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= 0001.1370.p (322 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310861|ref|YP_003774953.1| dipeptide/oligopeptide/nickel A... 469 e-133 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 165 4e-42 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 157 1e-39 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 132 3e-32 gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 126 2e-30 >gi|300310861|ref|YP_003774953.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 469 bits (1207), Expect = e-133, Method: Compositional matrix adjust. Identities = 284/321 (88%), Positives = 297/321 (92%) Query: 1 LTRLLPRSAARQLAGALGQRLLQASLVALLVGTLCFFMTRLLPGDMAYRIAAGRYGYDMV 60 L R L + ++LA AL RLLQA LVALLVGTLCFFMTR+LPGDMAYRIAAGRYGYDMV Sbjct: 3 LNRFLSARSGQRLAAALVPRLLQAVLVALLVGTLCFFMTRMLPGDMAYRIAAGRYGYDMV 62 Query: 61 TTEAALAVRAELGLDQPWFMALGQWWSRLLHLDLGTSQVTALPVLVEIAHQLGPTLRLSL 120 TTEAALAVR ELGLD+PWFMAL +WWSRLLHLDLG SQV++ PVL EIAHQLGPTLRLSL Sbjct: 63 TTEAALAVRDELGLDRPWFMALSEWWSRLLHLDLGVSQVSSQPVLAEIAHQLGPTLRLSL 122 Query: 121 LALALSLLFGPTLGILAGLNPGGWLDRSTLALSVLLRALPSFLLGLILVLLFSVQLGALP 180 LA+ALSLL GPTLG+LAGL+PG WLDR+TLALSV LRALPSFLLGLILVLLFSVQLGALP Sbjct: 123 LAMALSLLVGPTLGVLAGLHPGRWLDRATLALSVGLRALPSFLLGLILVLLFSVQLGALP 182 Query: 181 AAGHVDHGGILLPALTLALGLAAVSCRVARDAMVQVRASEYFAFALTKGLSPAQALARHG 240 AAGH DHGGILLPALTLALGLAAVSCRVARDAMVQVR S YFAFALTKGLSPAQALARHG Sbjct: 183 AAGHGDHGGILLPALTLALGLAAVSCRVARDAMVQVRQSAYFAFALTKGLSPAQALARHG 242 Query: 241 VRNVAAPVVAYLGVQLVMLVEGVVLVETIFAWPGIGHALVHAIFGRDVPMIQGTALVLGL 300 +RNVAAPV AYLGVQLVMLVEGVVLVETIFAWPGIGHALVHAIFGRDVPMIQGTALVLGL Sbjct: 243 LRNVAAPVTAYLGVQLVMLVEGVVLVETIFAWPGIGHALVHAIFGRDVPMIQGTALVLGL 302 Query: 301 MFVLFNALVDTTCAFLDPRGR 321 MFVLFNALVD CAFLDPRGR Sbjct: 303 MFVLFNALVDAACAFLDPRGR 323 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 165 bits (418), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 104/281 (37%), Positives = 156/281 (55%), Gaps = 5/281 (1%) Query: 41 LLPGDMAYRIAAGRYGYDMVTTEAALAVRAELGLDQPWFMALGQWWSRLLHLDLGTSQVT 100 LLPGD A R+AAG D + VRA+LGLD+P ++ D G S T Sbjct: 29 LLPGDPA-RLAAGPEADD----KTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHSIRT 83 Query: 101 ALPVLVEIAHQLGPTLRLSLLALALSLLFGPTLGILAGLNPGGWLDRSTLALSVLLRALP 160 PV EI+ + PTL L+++A+ ++LFG +GI + + W DR + L+V + P Sbjct: 84 KRPVSEEISARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFP 143 Query: 161 SFLLGLILVLLFSVQLGALPAAGHVDHGGILLPALTLALGLAAVSCRVARDAMVQVRASE 220 +F LG++LV +FSV+LG LP G +LP++TL +AAV R R + +++ + Sbjct: 144 AFSLGILLVQVFSVKLGWLPTVGDDTWLHYILPSITLGAAVAAVMARFTRSSFIEILQED 203 Query: 221 YFAFALTKGLSPAQALARHGVRNVAAPVVAYLGVQLVMLVEGVVLVETIFAWPGIGHALV 280 + A KGL+ + +H +RN PVV +G+Q L+ G +LVE +F WPG+G LV Sbjct: 204 FVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVFNWPGMGRLLV 263 Query: 281 HAIFGRDVPMIQGTALVLGLMFVLFNALVDTTCAFLDPRGR 321 A+ RD P+IQ L+ L F+ N +VD A ++P R Sbjct: 264 DAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIR 304 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 157 bits (397), Expect = 1e-39, Method: Compositional matrix adjust. Identities = 104/303 (34%), Positives = 159/303 (52%), Gaps = 6/303 (1%) Query: 19 QRLLQASLVALLVGTLCFFMTRLLPGDMAYRIAAGRYGYDMVTTEAALAVRAELGLDQPW 78 +RL A VA+ V + F + + GD+A IA T +VR + GLD+P Sbjct: 7 RRLAIALCVAVTVSVVSFTLLHM-SGDLAVSIAGPE-----ATAAQVESVRTQFGLDRPM 60 Query: 79 FMALGQWWSRLLHLDLGTSQVTALPVLVEIAHQLGPTLRLSLLALALSLLFGPTLGILAG 138 W R + LD G S PV+ IA +L T +L AL L++L LG+LA Sbjct: 61 ATQYLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAA 120 Query: 139 LNPGGWLDRSTLALSVLLRALPSFLLGLILVLLFSVQLGALPAAGHVDHGGILLPALTLA 198 + WLDR+ L ++V+ +A+PSF GL L+L+F+V L LP AG+ +LPA+ L Sbjct: 121 IYRDTWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPVAGNESWQHFILPAVALG 180 Query: 199 LGLAAVSCRVARDAMVQVRASEYFAFALTKGLSPAQALARHGVRNVAAPVVAYLGVQLVM 258 R+ R M++V S+Y A KGLS ++ + +H +RN PVVA V+L Sbjct: 181 YYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAAVELGF 240 Query: 259 LVEGVVLVETIFAWPGIGHALVHAIFGRDVPMIQGTALVLGLMFVLFNALVDTTCAFLDP 318 ++ G V++E++++ G+G AI D P++Q L++ + ++ L D A LDP Sbjct: 241 MLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVINALLDP 300 Query: 319 RGR 321 R R Sbjct: 301 RIR 303 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 132 bits (333), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 105/325 (32%), Positives = 168/325 (51%), Gaps = 22/325 (6%) Query: 13 LAGALGQRLLQASLVALLVGTLCFFMTRLLPGDMAYRIAAGRYGYDMVTTEAALAVRAEL 72 ++GA+ + ++QA +V LL+ + FF ++ + I G D V L + EL Sbjct: 1 MSGAIARSVVQALMVVLLMTVIVFFGLHMIGNPVDILI-----GQD-VDQVDRLRIIQEL 54 Query: 73 GLDQPWFMALGQWWSRLLHLDLGTSQVTALPVLVEIAHQLGPTLRLSLLALALSLLFGPT 132 GLDQP + + + LH +LG S V P ++ I +L TL L+ AL L+L+ G Sbjct: 55 GLDQPVWRQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVP 114 Query: 133 LGILAGLNPGGWLDRSTLALSVLLRALPSFLLGLILVLLFSVQLGALPAAGHVDHGGI-- 190 LG+ AG+ P R + S+ +LP+F +GL+L++ FSV LG LP+ G + Sbjct: 115 LGLFAGMKPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFG 174 Query: 191 --------------LLPALTLALGLAAVSCRVARDAMVQVRASEYFAFALTKGLSPAQAL 236 +LPA+ L+L ++ R+ R + +V ++ FA KGLSPA+ + Sbjct: 175 VQWSWLTADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVV 234 Query: 237 ARHGVRNVAAPVVAYLGVQLVMLVEGVVLVETIFAWPGIGHALVHAIFGRDVPMIQGTAL 296 + +RN P+V +G++ + V+ E+IFAWPG G ++ +I D P+I + Sbjct: 235 LMYVLRNTLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLM 294 Query: 297 VLGLMFVLFNALVDTTCAFLDPRGR 321 V+ MFV N +VD LDPR R Sbjct: 295 VIVCMFVTINLVVDVLYKLLDPRVR 319 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 126 bits (317), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 88/292 (30%), Positives = 145/292 (49%), Gaps = 13/292 (4%) Query: 36 FFMTRLLPGDMAYRIAAGRYGYDMVTTEAALAVRAELGLDQPWFMALGQWWSRLLHLDLG 95 FF+T LLPGD A + A G+ T E A+R + GLD P + W LL + G Sbjct: 28 FFITNLLPGDAA-QTALGQAA----TPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPG 82 Query: 96 TSQVTALPVLVEIAHQLGPTLRLSLLALALSLLFGPTLGILAGLNPGGWLDRSTLALSVL 155 S V +PV I +L +L L+ + +S+ LGI + + G + DR+ +V Sbjct: 83 MSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVS 142 Query: 156 LRALPSFLLGLILVLLFSVQLGALPAAGHVDHGGIL--------LPALTLALGLAAVSCR 207 + ++P FL+ + V++F+V+L L A H L +P LTL + A R Sbjct: 143 MVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTR 202 Query: 208 VARDAMVQVRASEYFAFALTKGLSPAQALARHGVRNVAAPVVAYLGVQLVMLVEGVVLVE 267 + R A++ S Y AL KG+ + + RH + N P+ + + L L+ GV++VE Sbjct: 203 MTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVE 262 Query: 268 TIFAWPGIGHALVHAIFGRDVPMIQGTALVLGLMFVLFNALVDTTCAFLDPR 319 +IF +PGI ++ A+ RD+P++Q +++ ++L D +PR Sbjct: 263 SIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPR 314 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 0.328 0.142 0.428 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: 766,047 Number of extensions: 24836 Number of successful extensions: 163 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 157 Number of HSP's successfully gapped: 6 Length of query: 322 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 237 Effective length of database: 1,217,395 Effective search space: 288522615 Effective search space used: 288522615 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 130 (54.7 bits)