RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 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* (6:)
Length = 181
Score = 167 bits (425), Expect = 7e-43
Identities = 86/160 (53%), Positives = 118/160 (73%), Gaps = 2/160 (1%)
Query: 21 KVDADFSRISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLE 80
+ F R E+ +G L T++++LV W R+ SL TFGLACCA+EMM ++ R DL
Sbjct: 2 ALKDLFERDVQELEREGILFTTLEKLVAWGRSNSLWPATFGLACCAIEMMASTDARNDLA 61
Query: 81 RFGFAP-RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYS 139
RFG RASPRQ+DVMIVAG L+ KMA +RRV++QMP+P++VISMG+CA+ GG ++ +
Sbjct: 62 RFGSEVFRASPRQADVMIVAGRLSKKMAPVMRRVWEQMPDPKWVISMGACASSGGMFN-N 120
Query: 140 YSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
Y++V+ D +VPVD+YVPGCPP EALIY ++ LQKK+R
Sbjct: 121 YAIVQNVDSVVPVDVYVPGCPPRPEALIYAVMQLQKKVRG 160
>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase,
oxidoreductase; 2.15A {Desulfovibrio baculatus}
(S:1-198)
Length = 198
Score = 159 bits (403), Expect = 2e-40
Identities = 20/160 (12%), Positives = 54/160 (33%), Gaps = 17/160 (10%)
Query: 34 THKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQS 93
+ + +++ ++M A+ M +++ F A P
Sbjct: 28 AVHPRIKEILLDVISLEFHPTVM---ASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAK 84
Query: 94 DVM------IVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV----- 142
+ + + + + + D P+ +++G+C+ GG +V
Sbjct: 85 EGRYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKS 144
Query: 143 ---VRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
++I + + VPGCPP + ++ ++ +
Sbjct: 145 VRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLN 184
>2wpn_A Periplasmic [nifese] hydrogenase, small subunit;
metal-binding, oxidoreductase, oxygen tolerance; HET:
FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} (A:1-240)
Length = 240
Score = 156 bits (395), Expect = 2e-39
Identities = 27/158 (17%), Positives = 55/158 (34%), Gaps = 9/158 (5%)
Query: 31 SEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASP 90
S + D L+ + A+E M+ ++ + F + P
Sbjct: 56 SVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVP 115
Query: 91 -RQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV------- 142
+ G + S + + + P V+++G+CA GG S
Sbjct: 116 VEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVS 175
Query: 143 -VRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
G + I + +PGCPP + ++ ++L I++
Sbjct: 176 KFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKK 213
>1yq9_A Periplasmic [NIFE] hydrogenase small subunit;
oxidoreductase; 2.35A {Desulfovibrio gigas} (A:1-177)
Length = 177
Score = 145 bits (366), Expect = 4e-36
Identities = 24/168 (14%), Positives = 49/168 (29%), Gaps = 34/168 (20%)
Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGF-------------------AP 86
L R + C+ +++ P D A
Sbjct: 1 LTAKKRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEAL 60
Query: 87 RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGYY- 136
+ + V ++ G + + + P+ + VI++G+CA GG
Sbjct: 61 HEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQA 120
Query: 137 -HYSYSVVRGCDR----IVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179
+ + G + + I + GCPP + ++ L K
Sbjct: 121 AKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMP 168
>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 (A:1-182)
Length = 182
Score = 145 bits (366), Expect = 5e-36
Identities = 23/166 (13%), Positives = 44/166 (26%), Gaps = 33/166 (19%)
Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAP------------------- 86
L R + C ++ P D
Sbjct: 1 LTAKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAAL 60
Query: 87 --RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGY 135
+ ++V G L + + + +I +G+C+ GG
Sbjct: 61 HQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGV 120
Query: 136 Y--HYSYSVVRGCDRIVPVD-IYVPGCPPTAEALIYGILLLQKKIR 178
+ S +G + V I +PGCPP + ++ + K
Sbjct: 121 QKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGI 166
>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high
resolution [NIFE]hydrogenase, oxidoreductase, NI-A
state, unready state; HET: NFC; 1.04A {Desulfovibrio
vulgaris str} (S:1-180)
Length = 180
Score = 142 bits (358), Expect = 4e-35
Identities = 26/170 (15%), Positives = 50/170 (29%), Gaps = 36/170 (21%)
Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAP------------------- 86
L+ R + C+ +++A P D
Sbjct: 1 LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAAL 60
Query: 87 --RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGY 135
+ + +V G + + L +P+ + VI+ G+CA GG
Sbjct: 61 EQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGV 120
Query: 136 Y--HYSYSVVRGCDRIVPV----DIYVPGCPPTAEALIYGILLLQKKIRR 179
+ + +G + + I + GCPP L+ I+ K
Sbjct: 121 QAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAA 170
>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR,
MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str}
(S:1-236)
Length = 236
Score = 141 bits (356), Expect = 7e-35
Identities = 27/180 (15%), Positives = 51/180 (28%), Gaps = 36/180 (20%)
Query: 36 KGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAP--------- 86
F L+ R + C+ +++A P D
Sbjct: 41 PAFAPEVARALMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMA 100
Query: 87 ------------RASPRQSDVMIVAGTLTNKMA---------SALRRVYDQMPEPRYVIS 125
+ + +V G + + L +P+ + VI+
Sbjct: 101 AAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIA 160
Query: 126 MGSCANGGGYY--HYSYSVVRGCDRIVP----VDIYVPGCPPTAEALIYGILLLQKKIRR 179
G+CA GG + + +G + + I + GCPP L+ I+ K
Sbjct: 161 YGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAA 220
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
translation termination, ATP-binding, cytoplasm,
hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
(A:1-326)
Length = 326
Score = 29.7 bits (66), Expect = 0.27
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 94 DVMIVAGTLTNKMAS----ALRRVYDQMPEPRYVI 124
+++ + + T K A+ L RV +P+P+ +
Sbjct: 160 NMIGQSQSGTGKTAAFALTMLSRVDASVPKPQAIC 194
>3i4a_A N(G),N(G)-dimethylarginine dimethylaminohydrolase 1; DDAH,
nitric oxide synthase regulation, acetylation,
metal-binding, zinc; HET: LN5; 1.90A {Homo sapiens} PDB:
3i2e_A* (A:1-96,A:292-308)
Length = 113
Score = 27.9 bits (62), Expect = 0.85
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 117 MPEPRYVISMGSCANGGGYYHYSYSVVRG 145
+P ++ SM + + +++VVR
Sbjct: 15 VPRGSHMASMAGLGHPAAFGRATHAVVRA 43
>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, 4Fe-4S,
iron-sulfur, metal-binding, oxidoreductase; HET: HCN;
1.39A {Clostridium pasteurianum} (A:210-268,A:344-406)
Length = 122
Score = 27.7 bits (62), Expect = 0.98
Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 21/70 (30%)
Query: 67 VEMMQASMPRYDL-ERFGFAPRASPRQSDVMIVAGTLT-NKMASALRR-----VYDQMPE 119
V + A R + E F G K+ +ALR+ ++D +P+
Sbjct: 16 VIVAMAPSVRASIGELFNMGF-------------GVDVTGKIYTALRQLGFDKIFD-IPK 61
Query: 120 PRYVISMGSC 129
+ +++ C
Sbjct: 62 NVFTVTVMPC 71
>2v6q_A BHRF1 protein; alternative splicing, membrane, apoptosis,
epstein-BARR virus; 2.7A {Epstein-barr virus} PDB:
1q59_A (A:)
Length = 173
Score = 27.3 bits (60), Expect = 1.4
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
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006)
Length = 120
Score = 27.0 bits (60), Expect = 1.6
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 17/39 (43%)
Query: 40 VTSVDQLVTWARTGSLMWMTF--GLACCAVEMMQASMPR 76
V S++ LV ++ F G+ MQ ++PR
Sbjct: 5 VMSIESLV------EVV---FYRGMT------MQVAVPR 28
>1m1n_A Nitrogenase molybdenum-iron protein alpha chain; atomic
resolution, FEMO cofactor, nitrogen fixation, central
nitrogen ligand; HET: HCA CLF CFN; 1.16A {Azotobacter
vinelandii} (A:56-212)
Length = 157
Score = 26.5 bits (58), Expect = 2.1
Identities = 13/87 (14%), Positives = 23/87 (26%), Gaps = 4/87 (4%)
Query: 46 LVTWARTGSLMWMTFGLACCAVEMMQASMPRY---DLERFGFAPRASPRQSDVMIVAGTL 102
V W ++ ++ G C Y + + IV G
Sbjct: 13 GVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGG- 71
Query: 103 TNKMASALRRVYDQMPEPRYVISMGSC 129
K+A + V P + + C
Sbjct: 72 DKKLAKLIDEVETLFPLNKGISVQSEC 98
>3beo_A UDP-N-acetylglucosamine 2-epimerase; UDP-GLCNAC, allosteric,
regulation, isomerase; HET: UD1 UDP; 1.70A {Bacillus
anthracis} PDB: 1o6c_A (A:1-192,A:357-375)
Length = 211
Score = 26.3 bits (57), Expect = 2.5
Identities = 14/98 (14%), Positives = 27/98 (27%), Gaps = 10/98 (10%)
Query: 85 APRASPRQSDVMIVAGTL--TNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSV 142
P + VM + GT KMA + + + +++ +
Sbjct: 1 GPVDMTERLKVMTIFGTRPEAIKMAPLVLELQKHPEKIESIVT------VTAQHRQMLDQ 54
Query: 143 VRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRV 180
V I P + LI + + +V
Sbjct: 55 VLSIFGITPDFDLNIMKDR--QTLIDITTRGLEGLDKV 90
>1dku_A Protein (phosphoribosyl pyrophosphate synthetase); open
alpha-beta structure, domain duplication,
phosphoribosyltransferase type I fold; HET: AP2 ABM;
2.20A {Bacillus subtilis} (A:1-153,A:296-317)
Length = 175
Score = 25.3 bits (55), Expect = 5.8
Identities = 15/89 (16%), Positives = 32/89 (35%), Gaps = 4/89 (4%)
Query: 92 QSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVP 151
++ I + ++A + + D + S+ ++G + S+ RGCD +
Sbjct: 7 DKNLKIFSLNSNPELA---KEIADIVGVQLGKCSVTRFSDGEVQINIEESI-RGCDCYII 62
Query: 152 VDIYVPGCPPTAEALIYGILLLQKKIRRV 180
P E LI L + + +
Sbjct: 63 QSTSDPVNEHIMELLIMVDALKRASAKTI 91
>3fz0_A Nucleoside hydrolase, putative; NH fold, open alpha/beta
structure, glycosidase; HET: BTB; 2.50A {Trypanosoma
brucei} (A:)
Length = 360
Score = 24.9 bits (53), Expect = 7.8
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 94 DVMIVA-GTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY 138
+VA G LTN +A ALR D + G G
Sbjct: 128 VYQLVALGPLTN-VALALRLNPDLFSKLGTDTIPGIVIMNGTSESK 172
>1bd0_A Alanine racemase; isomerase, pyridoxal phosphate, alanine
phosphonate; HET: IN5; 1.60A {Bacillus
stearothermophilus} (A:15-232)
Length = 218
Score = 24.5 bits (52), Expect = 9.1
Identities = 4/42 (9%), Positives = 17/42 (40%)
Query: 103 TNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVR 144
+ + + + +P ++ + A + ++++VR
Sbjct: 164 FSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVR 205
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
0.323 0.136 0.417
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,453,342
Number of extensions: 64572
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 19
Length of query: 185
Length of database: 4,956,049
Length adjustment: 83
Effective length of query: 102
Effective length of database: 2,150,234
Effective search space: 219323868
Effective search space used: 219323868
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: 52 (24.3 bits)