RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14392
(164 letters)
>3g5k_A Peptide deformylase, mitochondrial; actinonin, hydrolase, iron,
metal-bindi mitochondrion, protein biosynthesis, transit
peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_A
Length = 183
Score = 153 bits (389), Expect = 2e-48
Identities = 60/149 (40%), Positives = 85/149 (57%), Gaps = 2/149 (1%)
Query: 4 IILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFP-DPEESFSEGDIKKFEMQAFPHMVWI 62
+ ++ VM+R GLSAPQ+G+P ++ + P +M+ FP V++
Sbjct: 35 LTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFV 94
Query: 63 NPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQ 122
NP +++LD VT EGC S+ A VPR++ VQ++GLD G+ W A GWAARIIQ
Sbjct: 95 NPSLRVLD-SRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQ 153
Query: 123 HEMDHLDGLLFTDSMLPKSLECVCWQDIN 151
HEMDHL G LF D M ++ V W +N
Sbjct: 154 HEMDHLQGCLFIDKMDSRTFTNVYWMKVN 182
>1zxz_A PDF, peptide deformylase, mitochondrial; PDF1A, eukaryote, higher
plant, zinc ION, hydrolase; 2.80A {Arabidopsis thaliana}
PDB: 1zy0_A 1zy1_A
Length = 197
Score = 141 bits (357), Expect = 2e-43
Identities = 56/146 (38%), Positives = 80/146 (54%), Gaps = 2/146 (1%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESF-SEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+APQ+G+PLR+ ++ S+ + +I E + F MV +NP +K K
Sbjct: 49 GLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERS-NKKALF 107
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A V RY +V +TG D GK A GW ARI+QHE DHLDG L+ D M
Sbjct: 108 FEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKM 167
Query: 138 LPKSLECVCWQDINLQNGLLELRYYM 163
+P++ V D+ L G +L +
Sbjct: 168 VPRTFRTVDNLDLPLAEGCPKLGSHH 193
>3dld_A Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae
PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas
oryzae PV}
Length = 171
Score = 122 bits (308), Expect = 4e-36
Identities = 40/117 (34%), Positives = 58/117 (49%), Gaps = 9/117 (7%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + L+L + F E E A P N +++ L +
Sbjct: 46 GLAAPQIAVDLQLMVFGFEASER--------YPEAPAVPLTALANAQIEPLS-DEMENGW 96
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ L+A +PRYR ++ G G P AEG+ AR++QHE DHL G L+
Sbjct: 97 EGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPS 153
>1y6h_A Peptide deformylase; open and close conformation, PDF, hydrolase;
2.20A {Leptospira interrogans} SCOP: d.167.1.1 PDB:
1sv2_A* 1vey_A* 1vev_A 1vez_A 1szz_A*
Length = 177
Score = 120 bits (303), Expect = 2e-35
Identities = 36/117 (30%), Positives = 58/117 (49%), Gaps = 9/117 (7%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+G+ ++ +V D E P + +NP + L KD
Sbjct: 48 GLAAPQIGILKQIVVVGSEDNER--------YPGTPDVPERIILNPVITPLT-KDTSGFW 98
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ ++ V R ++++ +DE G T +G+ A + QHE DHL G+L+ D
Sbjct: 99 EGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVD 155
>1v3y_A Peptide deformylase; protein synthesis, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, hydrolase; 1.81A {Thermus thermophilus} SCOP:
d.167.1.1
Length = 192
Score = 114 bits (288), Expect = 7e-33
Identities = 44/118 (37%), Positives = 63/118 (53%), Gaps = 5/118 (4%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+GL RLF+ +E E + E+ V NP I + V
Sbjct: 44 GLAAPQIGLSQRLFVAV-EYADEPEGEEERPLRELVRRV-YVVANPV--ITYREGLVEGT 99
Query: 79 EGCASLKSLQA-KVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC SL L + +VPR ++++ DE G+ EG+ AR+ QHE+DHLDG+LF +
Sbjct: 100 EGCLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFE 157
>3l87_A Peptide deformylase; hydrolase, iron, metal-binding, PR
biosynthesis; 2.00A {Streptococcus mutans}
Length = 238
Score = 115 bits (289), Expect = 1e-32
Identities = 35/121 (28%), Positives = 62/121 (51%), Gaps = 10/121 (8%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+PE+ + E A V NP I+ + + AL
Sbjct: 106 GLAAPQLDISKRIIAVLIPNPED---KDGNPPKEAYALK-EVMYNPR--IIAHSVQDAAL 159
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ + ++ V R+ +V + D+ +G+ + ++QHE+DH +G++F
Sbjct: 160 ADGEGCLSVDRVVEGYVIRHSRVTIEYYDKNSDKKKLKLKGYQSIVVQHEIDHTNGIMFF 219
Query: 135 D 135
D
Sbjct: 220 D 220
>3svj_P Peptide deformylase 3; alpha-beta, metal binding protein, HYDR
hydrolase inhibitor complex; HET: 4LI; 1.55A
{Streptococcus pneumoniae} PDB: 3str_P* 3sw8_P* 1lm6_A
2aia_A* 2ai7_A* 2aie_P* 2os3_A*
Length = 203
Score = 111 bits (280), Expect = 1e-31
Identities = 32/121 (26%), Positives = 64/121 (52%), Gaps = 11/121 (9%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+ E + + + + NP+ I+ + + AL
Sbjct: 72 GLAAPQLDISKRIIAVLVPNIVE-----EGETPQEAYDLEAIMYNPK--IVSHSVQDAAL 124
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ +++ V R+ +V + D+ G+ +G+ + ++QHE+DH++G++F
Sbjct: 125 GEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFY 184
Query: 135 D 135
D
Sbjct: 185 D 185
>3e3u_A Peptide deformylase; metallo-enzyme, hydrolase, iron,
metal-binding, protein biosynthesis; HET: NVC; 1.56A
{Mycobacterium tuberculosis}
Length = 197
Score = 110 bits (277), Expect = 3e-31
Identities = 40/121 (33%), Positives = 53/121 (43%), Gaps = 15/121 (12%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDY----KDK 74
GL+A Q+G LRLF+ A V INP ++ + D
Sbjct: 51 GLAANQIGCSLRLFVYDCAADRAM-----------TARRRGVVINPVLETSEIPETMPDP 99
Query: 75 VTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
T EGC S+ R + ++TGLD G P S G AR++QHE HLDG L+
Sbjct: 100 DTDDEGCLSVPGESFPTGRAKWARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYL 159
Query: 135 D 135
D
Sbjct: 160 D 160
>2os0_A Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis}
PDB: 2os1_A* 3g6n_A 3cmd_A
Length = 188
Score = 108 bits (272), Expect = 1e-30
Identities = 33/121 (27%), Positives = 59/121 (48%), Gaps = 15/121 (12%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P + E + V NP+ IL + + L
Sbjct: 60 GLAAPQLDISKRIIAVHVPSNDP---ENETPSLST------VMYNPK--ILSHSVQDVCL 108
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ + + V R+ K+ ++ D G+ + + A ++QHE+DH++G++F
Sbjct: 109 GEGEGCLSVDRDVPGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFY 168
Query: 135 D 135
D
Sbjct: 169 D 169
>3pn3_A Peptide deformylase 1B, chloroplastic; PDF, N-terminal excision
pathway, N induced-FIT, hydrolase-hydrolase inhibitor
complex; HET: PN3; 1.30A {Arabidopsis thaliana} PDB:
3m6p_A* 3o3j_A* 3pn2_A 3m6o_A* 3pn4_A* 3pn5_A 3m6q_A
3pn6_A 3m6r_A 3cpm_A
Length = 193
Score = 108 bits (272), Expect = 1e-30
Identities = 40/117 (34%), Positives = 58/117 (49%), Gaps = 14/117 (11%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GLSAPQVGL ++L + + + +V +NP++K V
Sbjct: 43 GLSAPQVGLNVQLMVF------------NPAGEPGEGKE-IVLVNPKIKKYS-DKLVPFD 88
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S + A+V R + V++ D TG+ S + ARI QHE DHL+G+LF D
Sbjct: 89 EGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFD 145
>1rl4_A Formylmethionine deformylase; crystal engineering, drug design,
malaria, PDF, peptide DEFO plasmodium, hydrolase; HET:
BRR BL5; 2.18A {Plasmodium falciparum} SCOP: d.167.1.1
PDB: 1rqc_A 1jym_A
Length = 188
Score = 107 bits (270), Expect = 3e-30
Identities = 35/117 (29%), Positives = 53/117 (45%), Gaps = 13/117 (11%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GLSAPQV + R+ + + + + ++INP + K+ +
Sbjct: 51 GLSAPQVNISKRIIVW------------NALYEKRKEENERIFINPSIVEQS-LVKLKLI 97
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S ++ KV R V ++ D G +G +RI QHE DHL+G LF D
Sbjct: 98 EGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFID 154
>1ws0_A Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A
{Bacillus cereus} PDB: 1ws1_A*
Length = 156
Score = 104 bits (262), Expect = 2e-29
Identities = 40/117 (34%), Positives = 57/117 (48%), Gaps = 18/117 (15%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQVG+ L++ +V D + INP IL+ + +
Sbjct: 46 GLAAPQVGVSLQVAVVDVDDDTG----------------KIELINPS--ILEKRGEQVGP 87
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S L +V R +++ + GK AEG+ AR IQHE+DHL G+LFT
Sbjct: 88 EGCLSFPGLYGEVERADYIKVRAQNRRGKVFLLEAEGFLARAIQHEIDHLHGVLFTS 144
>2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A
{Helicobacter pylori} PDB: 2ew6_A* 2ew7_A
Length = 181
Score = 104 bits (262), Expect = 4e-29
Identities = 35/119 (29%), Positives = 57/119 (47%), Gaps = 16/119 (13%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPH--MVWINPEMKILDYKDKVT 76
GL+A QVGLPLR+ I+ ++ + + + INP+ ++ +
Sbjct: 45 GLAAIQVGLPLRMLII------------NLPQEDGVQHKEDCLEIINPK--FIETGGSMM 90
Query: 77 ALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ +V R+ KV++ + + A A IQHE+DHL+G+LF D
Sbjct: 91 YKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVD 149
>3u04_A Peptide deformylase 1; ssgcid, actinonin, ehrlichia chaffeensi
structural genomics; HET: BB2; 1.70A {Ehrlichia
chaffeensis} PDB: 3oca_A
Length = 190
Score = 103 bits (260), Expect = 9e-29
Identities = 35/121 (28%), Positives = 64/121 (52%), Gaps = 5/121 (4%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPH----MVWINPEMKILDYKDK 74
GL+A QVG+ R+ ++ P+ E + + + +++ + INP++ + ++K
Sbjct: 48 GLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDIS-QEK 106
Query: 75 VTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
V EGC S+ + R +++ + LD G A+GW AR +QHE+DHL+G +F
Sbjct: 107 VKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFL 166
Query: 135 D 135
Sbjct: 167 K 167
>1lme_A PDF, peptide deformylase; thermophIle, metalloenzyme,
deformylation, structural genomics, PSI, protein
structure initiative; 2.20A {Thermotoga maritima} SCOP:
d.167.1.1
Length = 176
Score = 102 bits (258), Expect = 1e-28
Identities = 36/117 (30%), Positives = 59/117 (50%), Gaps = 19/117 (16%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQVG+ R F++ D+ + INPE+ +D + A
Sbjct: 56 GLAAPQVGISQRFFVM------------DVGNGPV------AVINPEILEID-PETEVAE 96
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S + ++ R +++++ + G+ EG+AAR+ QHE DHL+G+L D
Sbjct: 97 EGCLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARVFQHEFDHLNGVLIID 153
>1lm4_A Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.45A
{Staphylococcus aureus} SCOP: d.167.1.1 PDB: 1lqw_A
2ai9_A 1lmh_A 1q1y_A*
Length = 194
Score = 103 bits (258), Expect = 2e-28
Identities = 34/121 (28%), Positives = 61/121 (50%), Gaps = 18/121 (14%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V PD +G K ++ + +NP+ I+ + + L
Sbjct: 71 GLAAPQINISKRMIAVLIPD------DGSGKSYDY------MLVNPK--IVSHSVQEAYL 116
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ ++ V R+ ++ + D G +G+ A + QHE+DHL+G++F
Sbjct: 117 PTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFY 176
Query: 135 D 135
D
Sbjct: 177 D 177
>3qu1_A Peptide deformylase 2; structural genomics, center for structural
genomics of infec diseases, csgid, metal binding; 1.80A
{Vibrio cholerae}
Length = 171
Score = 102 bits (257), Expect = 2e-28
Identities = 39/117 (33%), Positives = 57/117 (48%), Gaps = 17/117 (14%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQVG + ++ D ++ + P +V INP+ ++ +K
Sbjct: 49 GLAAPQVGREEAIVVI---DLSDNRDQ-----------P-LVLINPK--VVSGSNKEMGQ 91
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ A V RY V + LD GKP + A ++QHE+DHL G LF D
Sbjct: 92 EGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFID 148
>1xeo_A Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A
{Escherichia coli} SCOP: d.167.1.1 PDB: 1bs5_A 1bs6_A
1bs7_A 1bs8_A 1bsj_A* 1bsk_A* 1bsz_A* 1g27_A* 1bs4_A*
1icj_A* 1lru_A* 1xem_A 1xen_A 1g2a_A 2ai8_A* 4al3_A
4al2_A 3k6l_A* 1dff_A 1def_A ...
Length = 168
Score = 102 bits (256), Expect = 3e-28
Identities = 45/117 (38%), Positives = 60/117 (51%), Gaps = 17/117 (14%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+A QV + R+ ++ D E+ E +V INPE +L+ +
Sbjct: 45 GLAATQVDIHQRIIVI---DVSENRDE-----------R-LVLINPE--LLEKSGETGIE 87
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D
Sbjct: 88 EGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMD 144
>2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase,
metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A
Length = 188
Score = 102 bits (257), Expect = 3e-28
Identities = 45/117 (38%), Positives = 61/117 (52%), Gaps = 17/117 (14%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+A QV + R+ ++ D SE ++ +V INPE +L+ +
Sbjct: 45 GLAATQVDIHQRIIVI---D----VSENRDER--------LVLINPE--LLEKSGETGIE 87
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D
Sbjct: 88 EGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMD 144
>2okl_A Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus
cereus} PDB: 1lqy_A*
Length = 185
Score = 101 bits (254), Expect = 7e-28
Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 19/121 (15%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+G+ ++ V + + + NP+ I+ + + T L
Sbjct: 61 GLAAPQIGVSKKMIAV------------HVTDADGTLYS-HALFNPK--IISHSVERTYL 105
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ + + VPRY ++ + G+ +G A + QHE+DHL+G++F
Sbjct: 106 QGGEGCLSVDREVPGYVPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFY 165
Query: 135 D 135
D
Sbjct: 166 D 166
>1n5n_A Peptide deformylase; metalloenzyme, drug design, deformylation,
hydrolase; 1.80A {Pseudomonas aeruginosa} SCOP:
d.167.1.1 PDB: 1s17_A* 1ix1_A* 1lry_A*
Length = 180
Score = 98.3 bits (246), Expect = 8e-27
Identities = 44/117 (37%), Positives = 58/117 (49%), Gaps = 16/117 (13%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+A QV + R+ ++ D E SE P V+INPE + L ++
Sbjct: 58 GLAATQVNVHKRIVVM---DLSEDKSE-----------P-RVFINPEFEPLT-EEMDQYQ 101
Query: 79 EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ V R +KV++ LD G P AEG A IQHE DHL+G LF D
Sbjct: 102 EGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVD 158
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 36.0 bits (82), Expect = 0.004
Identities = 26/141 (18%), Positives = 51/141 (36%), Gaps = 32/141 (22%)
Query: 37 PDPEESFSEGDIKKFEMQAFPHMVWINPEMK-ILDYKDKVTA---LEGCASLKSLQAK-V 91
E++F + + ++Q P + E+ I+ KD V+ L L S Q + V
Sbjct: 23 SVFEDAFVD-NFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT--LLSKQEEMV 79
Query: 92 PRYRKVQLTGLDETGKPD-SWTAEGWAARIIQHEMD-----------HLDGLLFTDSMLP 139
++ ++E + + + Q M + D +F +
Sbjct: 80 QKF-------VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 140 KSLECVCWQDINLQNGLLELR 160
+ L+ + L+ LLELR
Sbjct: 133 R-LQPY----LKLRQALLELR 148
Score = 33.7 bits (76), Expect = 0.026
Identities = 32/180 (17%), Positives = 59/180 (32%), Gaps = 28/180 (15%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKF------EMQ 54
+ +L+ K FD + P +P L + + D +S + K E Q
Sbjct: 361 SSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420
Query: 55 AFPHMVWINPEMKILDYKDKVTALEGCASLKSLQAK-VPRYRKVQLTGLDETGKPDSWTA 113
+ I L+ K K + +L V Y + D +
Sbjct: 421 PKESTISIP--SIYLELKVK------LENEYALHRSIVDHYNIPK--TFDSDDLIPPYLD 470
Query: 114 EGWAARIIQH----EMDHLDGL---LFTD-SMLPKSL--ECVCWQDI-NLQNGLLELRYY 162
+ + + I H E L +F D L + + + W ++ N L +L++Y
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFY 530
>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 = 29.9 bits (66), Expect = 0.23
Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 17/44 (38%)
Query: 83 SLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMD 126
+LK LQA + Y DS A A I+ M+
Sbjct: 21 ALKKLQASLKLY------------ADDS--APALA---IKATME 47
>1hnr_A H-NS; histone-like protein H1, DNA-binding protein; NMR
{Escherichia coli} SCOP: a.155.1.1 PDB: 1hns_A
Length = 47
Score = 25.2 bits (55), Expect = 2.5
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 92 PRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMD 126
R K DE G+ +WT +G +I+ MD
Sbjct: 2 QRPAKYSYV--DENGETKTWTGQGRTPAVIKKAMD 34
>2l93_A DNA-binding protein H-NS; at HOOK; NMR {Salmonella typhimurium}
Length = 55
Score = 24.9 bits (54), Expect = 3.5
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 92 PRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMD 126
R K DE G+ +WT +G +I+ M+
Sbjct: 2 ARPAKYSYV--DENGETKTWTGQGRTPAVIKKAME 34
>2bw0_A 10-FTHFDH, 10-formyltetrahydrofolate dehydrogenase; nucleotide
biosynthesis, oxidoreductase; 1.7A {Homo sapiens} SCOP:
b.46.1.1 c.65.1.1 PDB: 2cfi_A* 1s3i_A
Length = 329
Score = 26.8 bits (60), Expect = 3.8
Identities = 5/23 (21%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 121 IQHEMDHLDGLLF-TDSMLPKSL 142
+ H H G+ T+++ +S+
Sbjct: 1 MHHHHHHSSGVDLGTENLYFQSM 23
>1pgl_2 Bean POD mottle virus large (L) subunit; comovirus, viral coat
protein, bean POD mottle virus (BPMV), icosahedral
virus, virus/RNA complex; 2.80A {Bean-pod mottle virus}
SCOP: b.121.4.2 b.121.4.2 PDB: 1bmv_2 1pgw_2
Length = 370
Score = 25.9 bits (56), Expect = 8.0
Identities = 8/44 (18%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 15 FDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPH 58
F++ +++P + + FI +++ +AFPH
Sbjct: 248 FEVSKMTSPYIKCTVSFFIAFGNLADDT--------INFEAFPH 283
>2nlz_A Cephalosporin acylase; structural genomics, protein structure
initiative, PSI, nysgxrc; 2.70A {Bacillus halodurans}
SCOP: d.153.1.6
Length = 547
Score = 25.6 bits (57), Expect = 9.6
Identities = 4/22 (18%), Positives = 11/22 (50%)
Query: 3 IIILQMKNVMKRFDLFGLSAPQ 24
++ L+ N++K F+ +
Sbjct: 274 LVALEALNIVKGFEFYHKDTVD 295
>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 = 25.8 bits (56), Expect = 10.0
Identities = 21/88 (23%), Positives = 31/88 (35%), Gaps = 29/88 (32%)
Query: 27 LPLRLFIVA------F----PDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVT 76
+P F +A F P+P E F+ D E +V K L Y
Sbjct: 22 VPTASFFIASQLQEQFNKILPEPTEGFAADD----EPTTPAELV-----GKFLGY----- 67
Query: 77 ALEGCASLKSLQAKVPRYRKVQLTGLDE 104
+SL +KV ++ +V L E
Sbjct: 68 ----VSSLVE-PSKVGQFDQVLNLCLTE 90
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
0.323 0.139 0.428
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,612,794
Number of extensions: 148605
Number of successful extensions: 401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 376
Number of HSP's successfully gapped: 36
Length of query: 164
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 78
Effective length of database: 4,300,587
Effective search space: 335445786
Effective search space used: 335445786
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: 53 (24.1 bits)