RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780853|ref|YP_003065266.1| NADH dehydrogenase subunit B
[Candidatus Liberibacter asiaticus str. psy62]
(185 letters)
>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport,
respiratory chain, 4Fe- 4S, cell membrane, flavoprotein,
FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8}
PDB: 2fug_6* 3iam_6* 3ias_6*
Length = 181
Score = 210 bits (535), Expect = 2e-55
Identities = 86/155 (55%), Positives = 117/155 (75%), Gaps = 2/155 (1%)
Query: 26 FSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFA 85
F R E+ +G L T++++LV W R+ SL TFGLACCA+EMM ++ R DL RFG
Sbjct: 7 FERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLARFGSE 66
Query: 86 -PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVR 144
RASPRQ+DVMIVAG L+ KMA +RRV++QMP+P++VISMG+CA+ GG ++ +Y++V+
Sbjct: 67 VFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-NYAIVQ 125
Query: 145 GCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
D +VPVD+YVPGCPP EALIY ++ LQKK+R
Sbjct: 126 NVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRG 160
>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD,
oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP:
e.19.1.1
Length = 317
Score = 81.1 bits (200), Expect = 1e-16
Identities = 30/190 (15%), Positives = 57/190 (30%), Gaps = 41/190 (21%)
Query: 25 DFSRISSEITHKGFLVTSVDQLVTWARTG----SLMWMTF-GLACCAVEMMQASMPRYDL 79
DF + + I + + V A G S++++ C+ +++A P D
Sbjct: 25 DFLKFCTAIAVTMGMGPAFAPEVARALMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDT 84
Query: 80 ERFGFAP---------------------RASPRQSDVMIVAGTLTNKMA---------SA 109
+ + +V G + +
Sbjct: 85 LILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTM 144
Query: 110 LRRVYDQMPEPRYVISMGSCANGGGY------YHYSYSVVRGCDRIVPVDIYVPGCPPTA 163
L +P+ + VI+ G+CA GG + V + I + GCPP
Sbjct: 145 LDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNP 204
Query: 164 EALIYGILLL 173
L+ I+
Sbjct: 205 YNLVGTIVYY 214
>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution
[NIFE]hydrogenase, oxidoreductase, NI-A state, unready
state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}
SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S
1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S
1wuk_S 1wul_S 1e3d_A*
Length = 267
Score = 80.0 bits (197), Expect = 3e-16
Identities = 25/161 (15%), Positives = 52/161 (32%), Gaps = 37/161 (22%)
Query: 50 ARTGSLMWMTF-GLACCAVEMMQASMPRYDLERFG-----FAP----------------R 87
R S++++ C+ +++A P D +
Sbjct: 4 PRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQA 63
Query: 88 ASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGYYH- 137
+ + +V G + + L +P+ + VI+ G+CA GG
Sbjct: 64 VNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAA 123
Query: 138 -YSYSVVRGCDRIVP----VDIYVPGCPPTAEALIYGILLL 173
+ + +G + + I + GCPP L+ I+
Sbjct: 124 KPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYY 164
>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A
{Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A
Length = 264
Score = 78.1 bits (192), Expect = 1e-15
Identities = 23/156 (14%), Positives = 51/156 (32%), Gaps = 37/156 (23%)
Query: 54 SLMWMTFGLAC--CAVEMMQASMPRYDLERFGF-------------------APRASPRQ 92
S++++ C C+ +++ P D A + +
Sbjct: 8 SVVYLHNA-ECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKG 66
Query: 93 SDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGG--YYHYSYS 141
V ++ G + + + P+ + VI++G+CA GG + +
Sbjct: 67 DFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPT 126
Query: 142 VVRGCDRIVP----VDIYVPGCPPTAEALIYGILLL 173
G + + I + GCPP + ++ L
Sbjct: 127 GTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHL 162
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase;
2.15A {Desulfovibrio baculatus} SCOP: e.19.1.1
Length = 283
Score = 70.4 bits (172), Expect = 2e-13
Identities = 16/131 (12%), Positives = 41/131 (31%), Gaps = 27/131 (20%)
Query: 78 DLERFGFAPRASPRQSDVMIVAGTLTNKM-------------------ASALRRVYDQMP 118
+ + ++V G + + + + D P
Sbjct: 56 MALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKAHHHEVTMMELIRDLAP 115
Query: 119 EPRYVISMGSCANGGGYYHYSYSV--------VRGCDRIVPVDIYVPGCPPTAEALIYGI 170
+ +++G+C+ GG +V ++I + + VPGCPP + ++ +
Sbjct: 116 KSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTL 175
Query: 171 LLLQKKIRRVG 181
+ +
Sbjct: 176 VAAWSHVLNPT 186
>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase
unready state, oxidoreductase; 1.83A {Desulfovibrio
fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S
Length = 264
Score = 70.3 bits (172), Expect = 3e-13
Identities = 22/155 (14%), Positives = 45/155 (29%), Gaps = 36/155 (23%)
Query: 54 SLMWMTFGLAC--CAVEMMQASMPRYDLERFGFAP---------------------RASP 90
S++W+ C C ++ P D
Sbjct: 8 SVVWLHNA-ECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEG 66
Query: 91 RQSDVMIVAGTLTNKM---------ASALRRVYDQMPEPRYVISMGSCANGGGYYH--YS 139
+ ++V G L + + + +I +G+C+ GG +
Sbjct: 67 KDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPN 126
Query: 140 YSVVRGCDRIVPVDIY-VPGCPPTAEALIYGILLL 173
S +G + V +PGCPP + ++ +
Sbjct: 127 PSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHV 161
>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase,
photosynthetic P sulfur bacterium, iron-sulfur cluster,
NI-A state; HET: SF4; 2.10A {Allochromatium vinosum}
Length = 269
Score = 69.2 bits (169), Expect = 5e-13
Identities = 23/108 (21%), Positives = 37/108 (34%), Gaps = 14/108 (12%)
Query: 78 DLERFGFAPRASPRQSDVMIVAGTLTNKMA----------SALRRVYDQMPEPRYVISMG 127
E R ++IV G++ A S + + + VI++G
Sbjct: 52 AAEAARLQAMDENRGQYLVIVDGSIPGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVG 111
Query: 128 SCANGGGYY--HYSYSVVRGCDRIVP--VDIYVPGCPPTAEALIYGIL 171
+CA GG + + +V I VPGCPP + I
Sbjct: 112 TCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPIPMVITGVIA 159
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris}
Length = 317
Score = 46.9 bits (111), Expect = 3e-06
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%)
Query: 100 GTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV--------VRGCDRIVP 151
G + S + + + P V+++G+CA GG S G + I
Sbjct: 126 GEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKT 185
Query: 152 VDIYVPGCPPTAEALIYGILLL 173
+ +PGCPP + ++ ++L
Sbjct: 186 PVVNIPGCPPHPDWIVGTVVLA 207
>3nb0_A Glycogen [starch] synthase isoform 2; glycogen synthase,
glucose-6-phosphate, yeast, allosteric AC transferase;
HET: G6P; 2.41A {Saccharomyces cerevisiae} PDB: 3nch_A
3naz_A 3o3c_A*
Length = 725
Score = 43.4 bits (101), Expect = 3e-05
Identities = 8/69 (11%), Positives = 15/69 (21%)
Query: 104 NKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTA 163
+M + Y ++ G V + VPG P
Sbjct: 620 KRMGLEYVKARQLALRRGYPDQFRELVGEELNDSNMDALAGGKKLKVARPLSVPGSPRDL 679
Query: 164 EALIYGILL 172
+ +
Sbjct: 680 RSNSTVYMT 688
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.3 bits (72), Expect = 0.059
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 11/37 (29%)
Query: 66 AVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTL 102
A++ +QAS+ Y A ++P + + T+
Sbjct: 21 ALKKLQASLKLY-------ADDSAP----ALAIKATM 46
>2wh6_A Early antigen protein R; mitochondrion, early protein,
transmembrane, viral protein, apoptosis; 1.50A {Human
herpesvirus 4} PDB: 2v6q_A 1q59_A
Length = 173
Score = 29.1 bits (64), Expect = 0.69
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 11/60 (18%)
Query: 20 EKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDL 79
E VD DF+ + EI H+G + R L WM + + C + Y +
Sbjct: 90 EHVDLDFNSVFLEIFHRG--------DPSLGRA--LAWMAWCMHAC-RTLCCNQSTPYYV 138
>2c40_A Inosine-uridine preferring nucleoside hydrolase family protein;
spine; 2.2A {Bacillus anthracis}
Length = 312
Score = 27.1 bits (59), Expect = 2.5
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 95 VMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138
++ G LT+ +A AL + + ++ MG G H
Sbjct: 121 TLLFTGPLTD-LARALYEAPIIENKIKRLVWMGGTFRTAGNVHE 163
>2v6q_A BHRF1 protein; alternative splicing, membrane, apoptosis,
epstein-BARR virus; 2.7A {Epstein-barr virus} PDB:
1q59_A
Length = 173
Score = 26.9 bits (59), Expect = 2.7
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 10/58 (17%)
Query: 20 EKVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRY 77
E VD DF+ + EI H+G + R +L WM + + C S P Y
Sbjct: 90 EHVDLDFNSVFLEIFHRGD--------PSLGR--ALAWMAWCMHACRTLCCNQSTPYY 137
>3ca8_A Protein YDCF; two domains, alpha/beta fold, helix bundle,
structural genomics, structure 2 function project, S2F,
unknown function; 1.80A {Escherichia coli K12}
Length = 266
Score = 26.9 bits (59), Expect = 2.7
Identities = 13/81 (16%), Positives = 23/81 (28%), Gaps = 8/81 (9%)
Query: 86 PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRG 145
P Q+D +I+AG A ++ P + GG H + +
Sbjct: 30 SGEVPYQADCVILAGNAVMPTIDAACKIARDQQIPLLIS--------GGIGHSTTFLYSA 81
Query: 146 CDRIVPVDIYVPGCPPTAEAL 166
+ + A L
Sbjct: 82 IAQHPHYNTIRTTGRAEATIL 102
>2k4z_A DSRR; ISCA/SUFA/HESB like fold, structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium, NESG; NMR {Allochromatium vinosum}
Length = 125
Score = 26.9 bits (59), Expect = 2.8
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 3/52 (5%)
Query: 90 PRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYS 141
PR S +M LT A + + Q + + + N G Y
Sbjct: 16 PRGSHMMF---KLTPAAAEQVLKAAKQGGTEGMCLRLAAGRNPDGSIDYRMG 64
>2x3d_A SSO6206; unknown function; 2.70A {Sulfolobus solfataricus}
Length = 96
Score = 26.7 bits (59), Expect = 2.9
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 5 TVNQKIISGQSSCSLEKVDADFSRISSEITHKGFLVTSVDQLV 47
T+ II +E +F I + +G + S+D++V
Sbjct: 47 TMGLMII-------IEGTSLNFDDIRKMLEEEGCAIHSIDEVV 82
>1ddg_A Sulfite reductase (NADPH) flavoprotein alpha- component; cytochrome
P450 reductase, FNR, modular protein, oxidoreductase;
HET: FAD; 2.01A {Escherichia coli} SCOP: b.43.4.1
c.25.1.4 PDB: 1ddi_A*
Length = 374
Score = 26.7 bits (58), Expect = 3.6
Identities = 15/118 (12%), Positives = 33/118 (27%), Gaps = 6/118 (5%)
Query: 23 DADFSRISSEITHKG--FLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLE 80
+S SS+ + + V + R + +F + + +
Sbjct: 160 PRLYSIASSQAEVENEVHVTVGVVRYDVEGRARAGGASSF---LADRVEEEGEVRVFIEH 216
Query: 81 RFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138
F A+P +MI GT + +++ P + + Y
Sbjct: 217 NDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADE-APGKNWLFFGNPHFTEDFLY 273
>1j1l_A Pirin; beta sandwich, cupin, iron, metatl binding protein; 2.10A
{Homo sapiens} SCOP: b.82.1.12
Length = 290
Score = 26.2 bits (57), Expect = 4.2
Identities = 19/119 (15%), Positives = 30/119 (25%), Gaps = 5/119 (4%)
Query: 51 RTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASAL 110
G L WMT G E MP + G + R S+ M+ K
Sbjct: 86 NPGDLQWMTAGRGILHAE-----MPCSEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIP 140
Query: 111 RRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYG 169
+ D + + + + D +P + I G
Sbjct: 141 KPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFKLDPGAKHSQPIPKGWTSFIYTISG 199
>1q14_A HST2 protein; histone deacetylase, hydrolase; 2.50A {Saccharomyces
cerevisiae} SCOP: c.31.1.5
Length = 361
Score = 26.3 bits (57), Expect = 4.3
Identities = 10/87 (11%), Positives = 28/87 (32%), Gaps = 5/87 (5%)
Query: 68 EMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPE--PRYVIS 125
+ + + R Q ++IV GT + + + +++P R + +
Sbjct: 195 SFSETWLNDSEWLREKITTSGKHPQQPLVIVVGT-SLAVYPF-ASLPEEIPRKVKRVLCN 252
Query: 126 MGSCANGGGYYHYSYSVVRG-CDRIVP 151
+ + + + +V D
Sbjct: 253 LETVGDFKANKRPTDLIVHQYSDEFAE 279
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
0.323 0.136 0.417
Gapped
Lambda K H
0.267 0.0436 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,630,635
Number of extensions: 73131
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 241
Number of HSP's successfully gapped: 22
Length of query: 185
Length of database: 5,693,230
Length adjustment: 87
Effective length of query: 98
Effective length of database: 3,584,002
Effective search space: 351232196
Effective search space used: 351232196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.3 bits)