RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780919|ref|YP_003065332.1| dTDP-4-dehydrorhamnose
3,5-epimerase [Candidatus Liberibacter asiaticus str. psy62]
(198 letters)
>1upi_A DTDP-4-dehydrorhamnose 3,5-epimerase; rhamnose pathway, PSI,
protein structure initiative, TB structural genomics
consortium, TB; HET: CME; 1.7A {Mycobacterium
tuberculosis} (A:)
Length = 225
Score = 200 bits (510), Expect = 1e-52
Identities = 54/186 (29%), Positives = 91/186 (48%), Gaps = 5/186 (2%)
Query: 1 MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRG 55
M + DSRG F + + + + V+ + G +RG
Sbjct: 21 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRG 80
Query: 56 LHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHG 115
LHF + P +QAK V C++G +FD+ VDIR SPT+G W S+ + + IY+ G AHG
Sbjct: 81 LHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHG 140
Query: 116 FMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQI 175
F+ L+ N+ V+Y + Y+ + + + D ++ + WPL+D PS+S++D P +
Sbjct: 141 FLALQDNSTVMYLXSAEYNPQREHTIXATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDV 200
Query: 176 DSPFEY 181
+
Sbjct: 201 RASGLL 206
>2c0z_A NOVW; isomerase, epimerase, antibiotic biosynthesis,
RMLC-like cupin; 1.60A {Streptomyces sphaeroides} (A:)
Length = 216
Score = 192 bits (488), Expect = 4e-50
Identities = 55/187 (29%), Positives = 79/187 (42%), Gaps = 10/187 (5%)
Query: 1 MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDV-FVQDNHSFSFDCGTIR 54
M + P V + + D RG F Y E + + Q N S S G +R
Sbjct: 10 MRLRPLGIEGVWEITPEQRADPRGVFLDWYHVDRFAEAIGRPLRLAQANLSVS-VRGVVR 68
Query: 55 GLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAH 114
G+HF P QAK V C+ G +FD+ VD+R SPTYGCW + + +Y+ G H
Sbjct: 69 GIHFVDVPPGQAKYVTCVRGAVFDVVVDLRVGSPTYGCWEGTRLDDVSRRAVYLSEGIGH 128
Query: 115 GFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174
GF + + Y + Y + GV D + I WP +L S +DQ+ L +
Sbjct: 129 GFCAISDEATLCYLSSGTYDPATEHGVHPLDPELAIDWPTGTPLL---SPRDQDALLLAE 185
Query: 175 IDSPFEY 181
Sbjct: 186 ARDAGLL 192
>1ep0_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; racemase,
DTDP-4-dehydrorhamnose epimerase, structural genomics,
PSI; 1.50A {Methanothermobacterthermautotrophicus} (A:)
Length = 185
Score = 189 bits (481), Expect = 2e-49
Identities = 77/184 (41%), Positives = 102/184 (55%), Gaps = 7/184 (3%)
Query: 1 MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRG 55
I++ + D RG+F +T++ + +E GL+ FVQDN S S G +RG
Sbjct: 4 FRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMS-VRGVLRG 62
Query: 56 LHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHG 115
LHFQR Q KLVR I G IFD+AVD+R+NS TYG W + +S N + +IP GFAHG
Sbjct: 63 LHFQREK-PQGKLVRVIRGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHG 121
Query: 116 FMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQI 175
F+ L V YK T+ Y E+DSG+ W D I I WPL +SEKD+N L +
Sbjct: 122 FLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLREN 181
Query: 176 DSPF 179
Sbjct: 182 PVYL 185
>1oi6_A PCZA361.16; epimerase, vancomycin group antibiotic, EVAD,
isomerase; HET: TMP; 1.4A {Amycolatopsis orientalis}
(A:)
Length = 205
Score = 188 bits (479), Expect = 4e-49
Identities = 49/188 (26%), Positives = 78/188 (41%), Gaps = 10/188 (5%)
Query: 1 MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQD--VFVQDNHSFSFDCGTI 53
M R F D RG Y + E Q HS S G +
Sbjct: 1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMS-KRGVV 59
Query: 54 RGLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFA 113
RG+H+ P AK V C G+ DI +DIR SPT+G W S+ + + +Y+P G
Sbjct: 60 RGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVG 119
Query: 114 HGFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLN 173
H F+ LE +T + Y ++ Y + + ++ D ++ + + P VS++D+ L
Sbjct: 120 HAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVE--PIVSDRDRVAITLA 177
Query: 174 QIDSPFEY 181
+
Sbjct: 178 EAQRQGLL 185
>1wlt_A 176AA long hypothetical DTDP-4-dehydrorhamnose 3,
5-epimerase; jelly roll-like topology, flattened barrel,
isomerase; 1.90A {Sulfolobus tokodaii} (A:)
Length = 196
Score = 186 bits (474), Expect = 2e-48
Identities = 58/186 (31%), Positives = 99/186 (53%), Gaps = 16/186 (8%)
Query: 1 MNINP------VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIR 54
M + ++K + F D RG+F + + S+ ++ + + +Q N SFS G +R
Sbjct: 21 MPFEFENLGMGIILIKPKVFPDKRGFFLEVFKSEDFTKMRIPN-VIQTNMSFS-RKGVVR 78
Query: 55 GLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAH 114
GLH+QR P Q K++ GRI D+AVD+R++SPT+G +V E++ N ++IP GFAH
Sbjct: 79 GLHYQRTPKEQGKIIFVPKGRILDVAVDVRKSSPTFGKYVKAELNEENHYMLWIPPGFAH 138
Query: 115 GFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174
GF LE + + + + YS H+ +++ I ++ S+KD P L +
Sbjct: 139 GFQALEDSIVIYFITHNEYSPPHERCISYSYIDWPIKEVII-------SDKDLQCPSLEK 191
Query: 175 IDSPFE 180
+ F+
Sbjct: 192 AE-VFD 196
>2ixk_A DTDP-4-dehydrorhamnose 3,5-epimerase; isomerase,
lipopolysaccharide biosynthesis, epimerise, epimerize;
HET: TDO; 1.7A {Pseudomonas aeruginosa} PDB: 2ixi_A*
2ixh_A* 1rtv_A* 2ixj_A* (A:)
Length = 184
Score = 184 bits (469), Expect = 5e-48
Identities = 71/181 (39%), Positives = 99/181 (54%), Gaps = 8/181 (4%)
Query: 1 MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRG 55
M V + + R F D RG+F ++Y+ + +E V ++ G +RG
Sbjct: 4 MKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRG 63
Query: 56 LHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHG 115
LH+Q AQ KLVR G +FD+AVD+RR SPT+G WV +SA N Q++IP GFAHG
Sbjct: 64 LHYQ-IRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHG 122
Query: 116 FMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQI 175
F+ L E +YK TDF++ EH+ + W D + I WPL D P +SEKD+
Sbjct: 123 FVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDA--PLLSEKDRQGKAFADA 180
Query: 176 D 176
D
Sbjct: 181 D 181
>1dzr_A DTDP-4-dehydrorhamnose 3,5-epimerase; isomerase, 3,
5-hexulose epimerase; 2.17A {Salmonella typhimurium}
(A:)
Length = 183
Score = 182 bits (464), Expect = 2e-47
Identities = 76/185 (41%), Positives = 108/185 (58%), Gaps = 8/185 (4%)
Query: 1 MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRG 55
M + V IL+ + F D RG+F ++Y+ + +EL + V ++ +RG
Sbjct: 2 MIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDNHSKSKKNVLRG 61
Query: 56 LHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHG 115
LHFQR AQ KLVRC G +FD+AVDIR+ SPT+G WV + +SA N Q++IP GFAHG
Sbjct: 62 LHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWVGVNLSAENKRQLWIPEGFAHG 121
Query: 116 FMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQI 175
F+TL E +YK T++YS + + W D++I I WP + LP +S KD P L+Q
Sbjct: 122 FVTLSEYAEFLYKATNYYSPSSEGSILWNDEAIGIEWPF--SQLPELSAKDAAAPLLDQA 179
Query: 176 DSPFE 180
E
Sbjct: 180 L-LTE 183
>1nxm_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; jelly
roll-like structure, beta sheet, isomerase; 1.30A
{Streptococcus suis} (A:)
Length = 197
Score = 158 bits (400), Expect = 6e-40
Identities = 51/187 (27%), Positives = 80/187 (42%), Gaps = 18/187 (9%)
Query: 6 VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDV-----FVQDNHSFSFDCGTIRGLHFQR 60
+ D+RGWF + + + + LG + +Q+N SFS +RGLH +
Sbjct: 21 MLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRK-NVLRGLHAEP 79
Query: 61 PPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTLE 120
+ G++ VD R T+G I I++P G A+GF L
Sbjct: 80 ---WDKYISVADGGKVLGTWVD-LREGETFGNTYQTVID--ASKSIFVPRGVANGFQVLS 133
Query: 121 MNTEVIYKVTDFYSVEH---DSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQIDS 177
Y V D++++E + V + D S+DI W L+ VSE D+N PFL +
Sbjct: 134 DFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEE--AEVSEADENHPFLKDVK- 190
Query: 178 PFEYDGL 184
P + L
Sbjct: 191 PLRKEDL 197
>3ejk_A DTDP sugar isomerase; YP_390184.1, structural genomics,
joint center for structural genomics, JCSG; HET: CIT;
1.95A {Desulfovibrio desulfuricans subsp} (A:)
Length = 174
Score = 134 bits (338), Expect = 8e-33
Identities = 21/161 (13%), Positives = 41/161 (25%), Gaps = 10/161 (6%)
Query: 1 MNINPVRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQR 60
+ + ++ + R+ G + F + S ++
Sbjct: 18 LPVEGAQLSELRQIPAEGGPVLHXLRLDSPQFSQ----FGEIYFSE-VLPRRVKAWKRHS 72
Query: 61 PPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEI-SANNGLQIYIPTGFAHGFMTL 119
+L G I + D R SPT G + + +N + IP +GF
Sbjct: 73 LX---TQLFAVPVGCIHVVLYDGREKSPTSGRLAQVTLGRPDNYRLLRIPPQVWYGFAAT 129
Query: 120 EMNTEV-IYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTIL 159
+ + I +W D
Sbjct: 130 GDTPALVANCTDIPHRQGESERAPQDAPFIPFSWAGADLSG 170
>2pa7_A DTDP-6-deoxy-3,4-keto-hexulose isomerase; deoxysugar
biosynthesis, S-layer biosynthesis, ketoisomerase; HET:
TYD; 1.50A {Aneurinibacillus thermoaerophilus} (A:)
Length = 141
Score = 96.6 bits (240), Expect = 2e-21
Identities = 17/149 (11%), Positives = 43/149 (28%), Gaps = 18/149 (12%)
Query: 6 VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPPYAQ 65
+++ +K DSRG +K + + + RG H +
Sbjct: 5 NKVINFKKIIDSRGSLVAIEENKNIPF----SIKRVYYIFDT-KGEEPRGFHAHKK---L 56
Query: 66 AKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTLEMNTEV 125
+++ C+ G + +D + + +Y+ H + +
Sbjct: 57 EQVLVCLNGS-CRVILDDGNIIQEITLD-------SPAVGLYVGPAVWHEMHDFSSDCVM 108
Query: 126 IYKVTDFYSVEHDSGVAWQDKSIDITWPL 154
+ +D+Y + D +
Sbjct: 109 MVLASDYYDETD--YIRQYDNFKKYIAKI 135
>2zkl_A Capsular polysaccharide synthesis enzyme CAP5F; rossmann
fold, isomerase; 2.61A {Staphylococcus aureus}
(A:249-369)
Length = 121
Score = 90.4 bits (224), Expect = 1e-19
Identities = 18/133 (13%), Positives = 38/133 (28%), Gaps = 19/133 (14%)
Query: 12 RKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPPYAQAKLVRC 71
D RG F++ Q + + S G +G H+ + +
Sbjct: 5 LMNVDDRGSFTEFIK---------TPDRGQVSVNIS-KPGITKGNHWHHT---KNEKFLV 51
Query: 72 IAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTL-EMNTEVIYKVT 130
++G+ + +S + + IP G+ H L + + I V
Sbjct: 52 VSGKGVIRFRH-----VNDDEIIEYYVSGDKLEVVDIPVGYTHNIENLGDTDMVTIMWVN 106
Query: 131 DFYSVEHDSGVAW 143
+ +
Sbjct: 107 EMFDPNQPDTYFL 119
>2fgy_A Carboxysome shell polypeptide; beta class of carbonic
anhydrase, lyase; 2.20A {Halothiobacillus neapolitanus}
(A:176-420)
Length = 245
Score = 24.8 bits (54), Expect = 9.3
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 7/39 (17%)
Query: 60 RPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEI 98
R P + AG +FDI D+ + W E+
Sbjct: 40 RLPLTAFTYRKAYAGSMFDIEDDLAQ-------WEKNEL 71
>2pef_A Serine protease inhibitor; serpin; 1.60A {Thermoanaerobacter
tengcongensis MB4} PDB: 2vh4_A 2pee_A
(A:36-174,A:266-338)
Length = 212
Score = 24.7 bits (53), Expect = 9.3
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 21 FSQTYS-SKLLKELGLQDVFVQDNHSFS 47
+ T ++ L+ LG+ D F+ D FS
Sbjct: 142 YEYTIKMNETLESLGMTDAFLPDKADFS 169
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 0.139 0.434
Gapped
Lambda K H
0.267 0.0567 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,520,022
Number of extensions: 65217
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 17
Length of query: 198
Length of database: 4,956,049
Length adjustment: 84
Effective length of query: 114
Effective length of database: 2,116,429
Effective search space: 241272906
Effective search space used: 241272906
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: 41 (21.9 bits)
S2: 52 (24.2 bits)