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= 0001.4104.p (260 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/sign... 497 e-142 gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/sign... 302 2e-83 gi|300310886|ref|YP_003774978.1| amino acid ABC transporter peri... 273 1e-74 gi|300313169|ref|YP_003777261.1| amino acid transport periplasmi... 179 3e-46 gi|300309582|ref|YP_003773674.1| amino acid ABC transporter/sign... 177 6e-46 >gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 497 bits (1280), Expect = e-142, Method: Compositional matrix adjust. Identities = 248/260 (95%), Positives = 257/260 (98%) Query: 1 MKLTKLLLGLLAGAMMFSASVAHADALDDIQKHGTLRVAVPADFPPFGSVDSDLKPQGLD 60 MKLTKLLLGL+AGAMMFSASVA ADALDDIQKHGTLRVAVPADFPPFGSVD+DLKPQGLD Sbjct: 1 MKLTKLLLGLMAGAMMFSASVARADALDDIQKHGTLRVAVPADFPPFGSVDADLKPQGLD 60 Query: 61 IDVAGLIAKKLGVKVELIPVSSANRIPYLTTRKVDLVISSMGKNAEREKVIDFTAAYAPF 120 IDVA LIAKKLGVKVELIPVSSANRIPYLTT+KVDLVISSMGKNAEREKVIDF+AAYAPF Sbjct: 61 IDVATLIAKKLGVKVELIPVSSANRIPYLTTKKVDLVISSMGKNAEREKVIDFSAAYAPF 120 Query: 121 FNGVFGPADLPVKSAADLAGKTIAVTRGSVEDLELSKIVPASATVKRYEDNNSTISSFLS 180 FNGVFGPADL VKSAADLAGKTIAVTRGSVEDLEL+KIVPASATVKRYEDNNSTISSFLS Sbjct: 121 FNGVFGPADLSVKSAADLAGKTIAVTRGSVEDLELTKIVPASATVKRYEDNNSTISSFLS 180 Query: 181 GQVQLVATGNVVAAAIIAKNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAEAKK 240 GQVQLVATGNVVAAAIIA+NPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAE+KK Sbjct: 181 GQVQLVATGNVVAAAIIARNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAESKK 240 Query: 241 DGSLNAISQKWLGLPLPAGL 260 DGSL+AISQKWLG+PLPAGL Sbjct: 241 DGSLSAISQKWLGMPLPAGL 260 >gi|300311590|ref|YP_003775682.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 302 bits (774), Expect = 2e-83, Method: Compositional matrix adjust. Identities = 148/260 (56%), Positives = 190/260 (73%) Query: 1 MKLTKLLLGLLAGAMMFSASVAHADALDDIQKHGTLRVAVPADFPPFGSVDSDLKPQGLD 60 M K +L ++ G +A ADAL DIQK+G +R+ VP DF PFGSV++DL+ QGLD Sbjct: 3 MSPRKTMLAVVLGLAAMQGGLARADALADIQKNGVVRIGVPQDFAPFGSVNTDLQLQGLD 62 Query: 61 IDVAGLIAKKLGVKVELIPVSSANRIPYLTTRKVDLVISSMGKNAEREKVIDFTAAYAPF 120 IDVA LIA+K+GVK++L+PV+SANRI YL T K DLVIS++G+NAEREKVIDF+ YAP+ Sbjct: 63 IDVARLIAQKMGVKLQLVPVASANRIAYLQTHKADLVISTLGRNAEREKVIDFSQPYAPY 122 Query: 121 FNGVFGPADLPVKSAADLAGKTIAVTRGSVEDLELSKIVPASATVKRYEDNNSTISSFLS 180 N VFG A + V ADLA KT+ V RG+ +DL+L+ P SAT+KRYEDNN+ IS+++S Sbjct: 123 NNSVFGVASVKVSGPADLADKTVGVARGTFQDLQLTDTAPKSATIKRYEDNNAMISAYVS 182 Query: 181 GQVQLVATGNVVAAAIIAKNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAEAKK 240 GQVQLV TG+ VA A+ K P KP K++I++S C +GLNKGE L KV+ L AKK Sbjct: 183 GQVQLVGTGDFVAYALAEKAPNNKPVLKYIIQESACNVGLNKGEPALLAKVNEALTAAKK 242 Query: 241 DGSLNAISQKWLGLPLPAGL 260 G LN I QKWL +PLPA + Sbjct: 243 SGELNGIVQKWLNVPLPAKM 262 >gi|300310886|ref|YP_003774978.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 265 Score = 273 bits (697), Expect = 1e-74, Method: Compositional matrix adjust. Identities = 134/257 (52%), Positives = 175/257 (68%) Query: 1 MKLTKLLLGLLAGAMMFSASVAHADALDDIQKHGTLRVAVPADFPPFGSVDSDLKPQGLD 60 M K + G M + A AD L DIQK G +++ VP DF P+GSV SDL+ QGLD Sbjct: 1 MNFIKTAIAASLGLMAVAVHPAMADTLADIQKAGVVKIGVPQDFAPYGSVTSDLQLQGLD 60 Query: 61 IDVAGLIAKKLGVKVELIPVSSANRIPYLTTRKVDLVISSMGKNAEREKVIDFTAAYAPF 120 IDVA L+AK +GVK EL+PV ++R+ +L T K+DL+IS++GKNAEREKVIDF+ YAP+ Sbjct: 61 IDVARLVAKGMGVKAELVPVPISSRMAFLQTHKIDLIISTLGKNAEREKVIDFSQGYAPY 120 Query: 121 FNGVFGPADLPVKSAADLAGKTIAVTRGSVEDLELSKIVPASATVKRYEDNNSTISSFLS 180 N VFG A + V ADLA +T+ V R + EDL L+ VP S +KRYEDNN I++++S Sbjct: 121 NNSVFGVAAIKVAGPADLANQTVGVARSTFEDLMLTDSVPKSTVIKRYEDNNGLIAAYVS 180 Query: 181 GQVQLVATGNVVAAAIIAKNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAEAKK 240 GQVQLV TG+ VA A+ K P KP K++I S C++G+NKGE L KV+ L +KK Sbjct: 181 GQVQLVGTGDFVAYALAEKTPANKPLLKYIINVSTCYVGMNKGEPALMAKVNEALTASKK 240 Query: 241 DGSLNAISQKWLGLPLP 257 G LN I +KWL +PLP Sbjct: 241 SGELNGIVKKWLNVPLP 257 >gi|300313169|ref|YP_003777261.1| amino acid transport periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 268 Score = 179 bits (453), Expect = 3e-46, Method: Compositional matrix adjust. Identities = 95/229 (41%), Positives = 140/229 (61%) Query: 29 DIQKHGTLRVAVPADFPPFGSVDSDLKPQGLDIDVAGLIAKKLGVKVELIPVSSANRIPY 88 DI+ + VA+ PPFG ++ L+PQG D++ A L+AK LGV++E++ V+ NRIP+ Sbjct: 32 DIKARKKVLVAIDLGAPPFGMTNAKLEPQGSDVETARLLAKDLGVELEIVQVTGPNRIPF 91 Query: 89 LTTRKVDLVISSMGKNAEREKVIDFTAAYAPFFNGVFGPADLPVKSAADLAGKTIAVTRG 148 L T K D+VISS ER+KV+ FT Y V P +KS DL GK +AV RG Sbjct: 92 LMTGKADMVISSFSITPERQKVVAFTQPYGASQFVVAAPKGENIKSLNDLVGKRVAVVRG 151 Query: 149 SVEDLELSKIVPASATVKRYEDNNSTISSFLSGQVQLVATGNVVAAAIIAKNPPKKPETK 208 +++D L+ I P + R++D+ + ++ +SGQV + T N +A+AI +NP K ETK Sbjct: 152 NMQDSLLTPIAPKGTNIVRFDDDATVTAAIISGQVDALCTPNSLASAIAKQNPSKNLETK 211 Query: 209 FLIKDSPCFIGLNKGEKKLQDKVDAILAEAKKDGSLNAISQKWLGLPLP 257 F IKD P IGL KGE L+ ++ ++ K+G L I Q+W+G P+P Sbjct: 212 FAIKDIPYAIGLRKGEPALEKWLNEWISANLKNGKLPGIYQQWVGSPMP 260 >gi|300309582|ref|YP_003773674.1| amino acid ABC transporter/signal transduction system periplasmic binding protein [Herbaspirillum seropedicae SmR1] Length = 269 Score = 177 bits (450), Expect = 6e-46, Method: Compositional matrix adjust. Identities = 92/235 (39%), Positives = 140/235 (59%) Query: 23 HADALDDIQKHGTLRVAVPADFPPFGSVDSDLKPQGLDIDVAGLIAKKLGVKVELIPVSS 82 AD LD I LRVA+ PP+ D L+ G D++ A +AK G+++E++P + Sbjct: 27 QADQLDTILAAKKLRVAIDLAVPPYSMKDDKLRLIGSDVETAQRMAKDFGLELEVVPTTL 86 Query: 83 ANRIPYLTTRKVDLVISSMGKNAEREKVIDFTAAYAPFFNGVFGPADLPVKSAADLAGKT 142 NR+PYL T K D+VIS+ ER KVIDF+ YAP V P + + S ADLAGK Sbjct: 87 TNRVPYLQTNKADIVISAFSITPERAKVIDFSVPYAPILVVVGAPRSMKITSPADLAGKK 146 Query: 143 IAVTRGSVEDLELSKIVPASATVKRYEDNNSTISSFLSGQVQLVATGNVVAAAIIAKNPP 202 I TRG+ D EL+KI P+SAT+ R++D+ +++++ +SGQ + AT ++ + KNP Sbjct: 147 IIATRGTTNDQELTKIAPSSATITRFDDDATSMTAMVSGQADIWATSPMLLKVVNQKNPS 206 Query: 203 KKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAEAKKDGSLNAISQKWLGLPLP 257 + E+K +K + +GL KGE +L++K+D + +G LN I +K+ LP Sbjct: 207 RDIESKLTLKANLLAVGLRKGEPRLKEKIDGWIRTNLSNGELNTIYKKYHEAELP 261 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 0.316 0.134 0.372 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: 692,601 Number of extensions: 26008 Number of successful extensions: 126 Number of sequences better than 1.0e-08: 16 Number of HSP's gapped: 114 Number of HSP's successfully gapped: 16 Length of query: 260 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 177 Effective length of database: 1,226,865 Effective search space: 217155105 Effective search space used: 217155105 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 (21.6 bits) S2: 129 (54.3 bits)