RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780855|ref|YP_003065268.1| NADH dehydrogenase subunit D
[Candidatus Liberibacter asiaticus str. psy62]
(396 letters)
>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport,
respiratory chain, 4Fe- 4S, cell membrane, flavoprotein,
FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8}
PDB: 2fug_4* 3iam_4* 3ias_4* (4:109-308,4:384-409)
Length = 226
Score = 239 bits (612), Expect = 3e-64
Identities = 77/198 (38%), Positives = 116/198 (58%)
Query: 92 IPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRM 151
+P R + IRV+ +E+ R+ SHL+ + T +D+GALTP + F ERE ++ +E +G R
Sbjct: 1 VPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRF 60
Query: 152 HAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLED 211
H Y R GGV +D+P E V ++ + P +++ L + IF +R +G + E
Sbjct: 61 HHNYIRIGGVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEV 120
Query: 212 AWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVK 271
A G +G +R SG +D+RK+ PY Y FD+P+G+ GD +DR LVR+ EMRESVK
Sbjct: 121 AIDLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVK 180
Query: 272 IIRQCVNRLLGKNKVGPV 289
II+Q + RL P
Sbjct: 181 IIKQALERLEPGPVRDPN 198
Score = 36.6 bits (84), Expect = 0.006
Identities = 33/170 (19%), Positives = 57/170 (33%), Gaps = 29/170 (17%)
Query: 243 LDFDIPIGKHGDCY---DRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPK---- 295
+ D+P + + R+ E R G VG +
Sbjct: 70 VKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARG---VGVIPPEVAIDLGL 126
Query: 296 IVPPKRA-----DMKRSMESLIHHFKLYTE-GYHVPV---GEVYAAVEAPKGEFGVYLIS 346
RA D++++ + + Y + VP+ G+V+ + E +
Sbjct: 127 TGGSLRASGVNYDVRKA-----YPYSGYETYTFDVPLGERGDVFDRMLVRIRE-----MR 176
Query: 347 DGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
+ + R CKG Q+ D+ AI+ SLD V G+VDR
Sbjct: 177 ESVKIIKQALERLEPGPVRDPNPQACKGEQVPDMVAIIASLDPVMGDVDR 226
>1yq9_H Periplasmic [NIFE] hydrogenase large subunit;
oxidoreductase; 2.35A {Desulfovibrio gigas} (H:56-492)
Length = 437
Score = 194 bits (492), Expect = 2e-50
Identities = 35/329 (10%), Positives = 68/329 (20%), Gaps = 36/329 (10%)
Query: 46 HRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSE 105
+Q + A + P R R LY E
Sbjct: 134 DLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRPERIAEFRKLYKE 193
Query: 106 IGRILSHLLNVTTQAMD---VGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVH 162
+ + + A+ E SR G
Sbjct: 194 VREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSRYTPQGVIWGNDL 253
Query: 163 QDIPPELVEDIG-----CWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGF 217
+ + I W + + F +
Sbjct: 254 SKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTKPKWTEFHGEDRYSWMKAPRYKGEAFE 313
Query: 218 SGVMIRGSGAAWDLRKSQPYECYSELD-FDIPIGKHGDCYDRYLVRMMEMRESVKIIRQC 276
G + A + L + R R ++ + + +
Sbjct: 314 VGPLASVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLGRTAARGIQCLTAAQEVEVW 373
Query: 277 VNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAP 336
+++L K LYT+ + + V AP
Sbjct: 374 LDKLEANVK--------------------------AGKDDLYTDWQYPTESQGVGFVNAP 407
Query: 337 KGEFGVYLISDGGNKPYRCKIRAPGYAHL 365
+G +++ GG K ++ P +L
Sbjct: 408 RGMLSHWIVQRGG-KIENFQLVVPSTWNL 435
Score = 83.8 bits (205), Expect = 4e-17
Identities = 23/286 (8%), Positives = 55/286 (19%), Gaps = 16/286 (5%)
Query: 61 AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA 120
A + R V A AV+ +G++IP L+R L + HL++
Sbjct: 2 AQHFTQRACGVCTYVHALASVRAVDNCVGVKIPENATLMRNLTMGAQYMHDHLVHFYHLH 61
Query: 121 MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSF 180
+ + + + + + + + I
Sbjct: 62 ALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQAKVKALVESGQLGIFTNAYFL 121
Query: 181 PSALNDI--------------SDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSG 226
+ L + + + G
Sbjct: 122 GGHPAYVLPAEVDLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRP 181
Query: 227 AAWDLRKSQPYECYSELDFDIPIGKH--GDCYDRYLVRMMEMRESVKIIRQCVNRLLGKN 284
+ E ++ Y + L
Sbjct: 182 ERIAEFRKLYKEVREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSR 241
Query: 285 KVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVY 330
+ + E + + + + +H G
Sbjct: 242 YTPQGVIWGNDLSKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTK 287
>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport,
respiratory chain, 4Fe- 4S, cell membrane, flavoprotein,
FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8}
PDB: 2fug_4* 3iam_4* 3ias_4* (4:76-108,4:309-383)
Length = 108
Score = 128 bits (324), Expect = 1e-30
Identities = 39/76 (51%), Positives = 56/76 (73%)
Query: 295 KIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYR 354
I PP R ++ SME++I+HFK YTEG+H P GEVY E+ +GE G Y++SDGG+ PYR
Sbjct: 33 VITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYR 92
Query: 355 CKIRAPGYAHLQAMEF 370
K+RAP + +LQ++ +
Sbjct: 93 VKVRAPSFVNLQSLPY 108
Score = 73.6 bits (181), Expect = 4e-14
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 59 LQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEI--PIRGQLIRVLYSEIGRILSHLLNV 116
LQ + Y R+DY+ + AYALAVEKLLG I P R L + + I H +
Sbjct: 1 LQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVITPPPRHLLETSMEAVIY----HFKHY 56
Query: 117 T 117
T
Sbjct: 57 T 57
>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high
resolution [NIFE]hydrogenase, oxidoreductase, NI-A
state, unready state; HET: NFC; 1.04A {Desulfovibrio
vulgaris str} (L:47-490)
Length = 444
Score = 121 bits (302), Expect = 2e-28
Identities = 19/236 (8%), Positives = 42/236 (17%), Gaps = 28/236 (11%)
Query: 131 WGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDL 190
E + R + D W + +
Sbjct: 234 TFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQT 293
Query: 191 LTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSG-AAWDLRKSQPYECYSELDFDIPI 249
+ +G + + + K + +
Sbjct: 294 QPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGP 353
Query: 250 GKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSME 309
R R +E + + + + P +
Sbjct: 354 EALFSTLGRTAARGIETAVIAEYVGVMLQEYKDN----IAKGDNVICAPWEM-------- 401
Query: 310 SLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHL 365
E V AP+G ++ + G K ++ P L
Sbjct: 402 --------------PKQAEGVGFVNAPRGGLSHWIRIEDG-KIGNFQLVVPSTWTL 442
Score = 119 bits (298), Expect = 5e-28
Identities = 24/235 (10%), Positives = 55/235 (23%), Gaps = 17/235 (7%)
Query: 53 IETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSH 112
++ + A + R V A V+ +G+ IP IR L + H
Sbjct: 1 LKGRDPRDAQHFTQRTCGVXTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDH 60
Query: 113 LLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYF-----------RPGGV 161
+++ + K S + AA G +
Sbjct: 61 IVHFYHLHALDFV-DVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVETGQL 119
Query: 162 HQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVM 221
+ + + L + L R+ + + ++
Sbjct: 120 GPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGG 179
Query: 222 IRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQC 276
+ A R ++ + + Y L+ + +
Sbjct: 180 VTCYDALTPQRIAEFEALW-----KETKAFVDEVYIPDLLVVAAAYKDWTQYGGT 229
>2wpn_B Periplasmic [nifese] hydrogenase, large subunit,
selenocysteine-containing; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris} (B:84-224,B:327-388)
Length = 203
Score = 102 bits (255), Expect = 9e-23
Identities = 16/152 (10%), Positives = 36/152 (23%), Gaps = 36/152 (23%)
Query: 92 IPIRGQLIRVLYSEIGRILSHLLNV---------------------------TTQAMDVG 124
+P G++ R L + SH+L+ ++ ++
Sbjct: 1 VPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKA 60
Query: 125 ALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSAL 184
+ + E R G H GG + E + + +
Sbjct: 61 GVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFV 120
Query: 185 NDISDLLTGNRIFKQRNVNIGTVKLEDAWGWG 216
+ + IG+ +
Sbjct: 121 ---------EQKYVPVVYTIGSKYKDMFKVLS 143
>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport,
respiratory chain, 4Fe- 4S, cell membrane,
flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus
thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4* (4:1-75)
Length = 75
Score = 94.5 bits (235), Expect = 2e-20
Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 2 DKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTF 58
+ ++ T+N GPQHP+ HGVLRL++ L GE V V PHIG LH G EK +E +T+
Sbjct: 19 KELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTY 75
>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase,
oxidoreductase; 2.15A {Desulfovibrio baculatus}
(L:61-92,L:242-280,L:406-454)
Length = 120
Score = 42.3 bits (99), Expect = 1e-04
Identities = 11/111 (9%), Positives = 20/111 (18%), Gaps = 32/111 (28%)
Query: 252 HGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESL 311
+ + + ++ S +I
Sbjct: 37 KNVIAFGVFPEDDDYKTFLLKPGVYIDGKDE----EFDSYVKSEIPDA------------ 80
Query: 312 IHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGY 362
E EAP+G YL K +I +
Sbjct: 81 ---------------AEGTGFTEAPRGALLHYLKIKDK-KIENYQIVSATL 115
>3bga_A Beta-galactosidase; NYSGXRC, protein structure initiative II
(PSI-II), glycosyl hydrolase family 2, jelly-roll fold;
2.10A {Bacteroides thetaiotaomicron vpi-5482} PDB:
3dec_A (A:1-225)
Length = 225
Score = 29.5 bits (65), Expect = 0.68
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 171 EDIGCWCDSFPSALNDISDLLT--GNRIFKQRNVNIGTVKLEDAWGWGFSGV 220
+ +G S +A DI+D+L+ N + + LE W SG+
Sbjct: 163 KLLGYNQGSKTAAEWDITDVLSEGENVVALEVYRWSSGAYLECQDXWRLSGI 214
>2qva_A GM27569P; translin, D. melanogaster, DNA binding protein;
3.40A {Drosophila melanogaster} PDB: 2qrx_A (A:)
Length = 247
Score = 28.7 bits (64), Expect = 1.3
Identities = 14/88 (15%), Positives = 32/88 (36%), Gaps = 1/88 (1%)
Query: 44 LLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIE-IPIRGQLIRVL 102
+ +K + + A Y+ D+ + Q + +A+ L + R + +L
Sbjct: 77 QVELCAQKYQKLAELVPAGQYYRYSDHWTFITQRLIFIIALVIYLEAGFLVTRETVAEML 136
Query: 103 YSEIGRILSHLLNVTTQAMDVGALTPPL 130
+I + L+V + + L L
Sbjct: 137 GLKISQSEGFHLDVEDYLLGILQLASEL 164
>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase,
oxidoreductase; 2.15A {Desulfovibrio baculatus}
(L:93-241,L:281-405)
Length = 274
Score = 27.2 bits (60), Expect = 3.5
Identities = 7/42 (16%), Positives = 10/42 (23%)
Query: 132 GFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDI 173
E R G H GG + + V +
Sbjct: 76 ALEIRRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEY 117
>2dn8_A Acetyl-COA carboxylase 2; biotin required enzyme,
transcarboxylase, structural genomics, NPPSFA; NMR {Homo
sapiens} (A:)
Length = 100
Score = 26.7 bits (59), Expect = 4.9
Identities = 12/61 (19%), Positives = 19/61 (31%)
Query: 288 PVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISD 347
S+ + RS + +G HV G YA +E K + +
Sbjct: 3 SGSSGTCVFEKENDPTVLRSPSAGKLTQYTVEDGGHVEAGSSYAEMEVMKMIMTLNVQER 62
Query: 348 G 348
G
Sbjct: 63 G 63
>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe
hydrogenase unready state, oxidoreductase; 1.83A
{Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q
3cur_H 1frf_L (Q:95-282,Q:382-458)
Length = 265
Score = 26.9 bits (59), Expect = 5.0
Identities = 9/99 (9%), Positives = 18/99 (18%), Gaps = 22/99 (22%)
Query: 92 IPIRGQLIRVLYSEIGRILSHLLNVTTQAM----DVGALTPPLWGFEE------------ 135
IP +++R L + HL++ DV A
Sbjct: 1 IPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPG 60
Query: 136 ------REKLMVFYERASGSRMHAAYFRPGGVHQDIPPE 168
+ ++
Sbjct: 61 NSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYL 99
>1h7b_A Anaerobic ribonucleotide-triphosphate reductase large chain;
oxidoreductase, allosteric regulation, substrate
specificity; 2.45A {Bacteriophage T4} (A:51-605)
Length = 555
Score = 26.4 bits (58), Expect = 6.5
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 312 IHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGG 349
+ YT +HV V E E E + I+ GG
Sbjct: 416 VTDKGWYTNSFHVSVEENITPFEKISREAPYHFIATGG 453
>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase
class II, ligase; 3.23A {Methanococcus maripaludis S2}
(A:550-614)
Length = 65
Score = 26.3 bits (57), Expect = 7.2
Identities = 5/10 (50%), Positives = 6/10 (60%), Gaps = 3/10 (30%)
Query: 201 NVNIGTVKLE 210
NV VK+E
Sbjct: 1 NVE---VKIE 7
>2bsj_A Chaperone protein SYCT; type III secretion, effector, YOPT;
1.83A {Yersinia enterocolitica} PDB: 2bho_A 2bsh_A
2bsi_A (A:)
Length = 133
Score = 26.1 bits (57), Expect = 7.7
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 57 TFLQAVP-YFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLN 115
TF + + F +L +N+ Y V+ + + I Q L+SE+G L N
Sbjct: 7 TFTELMQQLFLKLGLNHQVNENDVYTFEVDGHIQVLIACYHQQWVQLFSELGADLPTNDN 66
Query: 116 V 116
+
Sbjct: 67 L 67
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.322 0.141 0.433
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 3,249,309
Number of extensions: 154374
Number of successful extensions: 534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 523
Number of HSP's successfully gapped: 23
Length of query: 396
Length of database: 4,956,049
Length adjustment: 90
Effective length of query: 306
Effective length of database: 1,913,599
Effective search space: 585561294
Effective search space used: 585561294
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: 56 (25.5 bits)