRMAATNNMLKMSAP 54
>2gsm_A Cytochrome C oxidase subunit 1; transmembrane protein complex,
oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter
sphaeroides} SCOP: f.24.1.1 PDB: 1m56_A* 3dtu_A* 3fye_A*
3fyi_A* 1m57_A* 3oma_A* 3om3_A* 3omi_A* 3omn_A* 3hb3_A*
1ar1_A* 3ehb_A* 1qle_A*
Length = 566
Score = 26.9 bits (60), Expect = 7.6
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 102 WTIIITAGLLLLTCMLLVG-IT 122
W+I +TA L+LL +L G IT
Sbjct: 230 WSIFVTAWLILLALPVLAGAIT 251
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 25.4 bits (56), Expect = 8.8
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 12/38 (31%)
Query: 64 AASQIRRKKKRKRRRKRLRNAHGEVVMIDPSDLPKRAK 101
A + R +R R+ K+ DP + PKRA
Sbjct: 2 AGASDRTGVRRPRKAKK-----------DP-NAPKRAL 27
>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus
stearothermophilus} SCOP: c.55.4.1
Length = 120
Score = 25.6 bits (57), Expect = 9.3
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 66 SQIRRKKKRKRRRKRLRN 83
+++ R RK+R R+R
Sbjct: 3 TKVDRNAVRKKRHARIRK 20
>2i0k_A Oxidoreductase; MIX alpha beta, covalent FAD, flavoenzyme; HET:
FAD; 1.60A {Brevibacterium sterolicum} SCOP: d.58.32.3
d.145.1.1 PDB: 1i19_A*
Length = 561
Score = 26.7 bits (58), Expect = 9.4
Identities = 27/216 (12%), Positives = 56/216 (25%), Gaps = 32/216 (14%)
Query: 26 EAEKAAQTIAQRARRGGHDRSKRFTQTR----KVDNHHNSRPAASQIRRKKKRKRRRKRL 81
+T + G + + T KV ++P +S
Sbjct: 240 PKGADGRTFEKFVAESGGAEAIWYPFTEKPWMKVWTVSPTKPDSSNEVGSLGSAG----- 294
Query: 82 RNAHGEVVMIDPSDLPKRAKWTIIITAGLLLLTCMLLVGITLRMAPIIDQMVNGTTGEGV 141
+ G+ P ++ + + + + G +AP+ + T G+
Sbjct: 295 -SLVGKPPQAREVSGPYNYIFSDNLPEPITDMIGAINAGN-PGIAPLFGPAMYEITKLGL 352
Query: 142 SMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVLCLPELFF 201
+ T A + W + T A N+ V+
Sbjct: 353 AATNAN-----DIWGWSKDVQFYIK----ATTLRLTEGGGAVVTSRANIATVI------- 396
Query: 202 TPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVT 237
D ++ + E A F + P+ R
Sbjct: 397 -----NDFTEWFHERIEFYRAKGEFPLNGPVEIRCC 427
>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency
decline, ATP-binding, DNA DAMA repair, DNA-binding,
helicase, hydrolase; 1.95A {Escherichia coli} PDB:
2b2n_A* 4dfc_A
Length = 483
Score = 26.6 bits (59), Expect = 9.7
Identities = 4/16 (25%), Positives = 8/16 (50%)
Query: 69 RRKKKRKRRRKRLRNA 84
R +R++ +R N
Sbjct: 452 ERVARRRQDSRRTINP 467
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
0.320 0.132 0.382
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,690,652
Number of extensions: 223482
Number of successful extensions: 1161
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1115
Number of HSP's successfully gapped: 73
Length of query: 239
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 148
Effective length of database: 4,160,982
Effective search space: 615825336
Effective search space used: 615825336
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 (21.8 bits)
S2: 56 (25.3 bits)