BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0340.0028.p (190 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_866276.1| similar to shikimate kinase [Pirellula sp. 1] >... 79 7e-14 ref|ZP_00030403.1| hypothetical protein [Burkholderia fungorum] 77 2e-13 ref|NP_942223.1| sll5067 [Synechocystis sp. PCC 6803] >gi|384236... 68 1e-10 gb|EAJ99224.1| unknown [environmental sequence] 67 2e-10 ref|ZP_00024542.1| hypothetical protein [Ralstonia metallidurans] 66 3e-10 >ref|NP_866276.1| similar to shikimate kinase [Pirellula sp. 1] emb|CAD73962.1| similar to shikimate kinase [Pirellula sp.] Length = 168 Score = 78.6 bits (192), Expect = 7e-14, Method: Compositional matrix adjust. Identities = 52/148 (35%), Positives = 64/148 (43%), Gaps = 7/148 (4%) Query: 3 QLVFFLGPAGAGKTTXXXXXXXXXXXXXXDMDILLRPAADVIMQMHGLDPADRDSAEYKR 62 +L G AG GKTT D D + P + GL+PADRDS EYKR Sbjct: 5 ELHIVAGAAGVGKTTFGKDLASKLGGVLLDSDTVTEPVVRAGLSAAGLNPADRDSPEYKR 64 Query: 63 LCRDLGYRITMDAALDNMGLDCDVFVVGPFTKEAAEPDWIGGELARIGRTLEEIVVKVVL 122 L RD Y A DN+ V +VGPFT+E P+W R G V V Sbjct: 65 LFRDAVYECLFQTAADNLQ-HIPVVIVGPFTRELENPNWPSQLAERFG------VTPTVW 117 Query: 123 VSLGNTGLYRERIEGRHLPLDAWKFQNW 150 + + R+RIE R P D K +W Sbjct: 118 YLTCDDEVRRQRIEQRANPRDHAKLVDW 145 >ref|ZP_00030403.1| hypothetical protein [Burkholderia fungorum] Length = 205 Score = 76.6 bits (187), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 60/185 (32%), Positives = 80/185 (43%), Gaps = 13/185 (7%) Query: 1 MNQLVFFLGPAGAGKTTXXXXXXXXXXXXX------XDMDILLRPAADVIMQMHGLDPAD 54 M LVFF G AG GKTT D D L + M M DP D Sbjct: 1 MTHLVFFCGHAGTGKTTLAKNLHGPLTKASGTPFCLLDKDTLYGGYSAAAMAMLTGDPND 60 Query: 55 RDSAEYKRLCRDLGYRITMDAALDNMGLDCDVFVVGPFTKEAAEPDWIGGELARIGRTLE 114 RDS + + RD YR +D A DN+ L VVGP ++E E +G Sbjct: 61 RDSPLFLQHLRDPEYRGLLDTARDNLELGVSALVVGPLSREVRERRLFDRAWLGVG---A 117 Query: 115 EIVVKVVLVSLGNTGLYRERIEGRHLPLDAWKFQNWETFRTSLGTRTIAWPLPADNILQI 174 E+V++VV V R+RI R P DA+K +W+ +R R + D++L Sbjct: 118 EVVIRVVWVYTSEETA-RQRIVKRANPNDAYKLAHWDEYRQR---RFVPSGAICDDLLMF 173 Query: 175 DNSDP 179 DN+ P Sbjct: 174 DNTAP 178 >ref|NP_942223.1| sll5067 [Synechocystis sp. PCC 6803] dbj|BAD01837.1| sll5067 [Synechocystis sp. PCC 6803] Length = 174 Score = 67.8 bits (164), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 48/145 (33%), Positives = 65/145 (44%), Gaps = 7/145 (4%) Query: 9 GPAGAGKTTXXXXXXXXXXXXXXDMDILLRPAADVIMQMHGLDPADRDSAEYKRLCRDLG 68 G GAGKT D+D + +Q+ G DP DRDS +K R+ Sbjct: 10 GSPGAGKTFYGKELAKLKQAIFLDIDTATERLVRLALQLSGQDPNDRDSLYFKSNFRNPI 69 Query: 69 YRITMDAALDNMGLDCDVFVVGPFTKEAAEPDWIGGELARIGRTLEEIVVKVVLVSLGNT 128 Y D A DN+ L DV + GPFTKE +PDW R+G + V+V V Sbjct: 70 YEQLFDIAQDNL-LWNDVVITGPFTKEIKDPDWANKLSTRLG-----VPVQVHYV-FCPP 122 Query: 129 GLYRERIEGRHLPLDAWKFQNWETF 153 + + RI R+ P D K +WE + Sbjct: 123 SIRQARIRDRNNPRDLAKLASWEDY 147 >gb|EAJ99224.1| unknown [environmental sequence] Length = 202 Score = 67.0 bits (162), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 53/182 (29%), Positives = 79/182 (43%), Gaps = 13/182 (7%) Query: 4 LVFFLGPAGAGKTTXXXX------XXXXXXXXXXDMDILLRPAADVIMQMHGLDPADRDS 57 +VFF G AG GKTT D D L + M M DP DRDS Sbjct: 1 MVFFCGHAGTGKTTLAKKLIGPLMQASSSPFCLLDKDTLFGGYSAAAMSMLTGDPNDRDS 60 Query: 58 AEYKRLCRDLGYRITMDAALDNMGLDCDVFVVGPFTKEAAEPDWIGGELARIGRTLEEIV 117 + + R+ YR +D A DN+ + VVGP ++E E IG ++ Sbjct: 61 PLFLQHLREPEYRGLLDTARDNLEIGVSALVVGPLSREVRERRLFDRAWLGIG---TDVT 117 Query: 118 VKVVLVSLGNTGLYRERIEGRHLPLDAWKFQNWETFRTSLGTRTIAWPLPADNILQIDNS 177 ++VV ++ + +RI R P DA+K +W+ +R R + D++L DN+ Sbjct: 118 LRVVWITTSEETAH-QRIVERGNPNDAYKLAHWDEYRQR---RFVPSGEICDDLLMFDNT 173 Query: 178 DP 179 P Sbjct: 174 AP 175 >ref|ZP_00024542.1| hypothetical protein [Ralstonia metallidurans] Length = 192 Score = 66.2 bits (160), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 58/190 (30%), Positives = 78/190 (41%), Gaps = 23/190 (12%) Query: 1 MNQLVFFLGPAGAGKTTXXXXXXXXXXXXX------XDMDILLRPAADVIMQMHGLDPAD 54 M +L+FF G AG GKTT D D L + M+ DP D Sbjct: 1 MPRLIFFCGHAGTGKTTLAHKLIGPLMQATGEPFCLLDKDTLYGRYSAAAMRAITGDPND 60 Query: 55 RDSAEYKRLCRDLGYRITMDAALDNMGLDCDVFVVGPFTKEA-----AEPDWIGGELARI 109 RDS Y RD Y +D A +N+ L V VVGP ++E +P W+ Sbjct: 61 RDSPAYLDNLRDPEYEGLLDTARENLMLGISVIVVGPLSREIRAHQLTDPSWL------- 113 Query: 110 GRTLEEIVVKVVLVSLGNTGLYRERIEGRHLPLDAWKFQNWETFRTSLGTRTIAWPLPAD 169 R E VV V L + + RI R P DA+K +W+ +RT R + P Sbjct: 114 -RVPEGTQTHVVWVHLPESEA-QARIVRRGNPNDAYKLAHWDAYRTR---RFLPEPAEYP 168 Query: 170 NILQIDNSDP 179 ++ DN P Sbjct: 169 ELIYFDNVAP 178 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.322 0.140 0.436 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 261,107,964 Number of extensions: 9850653 Number of successful extensions: 32644 Number of sequences better than 1.0e-05: 10 Number of HSP's gapped: 32628 Number of HSP's successfully gapped: 10 Length of query: 190 Length of database: 757,237,578 Length adjustment: 119 Effective length of query: 71 Effective length of database: 434,140,797 Effective search space: 30823996587 Effective search space used: 30823996587 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: 122 (51.6 bits)