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= 0020.0416.p (318 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel A... 626 0.0 gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel A... 183 2e-47 gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel A... 174 1e-44 gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel A... 123 2e-29 gi|300310861|ref|YP_003774953.1| dipeptide/oligopeptide/nickel A... 116 2e-27 >gi|300310464|ref|YP_003774556.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 318 Score = 626 bits (1614), Expect = 0.0, Method: Compositional matrix adjust. Identities = 317/318 (99%), Positives = 317/318 (99%) Query: 1 MNGMVLRLIVRRLLQAVLTLLLVSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYG 60 MNGMVLRLI RRLLQAVLTLLLVSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYG Sbjct: 1 MNGMVLRLIARRLLQAVLTLLLVSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYG 60 Query: 61 LDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFL 120 LDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFL Sbjct: 61 LDLPAPLRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFL 120 Query: 121 GIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGA 180 GIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGA Sbjct: 121 GIFSAMYRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGA 180 Query: 181 FIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAI 240 FIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAI Sbjct: 181 FIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAI 240 Query: 241 GPIANAVALSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLL 300 GPIANAVALSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLL Sbjct: 241 GPIANAVALSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLL 300 Query: 301 VLTADVLAIVSNPRLKTR 318 VLTADVLAIVSNPRLKTR Sbjct: 301 VLTADVLAIVSNPRLKTR 318 >gi|300311170|ref|YP_003775262.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 306 Score = 183 bits (464), Expect = 2e-47, Method: Compositional matrix adjust. Identities = 104/287 (36%), Positives = 161/287 (56%), Gaps = 8/287 (2%) Query: 32 NLLPGDAAQTALGQAATPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPGMSLVNNVPV 91 +LLPGD A+ A G A +TVA +R GLD P P ++ ++ N G+ G S+ PV Sbjct: 28 HLLPGDPARLAAGPEADDKTVALVRADLGLDKPLPEQFVNFFLNAARGDFGHSIRTKRPV 87 Query: 92 AQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVSMVSVPEFLV 151 ++ I R +L L V + +V L +GI SA++R + DR AVS +S P F + Sbjct: 88 SEEISARFWPTLWLTVVAMVWAVLFGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSL 147 Query: 152 ATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTRMTRAAVIDQ 211 + V +F+VKL WL + GD L Y +P +TL + A M R TR++ I+ Sbjct: 148 GILLVQVFSVKLGWLPTV---GDDTWL-----HYILPSITLGAAVAAVMARFTRSSFIEI 199 Query: 212 LRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVESIFNYPGIA 271 L+ + A KG+ T +V++H L NA+ P+ + L +LLGG I+VE +FN+PG+ Sbjct: 200 LQEDFVRTARAKGLTETVVVIKHCLRNALIPVVTMMGLQFGFLLGGSILVEVVFNWPGMG 259 Query: 272 TLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPRLKTR 318 L++DAV RD P++QA ++F ++ + L DVL V NP ++ + Sbjct: 260 RLLVDAVEMRDYPVIQAEILLFSLEFIFINLVVDVLYAVINPSIRFK 306 >gi|300312480|ref|YP_003776572.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 174 bits (440), Expect = 1e-44, Method: Compositional matrix adjust. Identities = 105/310 (33%), Positives = 172/310 (55%), Gaps = 9/310 (2%) Query: 9 IVRRLLQAVLTLLLVSAGVFFITNLLPGDAAQTALGQAATPETVAALRLQYGLDLPAPLR 68 I+RRL A+ + VS F + ++ GD A + G AT V ++R Q+GLD P + Sbjct: 5 ILRRLAIALCVAVTVSVVSFTLLHM-SGDLAVSIAGPEATAAQVESVRTQFGLDRPMATQ 63 Query: 69 YAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYR 128 Y WLG + + G S PV +MI RLP + L L++V A+ LG+ +A+YR Sbjct: 64 YLDWLGRAVQLDFGKSFYFQGPVMEMIAERLPITFKLGGSALLLAVLTAIPLGVLAAIYR 123 Query: 129 GSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMP 188 ++ DRA + AV ++P F ++IFAV L WL AG+ + + + +P Sbjct: 124 DTWLDRAALLIAVVGQAMPSFWFGLTLILIFAVTLHWLPV---AGNESW-----QHFILP 175 Query: 189 VLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVA 248 + L + M R+TR+ +++ L S Y A KG+ ++R+V +HAL NA+ P+ A Sbjct: 176 AVALGYYAMPAMMRLTRSGMLEVLGSDYIRTARAKGLSKSRVVFKHALRNAVIPVVALAA 235 Query: 249 LSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLA 308 + L ++LGG +++ES+++ G+ L DA++ D P+VQA +I Y+ L ADV+ Sbjct: 236 VELGFMLGGSVVIESVYSMQGLGQLAWDAISRNDYPVVQAVVLIIAMFYIGLTFLADVIN 295 Query: 309 IVSNPRLKTR 318 + +PR++TR Sbjct: 296 ALLDPRIRTR 305 >gi|300310893|ref|YP_003774985.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 94/320 (29%), Positives = 164/320 (51%), Gaps = 13/320 (4%) Query: 9 IVRRLLQAVLTLLLVSAGVFFITNLLPGDAAQTALGQAATPETVAALRL--QYGLDLPAP 66 I R ++QA++ +LL++ VFF +++ G+ +GQ + V LR+ + GLD P Sbjct: 5 IARSVVQALMVVLLMTVIVFFGLHMI-GNPVDILIGQDV--DQVDRLRIIQELGLDQPVW 61 Query: 67 LRYAHWLGNLLSGNPGMSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAM 126 +Y +L L GN G S V N P +I RLPA+L LA L+++ + + LG+F+ M Sbjct: 62 RQYLAFLNGALHGNLGNSFVYNTPAILLIFQRLPATLELACAALLLALVVGVPLGLFAGM 121 Query: 127 YRGSFFDRAVNVSAVSMVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLG---AFIK 183 F R V +++ S+P F + + +M F+V L WL + A G +++ Sbjct: 122 KPDHPFSRLVMTTSIFGFSLPTFWIGLMLIMAFSVTLGWLPSGGRGQTAELFGVQWSWLT 181 Query: 184 AYA-----MPVLTLCCVIVAQMTRMTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPN 238 A +P + L ++ + R+TRA V + L + + A KG+ R+VL + L N Sbjct: 182 ADGWRHMILPAINLSLFKISLVIRLTRANVREVLPMDFVKFARAKGLSPARVVLMYVLRN 241 Query: 239 AIGPIANAVALSLSYLLGGVIIVESIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYL 298 + P+ V L + ++ ESIF +PG L++D++ D P++ A M+ ++ Sbjct: 242 TLIPLVTVVGLEFGSTIAFAVVTESIFAWPGAGKLILDSINALDRPVIVAYLMVIVCMFV 301 Query: 299 LLVLTADVLAIVSNPRLKTR 318 + L DVL + +PR++ Sbjct: 302 TINLVVDVLYKLLDPRVRVE 321 >gi|300310861|ref|YP_003774953.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 324 Score = 116 bits (290), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 86/292 (29%), Positives = 152/292 (52%), Gaps = 13/292 (4%) Query: 28 FFITNLLPGD-AAQTALGQAA----TPETVAALRLQYGLDLPAPLRYAHWLGNLLSGNPG 82 FF+T +LPGD A + A G+ T E A+R + GLD P + + W LL + G Sbjct: 38 FFMTRMLPGDMAYRIAAGRYGYDMVTTEAALAVRDELGLDRPWFMALSEWWSRLLHLDLG 97 Query: 83 MSLVNNVPVAQMIGGRLPASLMLAAVTALVSVPLALFLGIFSAMYRGSFFDRAVNVSAVS 142 +S V++ PV I +L +L L+ + +S+ + LG+ + ++ G + DRA +V Sbjct: 98 VSQVSSQPVLAEIAHQLGPTLRLSLLAMALSLLVGPTLGVLAGLHPGRWLDRATLALSVG 157 Query: 143 MVSVPEFLVATVAVMIFAVKLRWLSALSHAGDAATLGAFIKAYAMPVLTLCCVIVAQMTR 202 + ++P FL+ + V++F+V+L L A H GD + A+ + + C R Sbjct: 158 LRALPSFLLGLILVLLFSVQLGALPAAGH-GDHGGILLPALTLALGLAAVSC-------R 209 Query: 203 MTRAAVIDQLRSSYAEMALLKGVKRTRIVLRHALPNAIGPIANAVALSLSYLLGGVIIVE 262 + R A++ +S+Y AL KG+ + + RH L N P+ + + L L+ GV++VE Sbjct: 210 VARDAMVQVRQSAYFAFALTKGLSPAQALARHGLRNVAAPVTAYLGVQLVMLVEGVVLVE 269 Query: 263 SIFNYPGIATLMIDAVTTRDMPLVQACSMIFCAGYLLLVLTADVLAIVSNPR 314 +IF +PGI ++ A+ RD+P++Q +++ ++L D +PR Sbjct: 270 TIFAWPGIGHALVHAIFGRDVPMIQGTALVLGLMFVLFNALVDAACAFLDPR 321 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 0.138 0.396 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: 861,358 Number of extensions: 32981 Number of successful extensions: 241 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 234 Number of HSP's successfully gapped: 6 Length of query: 318 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 233 Effective length of database: 1,217,395 Effective search space: 283653035 Effective search space used: 283653035 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)