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= 0002.0260.p (363 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter perip... 117 2e-27 gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter perip... 85 1e-17 gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter perip... 83 4e-17 gi|300310860|ref|YP_003774952.1| dipeptide ABC transporter perip... 74 1e-14 gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter perip... 73 4e-14 >gi|300310897|ref|YP_003774989.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 528 Score = 117 bits (292), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 93/281 (33%), Positives = 134/281 (47%), Gaps = 24/281 (8%) Query: 57 SSILPLTTTAGGNTELGPKIVEGLLTYDFNLNPKPLLATSWSISKDGLQYRFNLRHGVKW 116 SS+ P G+ + + L+ D+N P LA SW + D + F LR VKW Sbjct: 40 SSLDPQLNNHAGDRSVDLHFWDLLVQNDYN-KLVPGLAVSWK-NIDPKTWEFKLRPNVKW 97 Query: 117 HDGKDFTSADVAFSILTLKVVHPRGRATFA----NVTEVQTPDPFTAVIVLSKPSPTLLT 172 DGK FT+ DV FS + V P ATFA V V DP T VI + P+P L Sbjct: 98 QDGKPFTADDVIFSYQRARAV-PGSVATFAGYLRTVESVTAKDPLTLVIKTNIPNPDLPL 156 Query: 173 ALAGAESPIVPRHLYDKTDILNSKYNSAPVGTGPFIFKEFVKGSHIVLERNPNYWDKPKP 232 LA IV +H+ +K+ N +A +GTGP+ F + G +V++RN +YW+ KP Sbjct: 157 NLASVH--IVSKHIGEKSTTENYNSGAAVIGTGPYKFVSYTPGDRVVMQRNDDYWNG-KP 213 Query: 233 YLDKVVVRFIPDALARATALESGAADLGGQAIPLSDVGRFSKLPKITVDTTNWAYIGLQQ 292 +KV R+I + AR AL SG D+ + + +SD+ + + P + V N + L Q Sbjct: 214 LWEKVNYRYINNGAARTAALLSGDVDVIDK-VSVSDLAKLKQSPNVKVYPYNGLRVLLIQ 272 Query: 293 QLYF-------------NLDTPVLQKIEVRRAISXSAPRPA 320 + LD L + VRRA+S + R A Sbjct: 273 PSFHQGPSPFITDNNGKQLDKNPLLDVRVRRAMSLAINRKA 313 >gi|300310463|ref|YP_003774555.1| dipeptide ABC transporter periplasmic peptide-binding protein [Herbaspirillum seropedicae SmR1] Length = 540 Score = 84.7 bits (208), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 79/248 (31%), Positives = 105/248 (42%), Gaps = 22/248 (8%) Query: 19 IVAALAAGVLAALAGTG------QAGAAEPKHGGTLNWIVTPEPSS---ILPLTTTAGGN 69 ++ L AG L + GTG A K GG + I T S+ + P T + Sbjct: 33 MMRTLLAGSLMTVGGTGLLTASGSVMAQTGKRGGKMR-IATQTSSTADTLDPAKTAHSTD 91 Query: 70 TELGPKIVEGLLTYDFNLNPKPLLATSWSISKDGLQYRFNLRHGVKWHDGKDFTSADVAF 129 GL D L P+ +LA ++ D + + LR GV +HDGK T ADV + Sbjct: 92 YTRVHMFYNGLTKLDGKLGPQMVLAEEM-LTNDAVTWTVKLRKGVNFHDGKPLTPADVVY 150 Query: 130 SILTLK--VVHPRGRATFANVTEVQTPDPFTAVIVLSKPSPTLLTALAGAESPIVPRHLY 187 SI+ K + + V+ P I L+ + L LA A+ I+ Sbjct: 151 SIMRHKDPATASKVKVVADQFESVKATGPNEVQIKLTSANADLPVILATAQFLII----R 206 Query: 188 DKTDILNSKYNSAPVGTGPFIFKEFVKGSHIVLERNPNYWDKPKPYLDKVVVRFIPDALA 247 D T S P GTG F KEF G + RN NYW PYLD+V + IPD A Sbjct: 207 DGTTNF-----STPNGTGAFKLKEFTPGVRTIGVRNENYWKPGLPYLDEVELFGIPDEAA 261 Query: 248 RATALESG 255 R AL SG Sbjct: 262 RVNALLSG 269 >gi|300311169|ref|YP_003775261.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 523 Score = 82.8 bits (203), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 63/239 (26%), Positives = 112/239 (46%), Gaps = 14/239 (5%) Query: 28 LAALAGTGQAGAAEPKHGGTLNWIVTPEPSSILPLTTTAGGNTELGPKIVEGLLTYDFNL 87 +AAL T Q AA T+ V +++ P + + +GL +D ++ Sbjct: 18 VAALGTTLQFAAAHAFAAKTVTLAVYSTFTTLDPYDANDTLSLSMAKSFYQGLFGFDKDM 77 Query: 88 NPKPLLATSWSISKDGLQYRFNLRHGVKWHDGKDFTSADVAFSILTLKVVHPRGRAT--- 144 P+LA + +SKDGL+Y L+ GVK+ DG F AD ++ +V +P + Sbjct: 78 KLIPVLAEGYLVSKDGLEYTIRLKQGVKFQDGTVF-KADAVKAVFD-RVTNPDNKLKRYN 135 Query: 145 -FANVTEVQTPDPFTAVIVLSKPSPTLLTALAGAESPIV-PRHL--YDKTDILNSKYNSA 200 F + + + + +T +VL +P + LA + ++ P L Y DI Sbjct: 136 LFNRIAKTEILNDYTVKVVLKEPFSAFINVLAHPSAVMISPTALKQYGNKDIAFH----- 190 Query: 201 PVGTGPFIFKEFVKGSHIVLERNPNYWDKPKPYLDKVVVRFIPDALARATALESGAADL 259 PVGTGPF F E+ + ++ + + YW P +D+++ + + D AR+ +++G A Sbjct: 191 PVGTGPFKFVEWKQTDYVKVAKFDGYWKPGYPKVDEIIWKPVVDNNARSAMMQTGEAQF 249 >gi|300310860|ref|YP_003774952.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 74.3 bits (181), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 90/311 (28%), Positives = 130/311 (41%), Gaps = 31/311 (9%) Query: 29 AALAGTGQAGAA--EPKHGGTLNWIVTPEPSSILPLTTTAGGNTELGPKIVEGLLTYDFN 86 AALA +AG A + H G + + P + L T G +++E LL D Sbjct: 32 AALAHGDEAGHAHGDIAHAGK-DMLTVVGPWELTGLDPTRSGYMFARMEVLETLLEVDDA 90 Query: 87 LNPKPLLATSWSISKDGLQYRFNLRHGVKWHDGKDFTSADVAFSILTLKVVHPRGRATFA 146 +P +A++WS+S DGLQ+RF LR G+++HDG T A + + L P G A Sbjct: 91 GQLQPSVASAWSVSADGLQWRFVLRSGLRYHDGSALTPASI-LACLQRAQARP-GVLRLA 148 Query: 147 NVTEVQTPDPFTAVIVLSKPSPTLLTALAGAESPIVPRHLYDKTDILNSKYNSAPVGTGP 206 ++ ++ + T V+VL +P L L + I+ +D + A +G+GP Sbjct: 149 DIAALRV-EGQTLVVVLRRPFGPLPYLLTHYTTQILAPASFDAQGNV-----VAIIGSGP 202 Query: 207 FIFKEFVKGSHIVLERNPNYWDKPKPYLD--KVVVRF----IPDALARATALESGAADLG 260 F + +ER D KVV R + A R ++SG ADL Sbjct: 203 FRIRSIALPQQFEVERVAGSVSGSGAGSDVGKVVQRARYISVSRAETRTLLVQSGQADLA 262 Query: 261 GQAIP-----LSDVGRFSKLPKITVDTTNWAYIGLQQQLYFNLDTPVLQKIEVRRAISXS 315 P L D R S L + TT L N P+L + VRRAIS Sbjct: 263 FSLDPPSIRALQDSPRASLLSAMLPRTT---------LLKLNAGHPLLADVRVRRAISLC 313 Query: 316 APRPADACARL 326 R A A L Sbjct: 314 IEREGIARALL 324 >gi|300312481|ref|YP_003776573.1| dipeptide ABC transporter periplasmic protein [Herbaspirillum seropedicae SmR1] Length = 512 Score = 72.8 bits (177), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 76/264 (28%), Positives = 116/264 (43%), Gaps = 28/264 (10%) Query: 90 KPLLATSWSISKDGLQYRFNLRHGVKWHDGKDFTSADVAFSILTLKVVHPRGRA-TFANV 148 KP LAT+W + +LR GV++ +G F++ DV F+ V P +A T N Sbjct: 79 KPQLATAWKW-ESPTALVLDLRQGVQFQNGDKFSADDVVFTFNY--AVSPESKAVTRQNT 135 Query: 149 TEVQTPDP---FTAVIVLSKPSPTLLTALAGAESPIVPRHLYDKTDILNSKYNSAPVGTG 205 +++ D + I L P P L LAG PI P + K + ++ AP+GTG Sbjct: 136 DWIKSVDKLADYKVRINLKGPFPAALEYLAGP-LPIYPAAYFKKVGL--EGFSKAPIGTG 192 Query: 206 PFIFKEFVKGSHIVLERNPNYW-DKP--KPYLDKVVVRFIPDALARATALESGAADLGGQ 262 P+ G + L +NP Y+ D P +P + + IPD RA L +GA D + Sbjct: 193 PYKVTSVTPGQGVTLVKNPGYFKDSPQGQPTIGNIKFVVIPDPETRAAQLMTGAIDWIWR 252 Query: 263 AIPLSDVGRFSKLPKITVDTTNWAYIGLQQQLYFNLDT-------PVLQKIEVRRAISXS 315 +P PK+ V + IG + LDT + + VR+A++ + Sbjct: 253 -VPPDQADSLKTNPKLAVQSGETMRIG-----FITLDTTGTSAPNSPFKDVRVRQAVNHA 306 Query: 316 APRP--ADACARLGSATIISARGR 337 R AD R GS + +A R Sbjct: 307 INRKGYADNLMRGGSQPVYTACFR 330 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 0.134 0.412 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: 1,071,620 Number of extensions: 45005 Number of successful extensions: 137 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 129 Number of HSP's successfully gapped: 6 Length of query: 363 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 277 Effective length of database: 1,212,660 Effective search space: 335906820 Effective search space used: 335906820 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: 131 (55.1 bits)