RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13219
(193 letters)
>2nzl_A Hydroxyacid oxidase 1; HAOX1, glycolate oxidase, GOX, GOX1,
structural genomics, structural genom consortium, SGC,
oxidoreductase; HET: FMN; 1.35A {Homo sapiens} PDB:
2rdu_A* 2rdt_A* 2rdw_A* 2w0u_A*
Length = 392
Score = 240 bits (616), Expect = 2e-79
Identities = 81/192 (42%), Positives = 117/192 (60%), Gaps = 6/192 (3%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
M+RNV + D +VLG R P+ + +AMQ++AH DGE+AT RA + M+LS +T
Sbjct: 75 MLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWAT 134
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
+S+EEV P WLQ+YI+KDR ++ ++V++AE+ GY AI +T+DT LG+R D++
Sbjct: 135 SSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVR 194
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
N+F +PP L + NF F D SGL YVA D S+ W+D++ L
Sbjct: 195 NRFKLPPQLRMKNFETSTLSFSPEENFGD------DSGLAAYVAKAIDPSISWEDIKWLR 248
Query: 181 QATKLPIVCKGI 192
+ T LPIV KGI
Sbjct: 249 RLTSLPIVAKGI 260
>1gox_A (S)-2-hydroxy-acid oxidase, peroxisomal; oxidoreductase
(oxygen(A)); HET: FMN; 2.00A {Spinacia oleracea} SCOP:
c.1.4.1 PDB: 1gyl_A* 1al8_A* 1al7_A* 2cdh_0
Length = 370
Score = 238 bits (610), Expect = 8e-79
Identities = 83/192 (43%), Positives = 119/192 (61%), Gaps = 10/192 (5%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
++ +V + D T+LG + P+ IAP+AMQK+AH +GE ATARAA IM LS +T
Sbjct: 52 ILIDVTNIDMTTTILGFKISMPIMIAPTAMQKMAHPEGEYATARAASAAGTIMTLSSWAT 111
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
+S+EEV + P + Q+Y++KDR + Q+V+RAER+G+ AI +T+DT LG R D+K
Sbjct: 112 SSVEEVASTGPGI-RFFQLYVYKDRNVVAQLVRRAERAGFKAIALTVDTPRLGRREADIK 170
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
N+F +PP+L+L NF + D + SGL+ YVA Q D S+ W DV L
Sbjct: 171 NRFVLPPFLTLKNFEGIDLGKMDKAN---------DSGLSSYVAGQIDRSLSWKDVAWLQ 221
Query: 181 QATKLPIVCKGI 192
T LPI+ KG+
Sbjct: 222 TITSLPILVKGV 233
>3sgz_A Hydroxyacid oxidase 2; flavoprotein, homology, INH
oxidoreductase-oxidoreductase inhibitor complex; HET:
FMN HO6; 1.35A {Rattus norvegicus} PDB: 1tb3_A*
Length = 352
Score = 229 bits (586), Expect = 2e-75
Identities = 63/192 (32%), Positives = 96/192 (50%), Gaps = 16/192 (8%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
+R++ D+ T+ G P+ I+P+A +A DGE +TARAA + ++S ++
Sbjct: 50 YLRDMSKVDTRTTIQGQEISAPICISPTAFHSIAWPDGEKSTARAAQEANICYVISSYAS 109
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
SLE++ A P W Q+Y+ D + QMVQRAE G+ A+VIT+DT VLG+R RD +
Sbjct: 110 YSLEDIVAAAPEGFRWFQLYMKSDWDFNKQMVQRAEALGFKALVITIDTPVLGNRRRDKR 169
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
N+ + + A R LK+ S W+D+ L
Sbjct: 170 NQLNLEANILKAALRALKEEK----------------PTQSVPVLFPKASFCWNDLSLLQ 213
Query: 181 QATKLPIVCKGI 192
T+LPI+ KGI
Sbjct: 214 SITRLPIILKGI 225
>2nli_A Lactate oxidase; flavoenzyme, FMN, D-lactate, oxidoreducta; HET:
FMN; 1.59A {Aerococcus viridans} PDB: 2zfa_A* 2du2_A*
2e77_A* 2j6x_A*
Length = 368
Score = 225 bits (577), Expect = 7e-74
Identities = 49/192 (25%), Positives = 81/192 (42%), Gaps = 15/192 (7%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
+ ++V D+ +LG + + P +AP A LAH E TARA IM +S S
Sbjct: 61 LAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHTTKEAGTARAVSEFGTIMSISAYSG 120
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
+ EE+ W Q+Y+ KD + ++ A+ G +AI++T D+ V G+R RD+K
Sbjct: 121 ATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKSDGATAIILTADSTVSGNRDRDVK 180
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
NKF P + + + + + D+ +
Sbjct: 181 NKFVYPFGMPIVQRYLRGTA---------------EGMSLNNIYGASKQKISPRDIEEIA 225
Query: 181 QATKLPIVCKGI 192
+ LP+ KGI
Sbjct: 226 GHSGLPVFVKGI 237
>1p4c_A L(+)-mandelate dehydrogenase; TIM barrel, hydroxy acid oxidizing
enzyme, oxidoreductase; HET: FMN MES; 1.35A {Pseudomonas
putida} SCOP: c.1.4.1 PDB: 1huv_A* 1p5b_A* 3giy_A*
2a7p_A* 2a85_A* 2a7n_A*
Length = 380
Score = 226 bits (578), Expect = 8e-74
Identities = 58/192 (30%), Positives = 93/192 (48%), Gaps = 11/192 (5%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMST 60
+ +V R VLG R P+ I P+ + G++A ARAA +LS S
Sbjct: 53 RLVDVSRRSLQAEVLGKRQSMPLLIGPTGLNGALWPKGDLALARAATKAGIPFVLSTASN 112
Query: 61 TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLK 120
S+E++ A+ LW Q+Y+ R ++ MV +A +GY+ +V+T D AV G R RDL
Sbjct: 113 MSIEDL-ARQCDGDLWFQLYVIH-REIAQGMVLKALHTGYTTLVLTTDVAVNGYRERDLH 170
Query: 121 NKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLV 180
N+F +PP+L+L NF + D + ++ Q D S +W+ +R L
Sbjct: 171 NRFKIPPFLTLKNFEGIDLGKMDKANL---------EMQAALMSRQMDASFNWEALRWLR 221
Query: 181 QATKLPIVCKGI 192
++ KG+
Sbjct: 222 DLWPHKLLVKGL 233
>1kbi_A Cytochrome B2, L-LCR; flavocytochrome B2, electron transfer,
oxidoreductase; HET: HEM FMN; 2.30A {Saccharomyces
cerevisiae} SCOP: c.1.4.1 d.120.1.1 PDB: 1fcb_A* 1lco_A*
1ldc_A* 1sze_A* 2oz0_A* 1szf_A* 1szg_A* 1ltd_A* 1kbj_A*
1qcw_A* 3ks0_A*
Length = 511
Score = 206 bits (525), Expect = 1e-64
Identities = 52/197 (26%), Positives = 96/197 (48%), Gaps = 20/197 (10%)
Query: 1 MMRNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHA---DGEVATARAAGMMDAIMILSL 57
++ +V D +LG+ P ++ +A+ KL + + +VA G+ ++S
Sbjct: 170 ILVDVRKVDISTDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMIST 229
Query: 58 MSTTSLEEVR--AQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSR 115
+++ S EE+ A + W Q+Y+ DR ++ +V+ E+ G A+ +T+D LG R
Sbjct: 230 LASCSPEEIIEAAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQR 289
Query: 116 YRDLKNKFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDD 175
+D+K KF+ A + +K+ N + S G + ++ D S+ W D
Sbjct: 290 EKDMKLKFSNTK----AGPKAMKKTNVEE-----------SQGASRALSKFIDPSLTWKD 334
Query: 176 VRSLVQATKLPIVCKGI 192
+ L + TKLPIV KG+
Sbjct: 335 IEELKKKTKLPIVIKGV 351
>3sr7_A Isopentenyl-diphosphate delta-isomerase; isopentenyl pyrophosphate
isomerase, TIM-barrel; 2.04A {Streptococcus mutans}
Length = 365
Score = 78.7 bits (194), Expect = 1e-17
Identities = 24/188 (12%), Positives = 48/188 (25%), Gaps = 34/188 (18%)
Query: 3 RNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTS 62
++ + D G + P I + A+ A + + S
Sbjct: 69 YDLAEIDLSTHFAGQDFDFPFYINAMTGGSQKGKEVNEKLAQVADTCGLLFVTGSYS--- 125
Query: 63 LEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYR-DLKN 121
K+ + V+++ A I +D
Sbjct: 126 -----------------TALKNPDDTSYQVKKSRPHLLLATNIGLDKPYQAGLQAVRDLQ 168
Query: 122 KFTMPPYLSLA----------NFRNLKQHNEDISKFRD--ISAEECSSGLTDYVANQFDD 169
+ +++L FR+ K+H D +K +E G+ D
Sbjct: 169 PLFLQVHINLMQELLMPEGEREFRSWKKHLSDYAKKLQLPFILKEVGFGMDVKTIQTAID 228
Query: 170 S-VDWDDV 176
V D+
Sbjct: 229 LGVKTVDI 236
>1p0k_A Isopentenyl-diphosphate delta-isomerase; terpene biosynthesis,
dimethylallyl diphosphate, flavoprotein; 1.90A {Bacillus
subtilis} SCOP: c.1.4.1 PDB: 1p0n_A*
Length = 349
Score = 57.4 bits (139), Expect = 3e-10
Identities = 19/117 (16%), Positives = 38/117 (32%), Gaps = 12/117 (10%)
Query: 3 RNVCDRDSGLTVLGTRYRCPVGIAPSAMQ-KLAHADGEVATARAAGMMDAIMILSLMST- 60
+ D + P+ I + + ARAA + + +
Sbjct: 38 LALEQVDISTKIGELSSSSPIFINAMTGGGGKLTYEINKSLARAASQAGIPLAVGSQMSA 97
Query: 61 -------TSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTA 110
S E VR +NP+ ++ + A + + V E G +A+ I ++
Sbjct: 98 LKDPSERLSYEIVRKENPNGLIFANLGSEATAAQAKEAV---EMIGANALQIHLNVI 151
>3vkj_A Isopentenyl-diphosphate delta-isomerase; type 2 isopentenyl
diphosphate isomerase; HET: FNR; 1.70A {Sulfolobus
shibatae} PDB: 2zrv_A* 2zrw_A* 2zrx_A* 2zry_A* 2zrz_A*
3b03_A* 3b04_A* 3b05_A* 3b06_A* 2zru_A*
Length = 368
Score = 51.0 bits (122), Expect = 5e-08
Identities = 20/192 (10%), Positives = 51/192 (26%), Gaps = 38/192 (19%)
Query: 3 RNVCDRDSGLTVLGTRYRCPVGIAP-SAMQKLAHADGEVATARAAGMMDAIMILSLMSTT 61
+ + ++ PV + + + + A A M +
Sbjct: 42 ISFSEINTKTKFFRKEISVPVMVTGMTGGRNELGRINK-IIAEVAEKFGIPMGVGSQR-V 99
Query: 62 SLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDTAVLGSRYRDLKN 121
++E+ A+ S +V++ + + M V G ++ ++
Sbjct: 100 AIEKAEARE-----------------SFAIVRKVAPTIPIIANLGMPQLVKGYGLKEFQD 142
Query: 122 KFTMPPYLSLANFRNLKQHNEDISKFRDISAEECSSGLTDYVANQFDDSVDWDDVRSLVQ 181
M ++A N Q + + +R + +
Sbjct: 143 AIQMIEADAIAVHLNPAQ------------------EVFQPEGEPEYQIYALEKLRDISK 184
Query: 182 ATKLPIVCKGIP 193
+PI+ K
Sbjct: 185 ELSVPIIVKESG 196
>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 = 45.8 bits (108), Expect = 3e-06
Identities = 44/267 (16%), Positives = 73/267 (27%), Gaps = 110/267 (41%)
Query: 11 GLTVLGTRYR--CPV-GIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSLEE-- 65
G+ L Y + G P ++ AT + G++ A+ I S S
Sbjct: 242 GVIQLA-HYVVTAKLLGFTPGELRSYLKG----ATGHSQGLVTAVAIAETDSWESFFVSV 296
Query: 66 -----------VRAQN--PSTTLWLQMYIFKD---------------RALSLQMVQ---- 93
VR P+T+L + +D L+ + VQ
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSIL--EDSLENNEGVPSPMLSISNLTQEQVQDYVN 354
Query: 94 --RAERSGYSAIVITMDTAVLGSRYRDLKN---KF--TMPPYLSLA----NFRNLK-QHN 141
+ + I+ L N + PP SL R K
Sbjct: 355 KTNSHLPAGKQVEIS------------LVNGAKNLVVSGPP-QSLYGLNLTLRKAKAPSG 401
Query: 142 EDISK--FRD-----------ISA-------EECSSGL-TDYVANQFD-----------D 169
D S+ F + +++ S + D V N D
Sbjct: 402 LDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYD 461
Query: 170 SVDWDDVR--------SLVQA-TKLPI 187
+ D D+R +V +LP+
Sbjct: 462 TFDGSDLRVLSGSISERIVDCIIRLPV 488
Score = 32.3 bits (73), Expect = 0.11
Identities = 40/216 (18%), Positives = 74/216 (34%), Gaps = 64/216 (29%)
Query: 3 RNVCDR-DS------GLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMIL 55
++V +R D+ G ++L PV + H GE I
Sbjct: 1643 QDVWNRADNHFKDTYGFSILDIVINNPVNLT-------IHFGGEKGKRIRENYSAMIFET 1695
Query: 56 SLMSTTSLEEV-RAQNPSTTLWLQMYIFK--DRALSL-QMVQRAERSGYSAIVITMDTAV 111
+ E++ + N +T Y F+ LS Q Q A + M+ A
Sbjct: 1696 IVDGKLKTEKIFKEINEHSTS----YTFRSEKGLLSATQFTQPA-------LT-LMEKAA 1743
Query: 112 LGSRYRDLKNKFTMPP-----------Y--L-SLANFRNLKQHNED---ISKFR----DI 150
+ DLK+K +P Y L SLA+ ++ E + +R +
Sbjct: 1744 ----FEDLKSKGLIPADATFAGHSLGEYAALASLADVMSI----ESLVEVVFYRGMTMQV 1795
Query: 151 SAEECSSGLTDY--VA---NQFDDSVDWDDVRSLVQ 181
+ G ++Y +A + S + ++ +V+
Sbjct: 1796 AVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVE 1831
Score = 28.1 bits (62), Expect = 2.3
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 38 GEV-ATARAAGMMDA-----IMILSLMSTTSLEEVRAQ 69
G++ A +++ I I+ L + SLEEV
Sbjct: 1857 GDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGH 1894
>1vcf_A Isopentenyl-diphosphate delta-isomerase; TIM barrel, structural
genomics, riken structural genomics/P initiative, RSGI;
HET: FMN; 2.60A {Thermus thermophilus} SCOP: c.1.4.1
PDB: 1vcg_A* 3dh7_A*
Length = 332
Score = 42.6 bits (100), Expect = 3e-05
Identities = 19/116 (16%), Positives = 33/116 (28%), Gaps = 8/116 (6%)
Query: 3 RNVCDRDSGLTVLGTRYRCPVGIAPSAMQKLAHADGEVATARAAGMMDAIMILSLMSTTS 62
+ + D LG + P I + +A A AA + M+L
Sbjct: 41 LALSEVDLTTPFLGKTLKAPFLIGAMTGGEENGERINLALAEAAEALGVGMMLGSGRILL 100
Query: 63 LEE-------VRAQNPSTTLWLQMYIFKDRALSLQMVQRA-ERSGYSAIVITMDTA 110
VR P L + + + R + R E A+ ++
Sbjct: 101 ERPEALRSFRVRKVAPKALLIANLGLAQLRRYGRDDLLRLVEMLEADALAFHVNPL 156
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 30.5 bits (69), Expect = 0.36
Identities = 22/119 (18%), Positives = 34/119 (28%), Gaps = 14/119 (11%)
Query: 77 LQMYIFKDRALS----LQMVQRAERSGYS----AIVITMDTAVLGSRYRDLKNKFTMPPY 128
L + + + QM RA R G AI+I +
Sbjct: 348 LYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIV-GKRDREIAVKRYIFGEPERIT 406
Query: 129 LSLANFRNLKQH-NEDISKFRDISAEECSSGLTD-YVANQFDDSVDW---DDVRSLVQA 182
L +L+ H I + EE D + Q + S+ + VR L
Sbjct: 407 SKLGVETHLRFHSLSIICDGYAKTLEELEDFFADTFFFKQNEISLSYELERVVRQLENW 465
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 29.4 bits (66), Expect = 0.79
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 6/71 (8%)
Query: 89 LQMVQRAERSGYS----AIVITMDTAVLGSRYRDLKNKFTMPPYLSLANFRNLKQH-NED 143
QM+ RA R Y I+++ + K + L+N NL+
Sbjct: 363 HQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGK-PEKLFSQLSNESNLRSQVLAL 421
Query: 144 ISKFRDISAEE 154
I+ F + EE
Sbjct: 422 IATFGYSTVEE 432
>1oe1_A Dissimilatory copper-containing nitrite reductase; denitrification;
HET: PG4; 1.04A {Alcaligenes xylosoxidans} SCOP: b.6.1.3
b.6.1.3 PDB: 1oe3_A* 2xwz_A* 2vn3_A 2zon_A* 1haw_A
1hau_A* 2vm4_A* 2vw4_A* 2vw6_A* 2vw7_A* 2vm3_A* 1oe2_A*
2jl0_A* 2xx1_A 2xxg_A* 2xxf_A* 1gs8_A 1wa1_X* 1wa2_X*
2jl3_A* ...
Length = 336
Score = 29.0 bits (65), Expect = 0.96
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 35 HADGEVATARAAGMMDAIMIL 55
+G V +GM +M+L
Sbjct: 131 APEGMVPWHVVSGMSGTLMVL 151
>2vha_A Periplasmic binding transport protein; periplasmic binding protein,
ligand binding, ultrahigh resolution; HET: GLU; 1.00A
{Shigella flexneri} PDB: 2ia4_A*
Length = 287
Score = 28.1 bits (63), Expect = 1.7
Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 9/65 (13%)
Query: 60 TTSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQ--RAERSGYSAIVITMDTAVLGSRYR 117
TTS + N + +++ KD S + ++ RA MD A+L
Sbjct: 139 TTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAV-------AFMMDDALLAGERA 191
Query: 118 DLKNK 122
K
Sbjct: 192 KAKKP 196
>3qy7_A Tyrosine-protein phosphatase YWQE; TIM barrel, polymerase and
histindinol phosphatase(PHP)-like phosphatase,
hydrolase; 1.62A {Bacillus subtilis} PDB: 3qy6_A
Length = 262
Score = 27.3 bits (60), Expect = 3.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 83 KDRALSLQMVQRAERSGYSAIVIT 106
D A S++M + A R G I+ T
Sbjct: 17 GDSADSIEMARAAVRQGIRTIIAT 40
>2bw4_A Copper-containing nitrite reductase; oxidoreductase,
denitrification, catalysis, enzyme mechanism, nitrate
assimilation; 0.90A {Achromobacter cycloclastes} SCOP:
b.6.1.3 b.6.1.3 PDB: 1nib_A 1nia_A 1nid_A 1nie_A 1nic_A
1nif_A 2bw5_A 2bwd_A 2bwi_A 2nrd_A 2y1a_A 1kcb_A 1rzp_A*
1rzq_A 2avf_A 1as6_A 1aq8_A 1as7_A 1as8_A 2afn_A ...
Length = 340
Score = 27.2 bits (60), Expect = 3.6
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 35 HADGEVATARAAGMMDAIMIL 55
+G V +GM AIM+L
Sbjct: 137 APEGMVPWHVTSGMNGAIMVL 157
>3dcp_A Histidinol-phosphatase; HISK, histidine biosynthesis, NESG, LMR141,
structural genomics, PSI-2, protein structure
initiative; 2.10A {Listeria monocytogenes str}
Length = 283
Score = 27.3 bits (60), Expect = 3.6
Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 4/89 (4%)
Query: 90 QMVQRAERSGYSAIVITMDTAVLGSRYRDLKNKFTMPPYLSLANFRNLKQHNEDISKFRD 149
+MV +A + I + A L S + + +L + + ++ +
Sbjct: 22 EMVLKAIELDFDEYSIV-EHAPLSSEFMKNTAGDKEAVTTASMAMSDLPYYFKKMNHIKK 80
Query: 150 ISAEECS--SGL-TDYVANQFDDSVDWDD 175
A + G DY+ D + D+ +
Sbjct: 81 KYASDLLIHIGFEVDYLIGYEDFTRDFLN 109
>3ks6_A Glycerophosphoryl diester phosphodiesterase; structural genomics,
joint center for structural genomics, JCSG; HET: MSE;
1.80A {Agrobacterium tumefaciens str} PDB: 3ks5_A*
Length = 250
Score = 26.8 bits (60), Expect = 3.9
Identities = 10/66 (15%), Positives = 21/66 (31%), Gaps = 1/66 (1%)
Query: 40 VATARAAGMMDAIMILSLMSTTSLEEVRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSG 99
+A M++ S S++E+ LWL + +++ A
Sbjct: 123 IAGLERHSMLERTTFSSF-LLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHS 181
Query: 100 YSAIVI 105
I +
Sbjct: 182 IHEIGV 187
>2yxo_A Histidinol phosphatase; metal-dependent, hydrolase; 1.60A {Thermus
thermophilus} PDB: 2yz5_A 2z4g_A
Length = 267
Score = 26.6 bits (59), Expect = 5.8
Identities = 8/57 (14%), Positives = 18/57 (31%), Gaps = 5/57 (8%)
Query: 90 QMVQRAERSGYSAIVIT--MDTAVLGSRYRDLKNKFTMPPYLSLANFRNLKQHNEDI 144
++ A G +V T + +P Y L +++ +D+
Sbjct: 20 AYLEEARAKGLKGVVFTDHSPMPPWYDPESRM-RLEALPFY--LLALERVRERAQDL 73
>1unf_X Iron superoxide dismutase; oxidoreductase, eukaryotic,
metalloprotein; 1.97A {Vigna unguiculata} SCOP: a.2.11.1
d.44.1.1
Length = 238
Score = 26.1 bits (58), Expect = 6.1
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 161 DYVANQFDDSVDWDDVRSLVQATK 184
DY++ D V WD V S ++ K
Sbjct: 211 DYISVFMDKLVSWDAVSSRLEQAK 234
>2wje_A CPS4B, tyrosine-protein phosphatase CPSB; capsule
biogenesis/degradation, manganese, hydrolase,
exopolysaccharide synthesis; 1.90A {Streptococcus
pneumoniae} PDB: 2wjd_A 2wjf_A 3qy8_A
Length = 247
Score = 26.5 bits (58), Expect = 6.1
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 83 KDRALSLQMVQRAERSGYSAIVIT 106
K R S ++ + R G IV T
Sbjct: 21 KSREESKALLAESYRQGVRTIVST 44
>1x60_A Sporulation-specific N-acetylmuramoyl-L-alanine amidase; CWLC,
CWLCR, peptidoglycan, cell WALL lytic amidase, tandem
repeats, hydrolase; NMR {Bacillus subtilis}
Length = 79
Score = 25.2 bits (55), Expect = 6.5
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 66 VRAQNPSTTLWLQMYIFKDRALSLQMVQRAERSGYSAIVITMDT 109
++ + S +Q+ FK +A + + AE G+ +IV+ D
Sbjct: 1 LKKTSSSGLYKVQIGAFKVKANADSLASNAEAKGFDSIVLLKDG 44
>2jxu_A TERB, KP-TERB; tellurite resistance protein, plasmid, unknown
function; NMR {Klebsiella pneumoniae ntuh-k2044}
Length = 153
Score = 26.1 bits (57), Expect = 6.5
Identities = 6/41 (14%), Positives = 14/41 (34%)
Query: 28 SAMQKLAHADGEVATARAAGMMDAIMILSLMSTTSLEEVRA 68
+ ++A A V++ M+ + + EV
Sbjct: 36 AVCARIAVASDGVSSEEKQKMIGFLRSSEELKVFDTAEVIE 76
>1m65_A Hypothetical protein YCDX; structural genomics, beta-alpha-barrel,
metallo-enzyme, STRU function project, S2F, unknown
function; 1.57A {Escherichia coli} SCOP: c.6.3.1 PDB:
1m68_A 1pb0_A
Length = 245
Score = 26.3 bits (58), Expect = 6.9
Identities = 10/86 (11%), Positives = 22/86 (25%), Gaps = 20/86 (23%)
Query: 90 QMVQRAERSGYSAIVITMDTAVLGSRYRDLKNKFTMPPYLSLANFRNLKQHNEDISKFRD 149
+ +A++ G IT D M +F N++ +
Sbjct: 22 DYIAQAKQKGIKLFAIT-DHGP------------DMEDAPHHWHFINMRIWPRVVDGVGI 68
Query: 150 ISAEEC-------SSGLTDYVANQFD 168
+ E + + + D
Sbjct: 69 LRGIEANIKNVDGEIDCSGKMFDSLD 94
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 26.2 bits (58), Expect = 7.4
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 5/79 (6%)
Query: 89 LQMVQRAERSGYS----AIVITMDTAVLGSRYRDLKNKFTMPPYLSLANFRNLKQH-NED 143
QM RA R G+ +IV+ D + ++ P L + R
Sbjct: 384 KQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIESKLGSERAFYTFLLGI 443
Query: 144 ISKFRDISAEECSSGLTDY 162
+S ++S ++ + +
Sbjct: 444 LSAEGNLSEKQLENFAYES 462
>3js4_A Superoxide dismutase; niaid, ssgcid, seattle structural genomics
center for infect disease, GRAM-negative bacteria; 1.95A
{Anaplasma phagocytophilum}
Length = 227
Score = 25.7 bits (57), Expect = 9.8
Identities = 4/25 (16%), Positives = 11/25 (44%)
Query: 161 DYVANQFDDSVDWDDVRSLVQATKL 185
Y+ + ++WD V ++ +
Sbjct: 202 KYIDVFLEHLLNWDFVLGRLEDAGV 226
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 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,891,398
Number of extensions: 162604
Number of successful extensions: 482
Number of sequences better than 10.0: 1
Number of HSP's gapped: 467
Number of HSP's successfully gapped: 36
Length of query: 193
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 105
Effective length of database: 4,244,745
Effective search space: 445698225
Effective search space used: 445698225
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: 55 (25.0 bits)