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= 0001.2456.p (255 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310494|ref|YP_003774586.1| amino acid ABC transporter/sign... 468 e-133 gi|300311472|ref|YP_003775564.1| amino acid ABC transporter/sign... 102 3e-23 gi|300313610|ref|YP_003777702.1| amino acid ABC transporter/sign... 95 5e-21 gi|300311601|ref|YP_003775693.1| glutamine ABC transporter perip... 91 1e-19 gi|300309409|ref|YP_003773501.1| glutamine ABC transporter perip... 85 6e-18 >gi|300310494|ref|YP_003774586.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 258 Score = 468 bits (1204), Expect = e-133, Method: Compositional matrix adjust. Identities = 234/258 (90%), Positives = 243/258 (94%), Gaps = 3/258 (1%) Query: 1 MKPFHHLLKQLFGAIALGSMLV---AAPAMAQSSYNVGATSTGVPFTFLDIKTNKLQGMM 57 MKPFH L K L G++AL + + +APAMAQ+SYNVGATSTGVPFTFLDIKTNKLQGMM Sbjct: 1 MKPFHCLFKHLVGSVALAAAVATLGSAPAMAQASYNVGATSTGVPFTFLDIKTNKLQGMM 60 Query: 58 IDTVTAVGSKAGFSVNIQQTPFAALIPSLTGNKIDIIAAAMLKTEARAQIVDFSDPVYSY 117 +DTVTAVG+KAGFSVNIQQTPFAALIPSLTGNKIDIIAAAMLKTEARAQIVDFSDPVYSY Sbjct: 61 VDTVTAVGNKAGFSVNIQQTPFAALIPSLTGNKIDIIAAAMLKTEARAQIVDFSDPVYSY 120 Query: 118 GEGLFVNAQDQKVYKTLDDLKGEIVGAQVGTVFVDALNKKGGFKEVKTYDSVADMMRDVG 177 GEGLFVNAQD K YK LDDLKGEIVGAQVGTVFVDALNKKGGFKEVKTYDSVADMMRDV Sbjct: 121 GEGLFVNAQDGKSYKNLDDLKGEIVGAQVGTVFVDALNKKGGFKEVKTYDSVADMMRDVA 180 Query: 178 LGRIKAGFGDRPIVAYQLSQGANAQVRLVKEYQPTLMGDVCLVIRKGDPKLMERLNKAIA 237 LGRIKAGFGDRPIVAYQL+QGAN QVRLVKEYQPTLMGDVCLVIRKGDPKLMERLNKAIA Sbjct: 181 LGRIKAGFGDRPIVAYQLAQGANPQVRLVKEYQPTLMGDVCLVIRKGDPKLMERLNKAIA 240 Query: 238 ELKADGTLARIVEQWKLN 255 ELKADGTLARIVEQWKLN Sbjct: 241 ELKADGTLARIVEQWKLN 258 >gi|300311472|ref|YP_003775564.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 102 bits (254), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 73/253 (28%), Positives = 118/253 (46%), Gaps = 9/253 (3%) Query: 5 HHLLKQLFGAIALGSMLVAAPAMAQSSYNVGATSTGV-----PFTFLDIKTNKLQGMMID 59 LL + A+ S+ V+A + QS + G + PF F D KT +L G +D Sbjct: 7 QWLLAGVGAALLASSLSVSAADLLQSVKSSGTLKVALEGNYPPFNFKDPKTGELTGFEVD 66 Query: 60 TVTAVGSKAGFSVNIQQTPFAALIPSLTGNKIDIIAAAMLKTEARAQIVDFSDPVYSYGE 119 + +K G T ++ ++ L K D+I + T+ R + DFSDP Sbjct: 67 VAKLLAAKLGVKPVFTTTEWSGILAGLGAGKYDVIINQVGITDERQKAFDFSDPYTLSSA 126 Query: 120 GLFVNAQDQKVYKTLDDLKGEIVGAQVGTVFVDALNKKGGFKEVKTYDSVADMMRDVGLG 179 L V +++ +K+L+DLKG+ +G GT F G +V+TY + + D+ G Sbjct: 127 QLIVRKDEKREFKSLEDLKGKKLGLGQGTNFEQKAKAVPGI-DVRTYPGSPEYLADLAAG 185 Query: 180 RIKAGFGDRPIVAYQLSQGANAQVRLVKEYQPTLMGDVCLVIRKGDPKLMERLNKAIAEL 239 RI A D +V Y L + + L + + + RKG+P+ LNKA+A++ Sbjct: 186 RIDAALNDSLLVGYILK---STNLPLKAGSPIGAVDKIGIPFRKGNPEFKAALNKALADI 242 Query: 240 KADGTLARIVEQW 252 KADG+ E+W Sbjct: 243 KADGSFKAASEKW 255 >gi|300313610|ref|YP_003777702.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 271 Score = 95.1 bits (235), Expect = 5e-21, Method: Compositional matrix adjust. Identities = 68/226 (30%), Positives = 114/226 (50%), Gaps = 11/226 (4%) Query: 32 YNVGATSTGVPFTFLDIKTNKLQGMMIDTVTAVGSKAGFSVNIQQTPFAALIPSLTGNKI 91 Y VG S PF+ + + + G ID + A+ K G V TPF L Sbjct: 49 YVVGVESAYAPFS-SENEQKDVVGFDIDIMKALAKKIGIEVKFVPTPFEGFFNFLAQGDR 107 Query: 92 DIIAAAMLKTEARAQIVDFSDPVYSYGEGLFVNAQDQKVYKTLDDLKGEIVGAQVGT--- 148 D++ +A+ T+ R + V FS+P + + + + A D KV K ++DLK VG Q T Sbjct: 108 DLLISAITITDERKKSVAFSEPYFVATQTIALPAADTKVSK-MEDLKPLTVGTQSATSGD 166 Query: 149 -VFVDALNKKGGFKEVKTYDSVADMMRDVGLGRIKAGFGDRPIVAYQLSQGANAQVRLVK 207 + L K ++K +DS ++++ G + A D P+V ++ N+++R V Sbjct: 167 ELVQQVLGKNSA--KIKRFDSTPLALKELESGGVDAVVADEPVVKNYIANNPNSKLRTVT 224 Query: 208 EYQPTL-MGDVCLVIRKGDPKLMERLNKAIAELKADGTLARIVEQW 252 + P+ D + +RK DP+L+ ++NK +AE+KADG+ A I Q+ Sbjct: 225 D--PSFPKEDYGIAVRKDDPELLAKINKGLAEMKADGSFAAISAQY 268 >gi|300311601|ref|YP_003775693.1| glutamine ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 251 Score = 90.5 bits (223), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 82/258 (31%), Positives = 120/258 (46%), Gaps = 18/258 (6%) Query: 1 MKPFHHLLKQLFGAIALGSMLVAAPAMAQSS---YNVGATSTGVPFTFLDIKTNKLQGMM 57 MK F LL +A S+L+AA A ++ VG +T P F +K K G Sbjct: 1 MKTFSKLL---CAGMASLSLLIAAVPAAHANGEVIRVGTDATFPPMEF--VKDGKRTGFD 55 Query: 58 IDTVTAVGSKAGFSVNIQQTPFAALIPSLTGNKIDIIAAAMLKTEARAQIVDFSDPVYSY 117 ++ + A+ G V F LIP L N+ DI A+A+ T+ R ++V+FSDP Y Sbjct: 56 VELIEALAKTMGKKVQWIDIDFKGLIPGLVSNRFDIAASAIYMTDERRKVVNFSDPYYRG 115 Query: 118 GEGLFVNAQDQKVYKTLDDLKGEIVGAQVGTVFVDALNKK-GGFKEVKTYDSVADMMRDV 176 G + V D + D KG+ V QVGT V L G + V+ + A M + Sbjct: 116 GLAVLVRRDDNSIKVPEDLNKGKRVSVQVGTKSVGYLKDNFPGVERVEVEKNQA-MFDLL 174 Query: 177 GLGRIKAGFGDRP-IVAYQLSQGANAQVRLV-KEYQPTLMGDVCLVIRKGDPKLMERLNK 234 GR+ A RP V Y +Q VR++ K L G +RK D +L +LNK Sbjct: 175 ATGRVNAVVTGRPAAVEYARTQ---PLVRVLDKGLTTELYG---FALRKSDTELTAQLNK 228 Query: 235 AIAELKADGTLARIVEQW 252 A+ L+ +GT + ++W Sbjct: 229 ALQTLRMNGTYTALTDKW 246 >gi|300309409|ref|YP_003773501.1| glutamine ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 259 Score = 84.7 bits (208), Expect = 6e-18, Method: Compositional matrix adjust. Identities = 61/229 (26%), Positives = 116/229 (50%), Gaps = 10/229 (4%) Query: 28 AQSSYNVGATSTGVPFTFLDIKTNKLQGMMIDTVTAVGSKAGFSVNIQQTPFAALIPSLT 87 A +Y VGA T PF F + +L G ID + A+ + F + + TP+ + +L Sbjct: 26 ADQTYVVGAGGTYRPFEF-ETPKKELVGFDIDLIKAISQASNFKIQLVSTPWEGIFATLG 84 Query: 88 GNKIDIIAAAMLKTEARAQIVDFSDPVYSYGEGLFVNAQDQKVYKTLDDLKGE---IVGA 144 DII + + T+ RAQ+VDFS P + + + NA D K+ +L DLK +V + Sbjct: 85 QGDRDIIISGITITDKRAQMVDFSLPYFPAEQVIITNA-DAKI-TSLSDLKKTQVAVVNS 142 Query: 145 QVGTVFV-DALNKKGGFKEVKTYDSVADMMRDVGLGRIKAGFGDRPIVAYQLSQGANAQV 203 G + V + L K + +D+ M+ ++ G + A GD ++ + + + Sbjct: 143 TAGDIVVSEELGKAS--TAIHRFDNTVLMLEELYRGGVDAAVGDVGVIKFYIKSHPEKKF 200 Query: 204 RLVKEYQPTLMGDVCLVIRKGDPKLMERLNKAIAELKADGTLARIVEQW 252 ++V + + + + ++KG+ +L++++N + ++ ADGT A+I + W Sbjct: 201 KVVGDSK-FVRQYFGIAVKKGNKELLDKINAGLKKIVADGTYAKIYKTW 248 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.319 0.135 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 758,890 Number of extensions: 30290 Number of successful extensions: 134 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 122 Number of HSP's successfully gapped: 12 Length of query: 255 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 172 Effective length of database: 1,226,865 Effective search space: 211020780 Effective search space used: 211020780 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 (21.8 bits) S2: 129 (54.3 bits)