RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254781067|ref|YP_003065480.1| elongation factor P [Candidatus Liberibacter asiaticus str. psy62] (189 letters) >1ueb_A EF-P, TT0860, elongation factor P; beta barrel, riken structural genomics/proteomics initiative, RSGI, structural genomics; 1.65A {Thermus thermophilus} (A:64-125) Length = 62 Score = 84.7 bits (210), Expect = 8e-18 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%) Query: 66 FVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSV 125 +VE + Q+LY + E FM+ ETY+Q V + + +F+EGM ++EG + V Sbjct: 1 YVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAE-FFKEGMTALGDMYEGQPIKV 59 Query: 126 EVP 128 P Sbjct: 60 TPP 62 >1yby_A Translation elongation factor P; conserved hypothetical protein, structural genomics, PSI, protein structure initiative; 1.95A {Clostridium thermocellum} (A:94-156) Length = 63 Score = 80.8 bits (200), Expect = 1e-16 Identities = 20/62 (32%), Positives = 38/62 (61%) Query: 67 VEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVE 126 +E + Q+LY D + ++F + ET++Q+ + ++ IGD + +E VK+L H+G +E Sbjct: 2 IERKDXQYLYNDGDLYYFXDTETFEQLPLGKDKIGDALKFVKENEIVKVLSHKGNVFGIE 61 Query: 127 VP 128 P Sbjct: 62 PP 63 >1yby_A Translation elongation factor P; conserved hypothetical protein, structural genomics, PSI, protein structure initiative; 1.95A {Clostridium thermocellum} (A:157-215) Length = 59 Score = 75.0 bits (185), Expect = 6e-15 Identities = 26/58 (44%), Positives = 29/58 (50%) Query: 130 HVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVERV 187 V V DTEP KG T T + KPAI+ VP +N GD I I T Y ERV Sbjct: 2 FVELEVTDTEPGFKGDTATGATKPAIVETGASIKVPLFVNKGDIIRIDTRTGEYXERV 59 >1ueb_A EF-P, TT0860, elongation factor P; beta barrel, riken structural genomics/proteomics initiative, RSGI, structural genomics; 1.65A {Thermus thermophilus} (A:126-184) Length = 59 Score = 74.6 bits (184), Expect = 8e-15 Identities = 20/56 (35%), Positives = 26/56 (46%) Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 V V+DT P +G TV+ KPA L VP + G+ I + T YV R Sbjct: 3 VELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGR 58 >1yby_A Translation elongation factor P; conserved hypothetical protein, structural genomics, PSI, protein structure initiative; 1.95A {Clostridium thermocellum} (A:1-93) Length = 93 Score = 72.1 bits (177), Expect = 4e-14 Identities = 13/65 (20%), Positives = 33/65 (50%) Query: 1 MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTE 60 + + A + G ++DG+++ V+ ++ PGKG + +++ I G + + T+ Sbjct: 29 GLXISAGDFKNGVTFELDGQIFQVIEFQHVKPGKGAAFVRTKLKNIVTGATIEKTFNPTD 88 Query: 61 QVERA 65 + +A Sbjct: 89 KXPKA 93 >1ueb_A EF-P, TT0860, elongation factor P; beta barrel, riken structural genomics/proteomics initiative, RSGI, structural genomics; 1.65A {Thermus thermophilus} (A:1-63) Length = 63 Score = 61.9 bits (151), Expect = 5e-11 Identities = 11/59 (18%), Positives = 27/59 (45%) Query: 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVER 64 + +R G + +DG L+ + ++ G+G + + + G V + + E++E Sbjct: 4 VTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLED 62 >3gxs_A Phenylacetate-coenzyme A ligase; APC62324.1, structural genomics, PSI-2, protein structure initiative; 1.43A {Bacteroides vulgatus atcc 8482} (A:) Length = 109 Score = 26.1 bits (57), Expect = 3.2 Identities = 15/100 (15%), Positives = 28/100 (28%), Gaps = 4/100 (4%) Query: 45 RISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQK 104 D + + Q+E ++ + Y N E +V +S+ D Sbjct: 2 NADDXIILKGVNIFPIQIETILLQFKELGSDYLITLETAESNDEXTVEVELSQLFTDDY- 60 Query: 105 VYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKG 144 + I + + V V P S+G Sbjct: 61 ---GRLQALTREITRQLKDEILVTPRVKLVPKGALPKSEG 97 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 0.318 0.135 0.381 Gapped Lambda K H 0.267 0.0550 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,437,473 Number of extensions: 62977 Number of successful extensions: 155 Number of sequences better than 10.0: 1 Number of HSP's gapped: 154 Number of HSP's successfully gapped: 11 Length of query: 189 Length of database: 4,956,049 Length adjustment: 84 Effective length of query: 105 Effective length of database: 2,116,429 Effective search space: 222225045 Effective search space used: 222225045 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.2 bits)