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= 0257.0028.p (380 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313169|ref|YP_003777261.1| amino acid transport periplasmi... 306 2e-84 gi|300309582|ref|YP_003773674.1| amino acid ABC transporter/sign... 218 6e-58 gi|300313886|ref|YP_003777978.1| amino acid ABC transporter peri... 199 3e-52 gi|300310311|ref|YP_003774403.1| AraC family transcription regul... 174 1e-44 gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/sign... 157 1e-39 >gi|300313169|ref|YP_003777261.1| amino acid transport periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 268 Score = 306 bits (783), Expect = 2e-84, Method: Compositional matrix adjust. Identities = 140/233 (60%), Positives = 185/233 (79%) Query: 148 RKKIVIAIDLGSPPFGMTDDKLQPYGSDVSAAKMLAKDLGVEMEIIQVTGPNRVPFLLTN 207 RKK+++AIDLG+PPFGMT+ KL+P GSDV A++LAKDLGVE+EI+QVTGPNR+PFL+T Sbjct: 36 RKKVLVAIDLGAPPFGMTNAKLEPQGSDVETARLLAKDLGVELEIVQVTGPNRIPFLMTG 95 Query: 208 KADIVIASFSITPERAKVINFSVPYSASESVVGAERSMQIKSLADLAGKRVGVVRGNLQD 267 KAD+VI+SFSITPER KV+ F+ PY AS+ VV A + IKSL DL GKRV VVRGN+QD Sbjct: 96 KADMVISSFSITPERQKVVAFTQPYGASQFVVAAPKGENIKSLNDLVGKRVAVVRGNMQD 155 Query: 268 TLLTPIVPKGTILVRYDDDSTNAAALLSGQVDAIGTAKELVTTTARKNPGRNIETKFSVK 327 +LLTPI PKGT +VR+DDD+T AA++SGQVDA+ T L + A++NP +N+ETKF++K Sbjct: 156 SLLTPIAPKGTNIVRFDDDATVTAAIISGQVDALCTPNSLASAIAKQNPSKNLETKFAIK 215 Query: 328 VVPHGIGVRKEDTALLAWINSWVVTNMKNGNLAKSYEAAAGAPLPDLSQYLPK 380 +P+ IG+RK + AL W+N W+ N+KNG L Y+ G+P+PDL+Q+ K Sbjct: 216 DIPYAIGLRKGEPALEKWLNEWISANLKNGKLPGIYQQWVGSPMPDLAQFAAK 268 >gi|300309582|ref|YP_003773674.1| amino acid ABC transporter/signal transduction system periplasmic binding protein [Herbaspirillum seropedicae SmR1] Length = 269 Score = 218 bits (555), Expect = 6e-58, Method: Compositional matrix adjust. Identities = 111/224 (49%), Positives = 149/224 (66%) Query: 149 KKIVIAIDLGSPPFGMTDDKLQPYGSDVSAAKMLAKDLGVEMEIIQVTGPNRVPFLLTNK 208 KK+ +AIDL PP+ M DDKL+ GSDV A+ +AKD G+E+E++ T NRVP+L TNK Sbjct: 38 KKLRVAIDLAVPPYSMKDDKLRLIGSDVETAQRMAKDFGLELEVVPTTLTNRVPYLQTNK 97 Query: 209 ADIVIASFSITPERAKVINFSVPYSASESVVGAERSMQIKSLADLAGKRVGVVRGNLQDT 268 ADIVI++FSITPERAKVI+FSVPY+ VVGA RSM+I S ADLAGK++ RG D Sbjct: 98 ADIVISAFSITPERAKVIDFSVPYAPILVVVGAPRSMKITSPADLAGKKIIATRGTTNDQ 157 Query: 269 LLTPIVPKGTILVRYDDDSTNAAALLSGQVDAIGTAKELVTTTARKNPGRNIETKFSVKV 328 LT I P + R+DDD+T+ A++SGQ D T+ L+ +KNP R+IE+K ++K Sbjct: 158 ELTKIAPSSATITRFDDDATSMTAMVSGQADIWATSPMLLKVVNQKNPSRDIESKLTLKA 217 Query: 329 VPHGIGVRKEDTALLAWINSWVVTNMKNGNLAKSYEAAAGAPLP 372 +G+RK + L I+ W+ TN+ NG L Y+ A LP Sbjct: 218 NLLAVGLRKGEPRLKEKIDGWIRTNLSNGELNTIYKKYHEAELP 261 >gi|300313886|ref|YP_003777978.1| amino acid ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 267 Score = 199 bits (506), Expect = 3e-52, Method: Compositional matrix adjust. Identities = 105/223 (47%), Positives = 139/223 (62%), Gaps = 1/223 (0%) Query: 150 KIVIAIDLGSPPFGMTDDKLQPYGSDVSAAKMLAKDLGVEMEIIQVTGPNRVPFLLTNKA 209 KI IA +P FG +D+KLQ GSDV AA++LA+DLGV++++I V RVP L N+A Sbjct: 39 KIRIATTSSTPLFGYSDEKLQLAGSDVEAARLLAQDLGVQLDLIPVANAARVPTLQANRA 98 Query: 210 DIVIASFSITPERAKVINFSVPYSASESVVGAERSMQIKSLADLAGKRVGVVRGNLQDTL 269 DIV+ S SITPER KVI+FS PY+ ++GA +SM IK ADL GKR+GV R DTL Sbjct: 99 DIVVGSLSITPERLKVIDFSTPYAVISLIIGAPKSMVIKDYADLNGKRIGVTRATPNDTL 158 Query: 270 LTPIVPKGTILVRYDDDSTNAAALLSGQVDAIGTAKELVTTTARKNPGRNIETKFSVKVV 329 T KG ++RY+DD+T ++++GQVD + + +K PG+N+E KF K Sbjct: 159 TTQNA-KGAEIMRYEDDATLITSMVTGQVDVFSSTPSNLQEMQKKAPGKNLEMKFEQKAF 217 Query: 330 PHGIGVRKEDTALLAWINSWVVTNMKNGNLAKSYEAAAGAPLP 372 GI + K L WI+ WV TNMKNG L Y+ G LP Sbjct: 218 DLGIAINKNQPRLKEWIDGWVKTNMKNGKLNAIYKKYHGRDLP 260 >gi|300310311|ref|YP_003774403.1| AraC family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 274 Score = 174 bits (440), Expect = 1e-44, Method: Compositional matrix adjust. Identities = 86/149 (57%), Positives = 108/149 (72%), Gaps = 12/149 (8%) Query: 5 RGGHLAQLILSEIDGAAAIPVVIPWPSDRRVVAVCEAILADPGNANSLAHWAEFVGASPR 64 R GH+A+LILSE+ A AIPV IPWP DRR+ A+CEAILADPG SLA WA GAS R Sbjct: 135 RAGHVAELILSELARAPAIPVAIPWPGDRRLQAICEAILADPGRQFSLADWAGMGGASVR 194 Query: 65 TLIRLFPKETGLHFRHWVQQVHITDALLRLSQGEAVERIAERLGYKSASAFTSMFRGVLG 124 T+IRLFPKETGL FRHWVQQVH+++AL+RLS+G+ V +A+ LGY+S SAF++MFR L Sbjct: 195 TVIRLFPKETGLQFRHWVQQVHLSEALVRLSRGDPVGVVAQALGYRSQSAFSNMFRKALR 254 Query: 125 KTPSQYGGLARRNIAVDMLQRXVRKKIVI 153 TP+ Y LQR R+++ + Sbjct: 255 TTPNHY------------LQRQERRRLSL 271 >gi|300313535|ref|YP_003777627.1| amino acid ABC transporter/signal transduction system periplasmic protein/domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 157 bits (397), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 90/258 (34%), Positives = 145/258 (56%), Gaps = 3/258 (1%) Query: 115 FTSMFRGVLGKTPSQYGGLARRNIAVDMLQRXVRKKIVIAIDLGSPPFGMTDDKLQPYGS 174 T + G++ +AR + A+D +Q+ ++ + D PPFG D L+P G Sbjct: 3 LTKLLLGLMAGAMMFSASVARAD-ALDDIQKHGTLRVAVPADF--PPFGSVDADLKPQGL 59 Query: 175 DVSAAKMLAKDLGVEMEIIQVTGPNRVPFLLTNKADIVIASFSITPERAKVINFSVPYSA 234 D+ A ++AK LGV++E+I V+ NR+P+L T K D+VI+S ER KVI+FS Y+ Sbjct: 60 DIDVATLIAKKLGVKVELIPVSSANRIPYLTTKKVDLVISSMGKNAEREKVIDFSAAYAP 119 Query: 235 SESVVGAERSMQIKSLADLAGKRVGVVRGNLQDTLLTPIVPKGTILVRYDDDSTNAAALL 294 + V + +KS ADLAGK + V RG+++D LT IVP + RY+D+++ ++ L Sbjct: 120 FFNGVFGPADLSVKSAADLAGKTIAVTRGSVEDLELTKIVPASATVKRYEDNNSTISSFL 179 Query: 295 SGQVDAIGTAKELVTTTARKNPGRNIETKFSVKVVPHGIGVRKEDTALLAWINSWVVTNM 354 SGQV + T + +NP + ETKF +K P IG+ K + L +++ + + Sbjct: 180 SGQVQLVATGNVVAAAIIARNPPKKPETKFLIKDSPCFIGLNKGEKKLQDKVDAILAESK 239 Query: 355 KNGNLAKSYEAAAGAPLP 372 K+G+L+ + G PLP Sbjct: 240 KDGSLSAISQKWLGMPLP 257 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 0.318 0.134 0.386 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: 1,203,845 Number of extensions: 49990 Number of successful extensions: 213 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 209 Number of HSP's successfully gapped: 17 Length of query: 380 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 293 Effective length of database: 1,207,925 Effective search space: 353922025 Effective search space used: 353922025 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: 131 (55.1 bits)